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Q-Tof 2 User's Guide, issue 1. 6666526

1. ISS aia DA Quadrupole Analyser Embedded Housing Control Computer RF Generator RF Lens 1 Z spray Housing Source Turbomolecular Pumps Instrument Description Page 12 Q Tof 2 User s Guide The main internal mechanical components of the instrument are The source housing containing the RF hexapole lens The MS1 analyser housing containing the quadrupole analyser hexapole collision cell and hexapole transfer lens The TOF analyser housing containing the pusher detector and reflectron assemblies Three 250 litre second turbomolecular pumps Two active inverted magnetron Penning gauges and two Pirani gauges Instrument Description Page 13 Q Tof 2 User s Guide Electronics The main electronics unit is located in the lower section of the instrument behind the operator control panel This contains e High voltage power supplies These supply the probe or corona Dynolite point detector reflectron TOF flight tube and lens circuits e Low voltage power supplies These supply the PCBs high voltage supplies and turbomolecular pumps e Main PCBs For communications lenses and quadrupole control B chi aaa PCBs Instrument Description Page 14 Q Tof 2 User s Gu
2. A second function is added by selecting the Parent button and the Function 2 Parent Scan window appears All parameters in this window should be set to be the same as in function 1 except the Step Mass which should be set to 5Da The third function is added in the same way and the step mass parameter is set to 1Da Thus the final experiment should appear as shown below There are three functions that differ only in the Step Mass parameters All other aspects of the three functions are the same NB The step mass in function 1 must be an integer multiple of the step mass in function 2 which must be an integer multiple of the step mass in function 3 For example the windows may be set to 20Da 5Da and 1Da as shown Failure to observe this requirement will prevent the experiment from proceeding and no data will be acquired Parent lon Scanning Page 95 Q Tof 2 User s Guide Scan Functions PARENTS_MULT MDB oi xi Fie Function Analog Help ms MSMS Survey Parent Solvent Delay Analog Channels Jo 00 Time mins 1 2 3 4 APcl Probe Temp m T Unused T Unused T Unused I Unused Mins IEG a5 20 s o oe o e SS OO oe oO Before the experiment can be performed a file containing the required product ion for which the precursors are sought e g POs z78 9 must be created Parent Scan Options In the Scan Function window select the Function tab in the top banner and then select Paren
3. 891 175 1209 812 1882 490 940 741 1302 952 2117 927 996 138 1411 615 2420 632 1058 460 1540 036 1129 091 1694 140 Mixture of Sugars Reference File SUGNEG REF 1151 37 1313 42 1475 48 Reference Information Page 147 Q Tof 2 User s Guide Sodium lodide and Caesium lodide or Rubidium lodide Mixture Reference Information Page 148 Reference File NAINEG REF 126 9045 1026 2699 1925 6353 2825 0008 3724 3662 276 7987 1176 1641 2075 5296 2974 8950 3874 2604 426 6929 1326 0584 2225 4238 3124 7892 576 5872 1475 9526 2375 3180 3274 6835 726 4814 1625 8469 2523 2123 3424 577171 876 3757 1775 7411 2675 1065 3574 4719 Q Tof 2 User s Guide Preparation of Calibration Solutions PEG Ammonium Acetate for Positive lon Electrospray and APcl Prepare a solution of polyethylene glycols at the following concentrations PEG 200 25 ng yl PEG 400 50 ng yl PEG 600 75 ng yl PEG 1000 250 ng pl Use 50 acetonitrile and 50 water containing 2 mmol ammonium acetate Use reference file PEGH1000 REF PEG Ammonium Acetate for Positive lon Electrospray Extended Mass Range Prepare a solution of polyethylene glycols at the following concentrations PEG 200 25 ng yl PEG 400 50 ng yl PEG 600 75 ng l PEG 1000 250 ng l PEG 1450 250 ng yl Use 50 acetonitrile and 50 water containing 2 mmol ammonium acetate Use reference file PEGH2000 REF
4. By viewing under magnification the spray emanating from the capillary may be examined and tuned by altering the nebulising tip such that a fine spray is observed Altering the gas slightly may also help in this tuning process Swing the stage back out of the source and place the cover over the sprayer ensuring that the tubing coming from the sprayer is threaded correctly through it Lock the cover in place with two screws Swing the stage back into the source and alter the translation stage in out direction such that the capillary is approximately 5mm from the cone Select Operate and set Capillary to approximately 2 5kV An ion beam should now be present Nanoflow Electrospray Page 67 Q Tof 2 User s Guide Optimise the ion beam by altering the position of the spray using the controls of the translation stage The sprayer can now be connected to the HPLC system The injection valve is plumbed as follows P from the pump e C to the column or to the union e S is the sample port attach a VISF sleeve here e W is a waste port A short tail of fused silica attached to the entrance port of the union and the use of low pressure PTFE connectors will remove the need to move the stage This will prevent accidental alteration of the sprayer s position when changing between tuning and HPLC operation Changing Options To change between the glass capillary and the nano LC options A Rotate the stage outwards
5. EJ File Edit Display Process Window Tools Help le x 2 ala selle wale olala Of ae lelle Precursors of miz 79 8 azi4 1 TOF Parent ES 79 8 100 e300 970 0 84 20 Da Step size 610 0 670 0 az14 2 TOF Parent ES 7325 827 5 9725 79 8 5 Da Step size 857 5 VASS 28 azi4 3 TOF Parent ES 79 8 100 9745 i 1 Da Step size Parent lon Scanning Page 103 Q Tof 2 User s Guide Parent lon Scanning Page 104 Q Tof 2 User s Guide Maintenance and Fault Finding Introduction Cleanliness and care are of the utmost importance whenever internal assemblies are removed from the instrument v Always prepare a clear clean area in which to work vV Make sure that any tools or spare parts that may be required are close at hand v Obtain some small containers in which screws washers spacers etc can be stored v Use tweezers and pliers whenever possible v If nylon or cotton gloves are used take care not to leave fibres in sensitive areas xX Avoid touching sensitive parts with fingers x Do not use rubber gloves Y Before reassembling and replacing dismantled components inspect O rings and other vacuum seals for damage Replace with new if in doubt Should a fault occur soon after a particular part of the system has been repaired or otherwise disturbed it is advisable first of all to ensure that this part has been correctly refitted and or adjusted and that adjacent components have not been
6. 61 62 65 65 66 66 67 67 67 68 68 69 70 Table of Contents Q Tof 2 User s Guide Atmospheric Pressure Chemical lonisation Introduction Preparation Checking the Probe Obtaining an Ion Beam Hints for Sample Analysis Tuning Mobile Phase Probe Temperature Desolvation Gas Removing the Probe Calibration and Accurate Mass Introduction Nominal Mass Accuracy Calibration Lock Mass Dead Time Correction Generation of an Instrument Calibration Lock Mass Correction Deadtime Correction Exact Mass Measurement Additional Hints Parent lon Scanning Introduction Unlocking the Parent Scan Facility Setting up the Mass Transmission of the Quadrupole Setting up a Scan Function for Precursor Scanning i Multi Step Mode ii Single Step Mode Multi Step mode Parent Scan Options Single Step Mode Acquiring the Data Displaying the Data The Precursor Scan Constant Neutral Loss or Gain Scans The Product Scan The Precursor Scan Multi Step Mode Table of Contents 71 73 73 T9 11 11 77 T11 T11 78 81 81 82 82 83 83 88 89 93 95 96 97 98 98 98 98 100 102 103 103 103 105 105 106 Q Tof 2 User s Guide Maintenance and Fault Finding Introduction 109 Removal and Replacement of Outer Panels 110 Electronics Maintenance 112 Cooling Fans and Air Filters 113 The Vacuum System 113 Vacuum Leaks 113 Pirani Gauge 114 Active Inverted Magnetron Gauge 114 Gas Ballasting 114 Oil Mist Filter 115 Rot
7. Caution Failure to use the stop and handle to rotate the stage can result in permanent damage to the three axis manipulator Remove the protective cover and release the captive screw located underneath the stage Lift off the holder and replace it with the alternative holder securing it with the captive screw Replace the protective cover ensuring that either the PTFE back pressure tubing glass capillary option or the fused silica transfer line is fed through the slot in the back of the protective cover along with the HV cabling Nanoflow Electrospray Page 68 Q Tof 2 User s Guide Atmospheric Pressure Chemical lonisation Introduction Corona Discharge Pin gt Exhaust eee H Exhaust affle gt Liner Sample Lf IN lt Cone Gas 4 Isolation Valv Nebuliser Desolvation ae _ Gas Gas a Extraction Analyser Cone Source Enclosure _ 4 i 4 i Tarpamo Reula Pumps Rotary Pump Atmospheric Pressure Chemical Ionisation APcI is an easy to use LC MS interface that produces singly charged protonated or deprotonated molecules for a broad range of involatile analytes The ability to operate with 100 organic or 100 aqueous mobile phases at flow rates up to 2 ml min makes APcI an ideal technique for standard analytical column 4 6mm i d normal phase and reverse phase LC MS The APc
8. Q Tof 2 User s Guide For a given sample concentration the ion currents observed in nanoflow are comparable to those seen in normal flow rate electrospray Great sensitivity gains are therefore observed when similar scan parameters are used due to the great reductions in sample consumption The nanoflow end flange consists of a three axis j Purge Gas manipulator a stage a aan gt Exhaust protective cover and a stop ts oad Cleanable Exhaust handle arrangement for AE i Liner rotation of the manipulator Sample lt L lt Cone Gas and stage Cone The manipulator and stage Isolation are rotated by 90 degrees to Valve change option or in the glass capillary option to load a Extraction Analyser new nanovial Cone Caution Failure to use the stop and handle to u i u rotate the stage can Source Turbomolecular Enclosure Rotary Pump result in permanent Pumps damage to the three axis manipulator Se Installing the Interface To change from the normal electrospray interface and install the nanoflow interface If fitted remove the probe Remove the moulded cover from around the source Undo the three thumb screws and withdraw the probe adjustment flange assembly and glass tube Place the glass tube end on on a flat surface and place the probe support flange assembly on top of the glass tube Remove the PTFE encapsulated sour
9. z A m Voltage use by gradually increasing the applied sav fo voltage over a long time period This is som po Cose necessary to allow escape of all absorbed water from within the microchannels p Time Duration mins 600 Under normal operation the analyser Step mins 5 automatically vents to dry nitrogen However if the nitrogen supply was not connected to the instrument when last vented or if the instrument has been left vented for more than one day a significant amount of water vapour may have entered the analyser Under these circumstances it is good practice to allow the instrument to pump for 12 hours before commencing the conditioning process In all cases the TOF pressure must be le 6 mbar prior to commencing MCP conditioning MCP conditioning should be repeated after every instrument venting It is not necessary to recondition the detector if the instrument has been left out of the operate mode while still under vacuum Routine Procedures Page 26 A Q Tof 2 User s Guide During routine cleaning of the source sample cone the source isolation valve is closed in order to maintain analyser vacuum It is not therefore necessary to recondition the detector after this procedure The procedure for MCP conditioning is as follows Ensure that the analyser pressure is le 6 mbar Check that the MCP Detector voltage is set to zero on the tune page Switch the instrument into Operate Select Oth
10. Probe Adjustment Small improvements may be gained by varying the position using the sample and solvent system under investigation The following information should be considered when setting the probe position e 10mm of movement is provided in each direction with 1 25mm of travel per revolution of the probe positioning controls e At higher liquid flow rates the probe tip should be positioned further away from the sample cone to achieve optimum stability and sensitivity The position is less critical than at lower flow rates Nebuliser Gas Optimum nebulisation for electrospray performance is achieved with a nitrogen flow between 10 and 20 litres per hour This can be achieved by fully opening the Nebuliser Gas flow control valve which is situated on the instrument s front panel Desolvation Gas The desolvation gas also nitrogen is heated and delivered as a coaxial sheath to the nebulised liquid spray by the desolvation nozzle Electrospray Page 49 User s Guide The position of the desolvation nozzle heater is fixed relative to the probe tip and requires no adjustment The Desolvation Gas flow rate is adjusted by the control value situated on the instrument s front panel The optimum Desolvation Temp and flow rate is dependent on mobile phase composition and flow rate A guide to suitable settings is given below The Desolvation Gas flow rate indicated on the flow meter represents total drying flow that i
11. Reference Information Page 149 Q Tof 2 User s Guide Sodium lodide Solution for Positive lon Electrospray Method 1 Prepare a solution of sodium iodide at a concentration of 2 ug ul micrograms per microlitre in 50 50 propan 2 ol IPA water with no additional acid or buffer Add caesium iodide to a concentration of 0 05 yg pl The purpose of the caesium iodide is to obtain a peak at z 133 Cs to fill the gap in the calibration file between z 23 Nat and the first cluster at z 173 which would lead to poor mass calibration in this mass range Do not add more CsI than suggested as this may result in a more complex spectrum due to the formation of NaCs I clusters Use reference file NAICS REF Method 2 Sodium Prepare a solution of sodium iodide at a concentration of 2 ug ul micrograms per microlitre in 50 50 propan 2 ol IPA water with no additional acid or buffer Add rubidium iodide to a concentration of 0 05 pg yl The purpose of the rubidium iodide is to obtain a peak at z 85 Rb with an intensity of about 10 of the base peak at z 173 Rubidium iodide has the advantage that no rubidium clusters are formed which may complicate the spectrum Note that rubidium has two isotopes Rb and Rb in the ratio 2 59 1 giving peaks at z 85 and 87 Use reference file NAIRB REF lodide Solution for Negative lon Electrospray Either of the above solutions is suitable for calibration in neg
12. filtered and stored under cover at all times Electrospray Page 44 Q Tof 2 User s Guide It is wise periodically to check the flow rate from the solvent delivery system This can be carried out by filling a syringe barrel or a graduated glass capillary with the liquid emerging from the probe tip and timing a known volume say 101 Once the rate has been measured and set a note should be made of the back pressure readout on the pump as fluctuation of this reading can indicate problems with the solvent flow Post column Splitting Although the electrospray source can accommodate flow rates up to ml min it is recommended that the flow is split post column to approximately 200 yl min Also even at lower flow rates a split may be required to save valuable samples The post column split consists of a zero dead volume tee piece connected as shown LC Column To Waste or 1 UV Cell The split ratio is adjusted by increasing or decreasing the back pressure created in the waste line by changing either the length or the diameter of the waste tube A UV cell may also be incorporated in the waste line avoiding the requirement for in line low volume Z cells As the back pressure is varied the flow rate at the probe tip should be checked as described above These principles apply to splitting for both megaflow and normal flow electrospray Electrospray Page 45 Q Tof 2 User s Guide Megaflow Megaflow electrospray
13. peghnha ref ka I Ait references Mass measure Cancel Click on OK to reveal the residual errors whilst making sure that a polynomial of order lhas been selected The deadtime distortion is revealed as the observed difference between the high and low intensity peaks Calibration and Accurate Mass Page 85 Q Tof 2 User s Guide Calibration DEFAULT CAL File Print Edit Display Cancel Default Data file peq06 Uncalibrated 22 matches of 29 tested references 100 327 37 14045 42 459 45 503 47 Reference file peghnhd 100 VF 11 195 12299 15203 1032720371 23415 25459 28503 31 Mass difference Raw Ref mass 283 34 547 50 eo 53 64 17737 23932 T 635 55 679 57 793 60 0 18 x dwi x x x x x x x TET 0 15 Residuals Mean residual 1 061604e 6 0 004171 0 01 x x x 7 x S amu m 0 01 ET Miz 150 200 250 300 350 400 450 500 550 600 650 700 750 800 Do not click on OK now as this would erase the instrument calibration This menu is being used only to set up the deadtime correction and not to create a new calibration Click on Cancel and re center the data using a Resolution of 5000 and Np Multiplier of 1 There should now be a reduction in the mass deviation observed between adjacent peaks of high and low intensity Repeat this process at subsequently lower values of Np until the deviation is minimised At this point the peaks should lie close to the
14. 100 psi Under no circumstances should the nitrogen pressure exceed 10 bar 140 psi Routine Procedures Page 31 Q Tof 2 User s Guide The preceding sections have outlined the software controls and connections to establish the physical conditions required as a prerequisite to mass spectrometer operation Within the source and analyser enclosures electric fields controlled via MassLynx are applied to the components to manage the ion beam generated according to the sample to be analysed the ionisation mode and the type of information required The ion optical system elements are indicated in the following schematic diagram a LL ny a a Q O Sample Cone Extraction Cone RF Hexapole eee Pre filter a Post filter PEELE iiie Differential Pumping Aperture Phosphor Anode MCP Transport RF Hexapole Analyser Quadrupole Gas Cell RF Hexapole Conversion Dynode Flight Tube Acceleration Lens Steering Focus Lens Reflectron Tube Tof Entry Photomultiplier Q 2 5 Q Q 8 Q D 8668668 Considering the variable nature of the beam with different samples the instrument should be tuned for signal strength and calibrated for accurate z using suitable reference compounds prior to the acquisition of sample data Tuning parameters have been grouped in MassLynx into 3 menus as described below Full details of source tuning procedures for ele
15. ESP File lonMode Gas Ramps Other Stop Window Help S t S fe S lal ieis 22 Mass Span Gi Transport Tune Peak 1 571 38 jo St Aperture 2 Tune Peak 2 AccY Tune Peak 3 Focus Tune Peak 4 Tube Lens er pseu 2 20e3 l Offset 2 Pusher TOF k Reflectron snd aaeh Time us 55_ gt Multiplier s g gt MCP meenen eea 571 Source MS MS 2 Acquire Transport E Fi rerara This sets the offset DC on the transport hexapole and the DC on the apertures of the gas cell The optimum setting is usually between 2 4V Aperture 2 Operating Aperture 2 at 5V generally gives best resolution but at some cost to sensitivity For maximum sensitivity it should be set to around 15V AccV Usually set to maximum voltage 200V in all modes of operation Focus This adds an equal voltage to both the top and bottom steering focus lens halfplates The optimum setting for the first detector is typically 80 130V but for maximum TOF resolution it is set to zero Routine Procedures Page 36 Q Tof 2 User s Guide Tube Lens This is set to its optimum value in the factory and by the engineer at installation It helps shape the ion beam on entry into the pusher and so has a large effect on resolution and peak shape The factory setting should be noted before attempting to improve resolution by changing its voltage Offset 1 This determines the voltage difference between the two
16. Initially set Corona to 2 5kV and Cone to 30V When Source Block Temp reaches 150 C Select API Gas to switch on the nitrogen gas Using the valves on the front of the instrument adjust Desolvation Gas to 150 litres hour and set Nebuliser Gas to its maximum setting Set one of the peak display boxes to show masses down to at least 100 Da Select Operate Set APcl Probe Temp to 350 C Atmospheric Pressure Chemical lonisation Page 73 Q Tof 2 User s Guide When APcl Probe Temp reaches 350 C Start the LC pump at a flow of 1 ml min Optimise Corona so that the peaks reach maximum intensity Optimise the probe position for intensity and stability The two screws can be adjusted singly or simultaneously to optimise the beam eee Probe Adjustment The position of the probe will affect sensitivity However if the sample is contained in a biological matrix or is contained in an involatile solvent the probe should be moved away from the sample cone and towards the corona discharge pin The tune page shows a typical reagent ion spectrum for a Sideways methanol water mobile phase Adjustment Warning It is normal for the source enclosure the glass tube and parts of the probe adjustment flange to reach temperatures of up to 60 C during prolonged APcI operation Care should be exercised when handling source components immediately after operation Warning Switch off the liquid flow and allow the probe to
17. are 42 56 83 and 101 The transmission of these ions will be dependent on the setting of RF Lens A lower RF Lens voltage is required for optimum transmission at lower Pz Acetonitrile adducting may be minimised by optimisation of the probe position as described in the chapter entitled Electrospray Atmospheric Pressure Chemical lonisation Page 70 Q Tof 2 User s Guide Preparation Ensure that the source is assembled as described in Maintenance and Fault Finding and that the instrument is pumped down and prepared for APcl operation as described in Routine Procedures a pee Exhaust Blanking Mounting Contact High Voltage Socket Cleanable Baffle APclI may be operated with or without the cleanable baffle fitted Ensure that a supply of nitrogen has been connected to the gas inlet at the rear of the instrument and that the head pressure is between 6 and 7 bar 90 100 psi Checking the Probe Ensure that the probe heater is off Unplug the probe from the instrument s front panel and remove the probe from the source Connect the PTFE tube to the Nebuliser Gas outlet on the front panel Atmospheric Pressure Chemical lonisation Page 71 Q Tof 2 User s Guide Remove the probe tip assembly by carefully loosening the two grub screws Disconnect the heater from the probe body by pulling parallel to the axis of the probe Ensure that 0 5 to Imm of fused silica
18. axis the line of best fit Calibration and Accurate Mass Page 86 Q Tof 2 User s Guide Calibration DEFAULT CAL OF Xx File Print Edit Display Cancel Default Data file peg06 Uncalibrated 19 matches of 29 tested references 100 307 38 i i 459 46 503 48 s 83 35 547 51 504 53 F 177 27 239 32 635 55 679 58 D Reference file peghnh4 100 177 11195 12239 15283 18327 20 371 23415 25459 28503 31 D Mass difference Raw Ref mass 0 18 amu 0 15 Residuals Mean residual 1 323458e 9 0 001508 0 01 amu 0 00 Typical values for Np Multiplier will be about 0 7 and the Resolution used should be as measured on the instrument at mass 500 Now that the deadtime correction has been set up the difference in reported areas and masses between corrected and uncorrected centered data can be seen In the example below the 371 peak has been shifted by 8 7 mDa Calibration and Accurate Mass Page 87 Q Tof 2 User s Guide Spectrum pegO6 Bel SB File Edit Display Process Tools Window Help la x e aja we lae aaaea a aa 5V pegd6 6 0 145 AM 5000 0 0 00 Cm 3 6 TOF MS ES 100 371 2261 _ 5 59e4 55692 372 2311 a512 1009 373 2283 3742284 3747062 795 2373 a7 369 1917 219 E 370 2220 370 7277 165 442 o peg06 6 0 145 AM 0 0 0 00y Cm 3 6 TOF MS ES 100 371 2174_ 3 50e4 34996 372 2295 5780 369 1917 219
19. cool lt 100 C before removing it from the source Caution Failure to employ a desolvation gas flow during APcI operation may lead to heat damage to the source Atmospheric Pressure Chemical lonisation Page 74 Q Tof 2 User s Guide Hints for Sample Analysis Tuning e Start by tuning on the solvent ions It is generally found that the most significant analyte tuning parameter to adjust following tuning on the solvent ions is Cone e Fine tuning on the analyte of interest can be performed either by large loop injections 100y1 or by constant infusion in the mobile phase typically at analyte concentrations of a few ng yl e 10y1 loop injections can be monitored using real time chromatogram updates Mobile Phase e The choice of mobile phase is an important compound specific factor in APcl For example steroids prefer methanol water mixtures as opposed to acetonitrile water e Analyte sensitivity is also dependent on mobile phase composition which can be varied from 100 aqueous to 100 organic for any particular mixture Probe Temperature This can be a critical factor for some analytes e Involatile samples for example steroids generally require high probe temperatures gt 400 C e Volatile samples for example pesticides can be analysed with low probe temperatures lt 400 C e In some cases too high a probe temperature can lead to thermal degradation of labile samples Desolvation Gas Althoug
20. deviations of less than 5 ppm cannot be expected unless the number of ions per peak is greater than 267 Calibration and Accurate Mass Page 90 Q Tof 2 User s Guide Parent lon Scanning Introduction Identification of the components of a mixture sharing a common structural motif by precursor scanning MS MS is a well recognised analytical strategy For example phosphopeptides may be selectively detected in protein digest mixtures by producing precursor scans for Yz79 SA Carr MJ Huddleston and RS Annan Anal Biochem 1996 239 180 192 and similarly glycopeptides from scans of Yz204 and 366 SA Carr MJ Huddleston and MF Bean Protein Science 1993 2 183 196 More recently it has been used to good effect to locate the peptide protonated molecular ions from the nano electrospray analysis of low level protein digests in a chemical background present at a high level M Wilm G Neubauer and M Mann Anal Chem 1996 68 527 533 In this case precursor scans of Yz86 the immonium ion from commonly occurring Leu He were used On a triple quadrupole instrument MS2 is set to transmit the mass of the chosen product ion for which the precursors are sought and MS 1 is scanned over the range of masses for which precursors are sought Any mass transmitted by MS1 which decomposes in the gas cell to form the mass being transmitted by MS2 is recorded as a precursor and it follows from this that each precursor scan must be a
21. distributions When the attenuator fails in this way the TDC Stop mV threshold can be increased to a significantly higher value than that used previously without reducing the beam intensity In normal operation setting the TDC threshold above 200 or 250mV will start to reduce the beam intensity If the attenuator has failed the TDC threshold can be increased to 500mV or higher before the beam intensity is reduced Maintenance and Fault Finding Page 138 Q Tof 2 User s Guide High Noise Levels High noise levels can either be chemical or electronic in nature Chemical Noise Chemical noise usually originates from contaminated samples solvents or source gases Chemical noise can be distinguished from electronic noise simply by stopping source ionisation If no liquid or gases are entering the source and all the source voltages are set to zero then the remaining noise will be electronic in nature Electronic Noise Electronic noise can be caused by setting the TDC Stop mV threshold too low Refer to the tune page settings section of Routine Procedures for information regarding the setting of this parameter The microchannel plate detector can be damaged by failure to properly condition the detector following venting of the system to atmosphere If the detector is producing microdischarges excessive noise will be apparent on the baseline of mass spectra in the absence of any ion beam Reducing the detector voltage will reduc
22. if the sharp end is touched With the stage rotated outwards unscrew the union from the end of the assembly Carefully remove the capillary from its case by lifting vertically while pressing down on the foam with two fingers Over the blunt end of the capillary pass the knurled nut approximately 5mm of conductive elastomer and finally the union Tighten the nut finger tight is sufficient so that 5mm of glass capillary is protruding from the end of it This distance is measured from the end of the nut to the shoulder of the glass capillary Capillary Load sample into the capillary using either a PTFE Back Pressure ait ii Ferrule fused silica syringe needle or a GELoader tip Tubing Screw the holder back into the assembly finger tight is sufficient ff pe es Ensure that Capillary is set to OV on the tune page Rotate the stage back into the interface using the i stop and handle we When using a GELoader tip break the nanovial y Knurled Nut in half by scoring with a fused silica cutter This aa Blue enables the GELoader to reach the tip of the 4 Conductive Elastomer nanovial an Glass Capillary ff ff ff fF fF A SOY Ff Nanoflow Electrospray Page 64 Q Tof 2 User s Guide Nanovial Tip Position Operation The position of the nanovial is adjusted as shown The tip is in line with the centre of the sample cone at a distance be
23. inadvertently disturbed Warning Many of the procedures described in this chapter involve the removal of possibly toxic contaminating deposits using flammable or caustic agents Personnel performing these operations should be aware of the inherent risks and should take the necessary precautions Maintenance and Fault Finding Page 105 Q Tof 2 User s Guide Removal and Replacement of Outer Panels Warning There are high voltages and hot surfaces present throughout the mass spectrometer The instrument outer panels must not be removed unless the instrument has been electrically isolated at the power outlet Damage to internal electronic components could result if the panel is allowed to drop Caution Ensure that each panel is adequately supported during removal To remove or replace the instrument panels for maintenance purposes follow in order the procedures described below Panel 1 Panel 1 covers the top of the TOF analyser MS2 and the associated housing containing the pusher electronics Remove by lifting vertically To replace lower the panel into position aligning the attached pins with the corresponding holes in the panels beneath Panel 2 Panel 2 encloses the quadrupole analyser MS1 with cut outs at the front for the source and at the rear for the TOF analyser MS2 This panel is also removed by lifting vertically It must be lowered into position with care and engaged with each of the l
24. is left on overnight However if the data system has been switched off switch it on as described in the preceding section Preparation for Electrospray Operation If the corona discharge pin is fitted proceed as follows Deselect Operate from the tune page to put the instrument into standby mode Disconnect the gas and electrical connections from the front panel Unscrew the probe thumb nuts and remove the probe Undo the three thumb screws and remove the probe adjustment flange and glass tube will be maintained at the set temperature when the source enclosure is removed f Warning The ion source block can be heated to temperatures of 150 C and Touching the ion block when hot may cause burns to the operator Disconnect the APcI high voltage cable from the socket positioned at the bottom right corner of the source flange Remove the corona discharge pin from its mounting contact and fit the blanking plug Replace the glass tube and adjustment flange Ensure that the source enclosure is in place The Z spray source enclosure consists of the glass tube and the probe adjustment flange Warning Operating the source without the source enclosure will result in solvent vapour escape and the exposure of hot surfaces and high voltages With the corona discharge pin removed the plug fitted and the source enclosure in place proceed as follows Connect the source s gas line to Desolvation Gas on the front panel Tighten the
25. is protruding from the stainless steel nebuliser tube Connect the LC pump to the probe with a flow of 50 50 acetonitrile water at 1 ml min Check that the liquid jet flows freely from the end of the capillary and that the LC pump back pressure reads 250 to 400 psi Check that the nitrogen supply pressure is 6 to 7 bar 90 to 100 psi Select API Gas and turn on Nitrogen Check that the liquid jet converts to a fine uniform aerosol Switch off the liquid flow Deselect API Gas and turn off Nitrogen Reconnect the probe tip assembly Insert the APclI probe into the source and secure it by tightening the two thumb screws Connect the probe cable to Probes on the instrument s front panel Atmospheric Pressure Chemical lonisation Page 72 Q Tof 2 User s Guide Obtaining an lon Beam A Ensure that the corona discharge pin is fitted as described in Routine Procedures Preparation for APcI Operation and that the pin is connected using the APcI HV cable Ensure that the APcI probe is fitted as described above that the desolvation gas tube is connected to the front panel and that the cone gas and purge gas outlets are plugged If necessary change the ionisation mode using the lon Mode command Set Source Block Temp to 150 C Caution The maximum operating temperature for the source heater is 150 C Do not set Source Block Temp higher than 150 C Set APcl Probe Temp to 20 C with no liquid flow and Nitrogen off
26. nut to ensure a good seal Check that the lead of the probe adjustment flange is plugged into the socket labelled Probes on the front panel Connect the electrospray probe s gas line to Nebuliser Gas on the front panel Routine Procedures Page 28 A Q Tof 2 User s Guide Connect the liquid flow of a LC system or syringe pump to the probe Insert the probe into the source and tighten the two thumb nuts to secure the probe firmly Plug the probe lead into Capillary Corona on the front panel If necessary change the ionisation mode using the lon Mode command Set Source Block Temp to 100 C and Desolvation Temp to 120 C Caution The maximum operating temperature for the source heater is 150 C Do not set Source Block Temp higher than 150 C Preparation for APcl Operation A If the corona discharge pin is not fitted proceed as follows Deselect Operate from the tune page to put the instrument into standby mode Disconnect the gas and electrical connections from the front panel Unscrew the probe thumb nuts and remove the probe After a period of operation at high flow rates allow the glass source enclosure to cool before removal Undo the three thumb screws and remove the probe adjustment flange and glass tube Warning The ion source block can be heated to temperatures of 150 C and will be maintained at the set temperature when the source enclosure is removed Touching the ion block when hot may cause burns
27. of 29 tested references 100 327 38 S140 415 43 459 46 s0348 ved 177 27 239 32 263 35 248 547 51 594 53 635 55 679 5 D Rereren ene peas 344 23 415 25 459 28 503 31 pong 171421215 256 18 300 20 344a 234154 45920 8 D Mass difference Raw Ref mass 0 18 amu 0 15 Residuals Mean residual 3 458101e 10 0 001378 0 01 amu x 0 00 Miz 200 250 300 350 400 450 500 550 600 650 Make sure that the residual errors are all less than 3 mDa The calibration parameters can be altered by clicking on Edit to reveal the box below Calibration Parameters Peak Match OK I Perform auto peak matching ok Peak window Dal fi 00 Initial error Da 2 oo 5 oo Cancel Intensity threshold Curve Fit Polynomial order ja T Intensity weighting Display Calibrate display Calibration and Accurate Mass Page 83 Q Tof 2 User s Guide A fifth order polynomial has been chosen here as a large mass range is being covered by the calibration After these parameters have been set exit the calibration window The following prompt appears Instrument calibration d zd Are you sure you want to update the current calibration Choose Yes and the calibration will be updated with the time of update displayed in the box as shown below Calibrate DEFAULT CAL yx File Edit Process Help Reference File peghnha ret ha Start Stop O1 May 98 St
28. one or two masses in the spectrum will produce this fragment In this case the data can be acquired in a survey mode to try to home in to the regions of the precursor spectrum containing this characteristic signal in as short a time as possible To do this the data can be acquired in a three tier hierarchical fashion using wide 20Da windows to rapidly survey the mass spectrum to find the areas of interest Any of these survey windows which contain the signal of interest can be re evaluated using 5Da windows As a final step the 5Da windows are re evaluated using 1Da windows to locate the precursor to within 0 5Da ii Single Step Mode Single step mode is most useful when there are large numbers of components and there would consequently be no great advantage in using the multi step approach In the single step mode the experiment is set up to step the quad over a given mass range in steps of constant width typically 1Da and acquire the MS MS spectrum at each step Multi Step mode After the MassLynx ini file has been modified log into MassLynx and open up the Scan Function editor This is accessed either by opening up the MS File in the Sample List window or by selecting Set Up Scan which is under the Acquire option in the top banner of the Acquisition Control Panel see Control Panel under the Run command in the Sample List window The Scan Functions window should now appear In the top banner select File and New to open
29. remove the probe from the source to allow the solvent to be seen at the probe tip The flows of desolvation gas and nebuliser gas are on and are set to the correct flow rates The source has been assembled correctly and is clean The source isolation valve is open If after performing the above checks the beam is still absent Acquire TOF data with a mass range extending down to Pz 20 Check that there is an interference peak at approximately yz 28 due to the pusher pulse being switched off If this interference peak is not present either the pusher is not pulsing or the output from the detector is not reaching the TDC time to digital converter The most likely cause of an absent pusher interference pulse is a faulty attenuator If the pusher interference peak is not present no data will be acquired Maintenance and Fault Finding Page 135 Q Tof 2 User s Guide Unsteady Beam Refer to the relevant chapters of this manual and check that Capillary electrospray and Sample Cone are tuned correctly The capillary is not protruding too far from the end of the probe The probe is not too far into the source The flow of solvent from the HPLC pump is correct and steady To do this remove the probe degas the solvent increase the flow rate for several minutes to purge any trapped air then reset and re measure the flow rate Solvents have been adequately degassed The nitrogen flow of desolvation gas and ne
30. than 1000 Da produce singly charged protonated molecules M H in positive ion mode Likewise these low molecular weight analytes yield M H ions in negative ion mode although this is dependent upon compound structure High mass biopolymers for example peptides proteins and oligonucleotides produce a series of multiply charged ions The acquired data can be transformed by the data system to give a molecular weight profile of the biopolymer Electrospray Page 43 Q Tof 2 User s Guide The source can be tuned to fragment ions within the ion block This can provide valuable structural information for low molecular weight analytes The most common methods of delivering sample to the electrospray source are e Syringe pump and injection valve A flow of mobile phase solvent passes through an injection valve to the electrospray source This is continuous until the pump syringes empty and need to be refilled Sample is introduced through the valve injection loop usually 10 or 20ul capacity switching the sample plug into the mobile phase flow Tuning and acquisition are carried out as the sample plug enters the source At a flow rate of 10 l min a 201 injection lasts 2 minutes e Reciprocating pump and injection valve A flow of mobile phase solvent passes through an injection valve to the electrospray source Sample injection and analysis procedure is the same as for the syringe pump The pump reservoirs are simply topped up fo
31. the main electronics unit On the top of this unit is a toggle switch marked PUMPS In normal operation this switch should be in the AUTO position For electronic maintenance and fault finding this switch may be set to the ON position which will allow the electronics circuit breaker to be switched off without venting the vacuum system Maintenance and Fault Finding Page 108 Q Tof 2 User s Guide A Caution Do not leave the instrument unattended with this switch in the ON position as a reduced level of vacuum protection is in operation Return the switch to the AUTO position at the earliest opportunity Cooling Fans and Air Filters Always ensure that none of the cooling fans is obstructed It is essential that the fan filter is checked and cleaned at regular intervals and replaced if there is any doubt about its effectiveness The Vacuum System The performance of the mass spectrometer will be severely impaired by the lack of a good vacuum in the ion transfer hexapole region or the analyser e An excessive analyser pressure results in a general loss in performance indicated by a loss of resolution and an increase in the background noise e As the vacuum deteriorates the vacuum becomes insufficient to maintain the instrument in the operate mode Before suspecting a leak the following points should be noted The turbomolecular pumps will not operate if the rotary pump has failed e If the ro
32. venting of the system to atmosphere or vacuum failure Caution It is strongly recommended that assistance is sought from Micromass if maintenance to any of the components within the TOF analyser housing are thought to be necessary e g excessive noise spikes loss of detector gain or abnormal TOF peak shapes Maintenance and Fault Finding Page 134 Q Tof 2 User s Guide Fault Finding Introduction The majority of faults that occur can be traced to a malfunction of the ion source or inlet system On systems equipped with more than one source this can often be confirmed by changing sources to see if the fault moves with the source Should a fault occur soon after a part of the system has been repaired or otherwise disturbed it is advisable first of all to ensure that this part has been correctly refitted and adjusted and that adjacent components have not been inadvertently disturbed No Beam Refer to the relevant chapters of this manual and check the following The tune page real time display is activated by pressing the appropriate button on the tool bar of the tune page Normal tuning parameters are set and where appropriate readback values are acceptable All necessary cables have been correctly attached to the source and probe Solvent is reaching the probe tip and the solvent flow rate is as required For solvent flow rates below 100 l min it may be necessary temporarily to turn off the nebulising gas and
33. 00 pl min the back pressure should not exceed 7 bar 100 psi Pressures in excess of this indicate a blockage in the solvent flow system Samples containing particulate matter or those of high concentrations are most likely to cause blockages Check for blockages at the tube connections and couplings to the injector the column and if used the flow splitter Maintenance and Fault Finding Page 123 Q Tof 2 User s Guide Concentrated formic acid can be injected to clear blockages Rinse thoroughly afterwards Blockage of the stainless steel sample capillary may occur if the desolvation heater is left on without liquid flow This is particularly relevant for samples contained in involatile solvents or high analyte concentrations To avoid this problem it is good practice to switch off the heater before stopping the liquid flow and flush the capillary with solvent A blocked stainless steel sample capillary can often be cleared by removing it and reconnecting it in the reverse direction thus flushing out the blockage e Gas flow problems Check all gas connections for leaks using soap solution or a suitable leak searching agent such as Snoop Maintenance and Fault Finding Page 124 Q Tof 2 User s Guide Replacement of the Stainless Steel Sample Capillary Stainless Steel Capillary Conductive Sleeve Couplin ji c p ay is O Ring Finger tight Nut amp Ferrule _ o PSO16GVF FP oa OF N Ferrule Line
34. 00IRER Reference Information Page 145 Q Tof 2 User s Guide Sodium lodide and Caesium lodide Mixture Reference File NAICS REF 22 9898 772 4610 1671 8264 2571 1918 3470 5572 132 9054 922 3332 1821 7206 2721 0861 3620 4515 172 8840 1072 2494 1971 6149 2870 9803 3770 3457 322 1182 1222 1437 2121 5091 3020 8745 3920 2400 472 6725 1372 0379 2271 4033 3170 7688 622 5667 1521 9321 2421 2976 Sodium lodide and Rubidium lodide Mixture Reference Information Page 146 Reference File NAIRB REF 3320 6630 22 9898 772 4610 1671 8264 2571 1918 3470 5572 84 9118 922 3552 1821 7206 2721 0861 3620 4515 172 8840 1072 2494 1971 6149 2870 9803 3770 3457 322 7782 1222 1437 2121 5091 3020 8745 3920 2400 472 6725 1372 0379 2271 4033 3170 7688 622 5667 1521 9321 2421 2976 3320 6630 Negative lon Q Tof 2 User s Guide Horse heart myoglobin M1882 16951 48 700 2400 General SUGNEG Sugar mixture of maltose M5885 raffinose RO250 maltotetraose M8253 corn syrup M3639 Low mass range 100 1500 Sodium Iodide Caesium Iodide or Rubidium Iodide mixture Horse Heart Myoglobin Reference File MYONEG REF ES 200 3900 calibration
35. 831 5 868 5 9975 399 TOF Parent ES sum 831 5 7 go7 5 8 Tr OR Oe gt Scan Constant Neutral Loss or Gain Scans Data acquired using the single step method can also be used to display constant neutral loss or constant neutral gain data Mass Chromatogram X File az14 Coo Description Loss m z Cancel 97 98 Mass Chromatogram x Function 7 TOF Parent 50 2 File az14 OK Type TETRIS _ Description Gain m z ae 204 1 File Function fi TOF Parent 50 2000 ES Dev 7 Type Neutral Gain x C Add trace Replace trace C New window The Product Scan The product scan data is displayed in the Spectrum window by using the pointer and right mouse button in the usual way to select a single scan or several scans over the range of interest In the example shown below four scans over the Yz582 5 peak have been summed together and annotated with the BioLynx package Parent lon Scanning Page 101 Q Tof 2 User s Guide T Spectrum asms41 Bik iE File Edit Display Process Tools Window Help la x 2 DB w a elaela gt BSA digest 1 pmol uL asms41 283 5 483 Cm 261 284 TOF Parent ES 20 100 185 Sum of 4 scans over m z 582 5 peak At low levels where precursor scanning of this type would be most valuable data of this quality is unlikely to be produced with only a few seconds acquisition time for a precursor ion and a product spectrum would need
36. I probe is required include The probe tip assembly becomes contaminated for example by involatile samples if the probe temperature is too low during operation 300 C The appearance of chromatogram peak broadening or tailing Samples that give rise to a good chromatogram peak shape in APcI for example reserpine and common pesticides should display peak half widths of the order 0 1 minutes for 10Oul loop injections at a flow rate of 1 ml min The appearance of significant peak broadening or tailing with these compounds is most likely to be due to a broken fused silica capillary or probe tip heater assembly Low LC pump back pressure For 50 50 acetonitrile water at a flow rate of 1 ml min a LC pump back pressure less than 14 bar 200 psi is indicative of a broken fused silica capillary or a leaking connector High LC pump back pressure For 50 50 acetonitrile water at a flow rate of 1 ml min a LC pump back pressure above 35 bar 500 psi is indicative of a blockage or partial blockage in the fused silica capillary in a LC connector or in the filter It is advisable to change the inner filter pad ona regular basis see Replacing the Fused Silica Capillary in the following pages Gas flow problems Check all gas connections for leaks using soap solution or a suitable leak searching agent such as Snoop Cleaning the Probe Tip Remove any visible deposits on the inner wall of the probe heater with a micro interdental b
37. If a polynomial of order I is requested the values for A amp B are calculated and the higher terms are set to zero For a polynomial of order 5 the highest supported in MassLynx there will be six terms generated When calibrating over a large mass range gt 500 Da it is advisable to use a higher order polynomial as the deviations from the straight line fit become more appreciable Once a calibration has been generated from a reference compound such as PEG it should be used as an instrument calibration to be applied to all subsequently acquired data The procedure for this is described below Lock Mass Temperature variations in the environment and in the instrument power supplies can cause drifts in measurements of a few hundred parts per milion ppm over the course of a day For accurate mass work the instrument should be kept in OPERATE at all times to enable stabilisation of the power supplies Users can compensate for instrument drift by applying a single point lock mass correction that recalculates the term B in the above equation The lock mass reference compound must be internal to the sample and may be introduced by teeing in post column on an LC system The following diagram shows a typical arrangement Calibration and Accurate Mass Page 78 Q Tof 2 User s Guide Lc 200 pl min PA Column 1 ml min amp Reference Compound To Waste Sie a 800 pl min Pump 1 pl min Dead Time Cor
38. Profile Dwell Time Ramp Time Mass of scan time scan time mlm a 2 fim fe fo Lc On the tune page choose RF Settings then set Offsets of 0 5 and Gains of zero A Cone voltage of 35 volts will give a good distribution of PEG peaks Acquire data for one minute over the range 100 to 1000 Da with a scan time of 1 second Combine at least 30 scans of data and check that the signal is not too intense center the data using the Spectrum Center menu as set up below QOTOF Spectrum Center OF Cancel Center method Min peak width at half E height channels Top Centroid top 80 00 Median Centered spectrum IV Create centered spectrum Add Heights New window i Areas C Replace The data acquired should not be above 500 counts sec or deadtime distortion will occur Calibration and Accurate Mass Page 80 Q Tof 2 User s Guide Check that no deadtime correction is employed at this stage Resolution 0 and Np Multiplier 0 QOTOF Accurate Mass TOF Constants Resolution Np Multiplier Lock Mass Correction Mass Window Lock Mass Re center the data using Resolution 10000 and Np Multiplier 0 7 as below OTOF Accurate Mass TOF Constants Resolution fioooa o Hp Multiplier o 700 Lock Mass Correction Cancel Mass Window 0 000 Lock Mass fo Oooo Check that any differe
39. Q Tof 2 User s Guide Micromass UK Limited Floats Road Wythenshawe M23 9LZ Tel 44 161 945 4170 Fax 44 161 998 8915 Tudor Road Altrincham WA14 5RZ Tel 44 161 282 9666 Fax 44 161 282 4400 http www micromass co uk The instrument is marked with this symbol where high voltages are present The instrument is marked with this symbol where hot surfaces are present The instrument is marked with this symbol where the user should refer to this User s Guide for instructions which may prevent damage to the instrument Warnings are given throughout this manual where care is required to avoid personal injury AAAAAA If the instrument is used in a manner not specified by the manufacturer the protection provided by the equipment may be impaired This manual is a companion to the MassLynx NT User s Guide supplied with the instrument All information contained in these manuals is believed to be correct at the time of publication The publishers and their agents shall not be liable for errors contained herein nor for incidental or consequential damages in connection with the furnishing performance or use of this material All product specifications as well as the information contained in this manual are subject to change without notice Micromass is a registered trade mark of Micromass Limited Reg U S Pat amp T M Off Code 6666526 Issue 1 Micromass Ltd Table of Contents Q To
40. RENTS MDB Oix File Function Analog Help MS MSMS Survey Parent Solvent Delay Analog Channels Time mins 0 00 APcl Probe Temp jo Mins 17 Unused 27 Unused 37 Unused 40 Unused o 5 b 15 a S amp S S 40 amp DO 5 e In this example MS1 would begin at Yz300 and step in 1Da intervals up to Yz1000 The spectrum integration time for each step would be 0 9 sec and each step would take 1 0 sec i e 0 9 sec 0 1 sec 700 steps at 1 sec step 11 66 minutes so the retention time is set to 11 7 min to terminate acquisition at the end of the cycle If the retention time is set to a longer period the cycle will begin again at z300 and continue until the retention time is reached The collision energy would be fixed and is set here to 28V Collision energy ramping will be available in a future version of MassLynx to allow the collision energy to be increased as MS1 moves to higher Yz At the completion of this experiment the data file should contain 700 scans of MS MS data Parent lon Scanning Page 98 Q Tof 2 User s Guide Function 1 Parent Scan xi Mass m z p Method 7 Step Mass a lonization Mode fesP gt Start 300 Data Continuum gt End frooo o Repeats fi SomefGpeciun J m Scan Duration secs Start Time fo 00 Scan Time fi 00 End Time 93 00 Inter Scan Delay fot 0 m Collision Energy r Cone Voltage I Use Tune Page Sett
41. S mode 4eV for Q Tof and 10eV for Q Tof 2 The HM setting should be the same for all transmission windows as shown in the example above Determine three sets of conditions giving a transmission of 20 5 and 1Da To allow the multi step method to operate requires the appropriate hardware This is standard on later instruments but may be retrofitted to earlier models If it has been fitted then the instrument configuration file should have the line RE 1 as shown in the example To test if in doubt if the hardware is in place and optimised the transmission on MS in the MS MS mode with the HM and LM sliders set to 0 should be about 30 35Da If this transmission window cannot be set to greater than 20Da then the instrument cannot be operated in the multi step mode without modification Instrum cfg Notepad ofj x File Edit Search Help Parent lon Scanning Page 93 Q Tof 2 User s Guide Setting up a Scan Function for Precursor Scanning There are two modes of data acquisition i Multi Step Mode The multi step mode is of most use when there are only a small number of components in the mixture For example proteins are usually phosphorylated at only one or two sites A digest of a phosphorylated protein will consequently contain only one or two phospho peptides If precursor scanning is being used to find these phospho peptides by looking in the negative ion MS MS mode for the characteristic 2778 9 signal for POs then only
42. SA amp Canada 1 314 771 5750 call collect and ask for the fax machine Direct fax Outside USA amp Canada 1 314 771 5757 this is a toll call Reference Information Page 143 Q Tof 2 User s Guide Positive lon Reference Information Page 144 Bovine Ubiquitin UBQ U6253 8564 85 650 1500 General HBA oe 15126 36 700 1500 Hb analysis H753 i y Superoxide dismutase Hb internal SOD S2515 15591 35 900 1500 al Human globin HBB H7379 15867 22 800 1500 Hb analysis Horse heart myoglobin MYO M1882 16951 48 700 1600 General nea ES and PEGH1000 80 1000 APcI M calibration PEG 200 400 600 1000 Polyethylene glycol ammonium acetate ES PEGH2000 mixture 80 2000 calibration PEG 200 400 600 1000 1450 Sodium Iodide Caesium General NAICS 20 4000 ES Iodide mixture calibration NAIRB Sodium iodide Rubidium 20 4000 ES l Iodide mixture calibration Horse Heart Myoglobin Reference File MYO REF Molecular Weight 16951 48 Q Tof 2 User s Guide 28 606 419 21 808 222 13 1304 969 616 177 20 848 583 12 1413 633 2T 628 841 19 893 192 11 1542 053 26 652 989 18 942 758 10 1696 158 25 679 068 17t 998 155 9 1884 508 24 707 320 16 1060 477 2119 945 23 738 030 15 1131 108 T 2422 651 22 771 531 14 1211 829 Polyethylene Glycol PEG NH4 Reference Files PEGH1000 REF BEGH20
43. a 370 2220 370 7277 371 5121 se 374 2284 Ae 165 442 795 447 a 369 370 371 372 373 374 379 The model successfully corrects for deviations of up to about 15 mDa at mass 500 at which point the limits of the model are reached with no correction applied at higher ion current Users should familiarise themselves with the ion current range over which successful mass measurements can be made Once the Resolution and Np Multiplier figures have been evaluated they can be left active in the menu without affecting centered data in any adverse way The procedure involved using the Spectrum Make Calibration commands is a post processing calibration producing a data file of a particular format and with the extension cal The file resulting from the commands Instrument Calibrate Save Calibration has the same file extension cal but it should be noted that because it is an instrument calibration file it is of an incompatible format to that described above Folders and naming conventions should be appropriately assigned Information concerning the calibration of Q Tof 2 is provided in the MassLynx NT Guide to Data Acquisition Calibration and Accurate Mass Page 88 Q Tof 2 User s Guide Exact Mass Measurement Additional Hints e Best results are obtained if the lock mass gives an intensity of approximately 100 to 200 counts per second as shown on the real time tune display e The lock mass should be chosen to b
44. ally set at 100mV a value high enough to prevent electronic noise being detected as ions Threshold This parameter should normally be set to zero Setting to 1 will cause all peaks in the spectrum with one count to be thresholded out Bunching This facility can reduce data file size although at the expense of resolution For most analyses it is generally set to 1 Routine Procedures Page 39 Q Tof 2 User s Guide Lteff This is used to make the TOF mass measurement nominally correct without a calibration The default value is 1800 To adjust the nominal mass scale as displayed on the tune page without calibration Acquire a TOF spectrum of a standard compound with Lteff set to 1800 Calculate the new value of Lteff from the relation Lteff 1800 mina Maci where Mina indicated Vz Mact actual Vz Enter the new Lteff value in the tune page Once the new Lteff value has been entered all subsequent acquisitions should nominally be correctly mass measured Centroid If data is acquired in centroid format the right hand section of the dialog displays the settings generated during the instrument calibration described in Calibration and Accurate Mass later in this document This feature was introduced with MassLynx Version 2 0 and is absent from previous versions of MassLynx Calibration Information concerning the calibration of Q Tof 2 is provided in Calibration and Accurate Mass later in this document an
45. any dust or particles Caution Tools carborundum paper or micromesh must not be used to remove contamination from the main filter rods It is not anticipated that the gas cell or hexapole transfer lens will require cleaning Replacing the MS1 and Gas Cell Optical Bench Assembly Reassembly is the reverse of the appropriate dismantling procedure Take extra care to ensure that all electrical connections are correctly and securely made and that the various mechanical assemblies are accurately aligned within the housing on their locating dowels Maintenance and Fault Finding Page 133 Q Tof 2 User s Guide The MS2 Analyser and Detector Assembly The tuning detector orthogonal acceleration cell reflectron and microchannel plate assemblies are separated from the MS1 and gas cell region by a differential pumping orifice It is anticipated that this region of the instrument will not require routine maintenance under normal operating conditions The tuning detector system has been designed for trouble free operation over many years The sealed photomultiplier is safe from contamination and pressure surges the traditional enemies of mass spectrometer multipliers and the conversion dynodes are tolerant of ion burn The phosphor has also proved to be reliable and long lasting No routine maintenance of this detector is therefore required The microchannel plate system is at risk from failure properly to condition the detector following
46. arging effects are apparent Charging is evidenced by a noticeable progressive drop in signal intensity often resulting in a complete loss of signal Switching the instrument out of and back into operate causes the beam momentarily to return The hexapole transfer lens should not require frequent cleaning If it is suspected that the lens does need cleaning it may be withdrawn from the front of the instrument after removing the ion block support Warning Cleaning the various parts of the source requires the use of solvents and chemicals which may be flammable and hazardous to AAA health The user should take all necessary precautions Maintenance and Fault Finding Page 112 Q Tof 2 User s Guide Cleaning the Sample Cone in Situ This may be necessary due to lack of sensitivity or fluctuating peak intensity or if deposited material is visible on the outside of the sample cone Proceed as follows On the MassLynx top level window launch the tune page Deselect Operate to put the instrument in standby mode Switch off the LC pumps Disconnect the liquid flow at the rear of the probe Set Source Block Temp and either APcl Probe Temp or Desolvation Temp to 20 C to switch off the heaters Warning Removal of the APcI probe or desolvation nozzle when hot may cause burns Caution Removal of the APcI probe when hot will shorten the probe heater s life gt e The cooling time will be significantly shortened if the API gase
47. ary Pump Oil 115 Foreliune Trap 115 The Source 116 Overview 116 Cleaning the Sample Cone in Situ 117 Removing and Cleaning the Sample Cone 119 Removing and Cleaning the Source Block and Extraction Cone 121 Removing and Cleaning the RF Lens Assembly 123 Reassembling and Checking the Source 125 The Corona Discharge Pin 126 The Electrospray Probe 127 Overview 127 Replacement of the Stainless Steel Sample Capillary 129 The APcI Probe 131 Cleaning the Probe Tip 131 Replacing the Probe Tip Heater 32 Replacing the Fused Silica Capillary 133 The Analyser 135 Removing the MS1 and Collision Cell Optical Bench Assembly 136 Dismantling and Cleaning the Entrance Prefilter 136 Cleaning the MS1 Analyser Assembly 137 Replacing the MS1 and Gas Cell Optical Bench Assembly 137 The MS2 Analyser and Detector Assembly 138 Fault Finding 139 Introduction 139 No Beam 139 Unsteady Beam 140 High Back Pressure 141 Loss of Sensitivity 142 Incorrect Isotope Distributions 142 High Noise Levels 143 Chemical Noise 143 Electronic Noise 143 Poor Analyser Vacuum 143 Cleaning Materials 144 Preventive Maintenance Check List 145 Table of Contents Q Tof 2 User s Guide Reference Information Overview Positive Ion Horse Heart Myoglobin Polyethylene Glycol PEG NH4 Sodium Iodide and Caesium Iodide Mixture Sodium Iodide and Rubidium Iodide Mixture Negative Ion Horse Heart Myoglobin Mixture of Sugars Sodium Iodide and Caesium Iodide or Rubidium Iod
48. ative ion mode In both cases the first negative reference peak appears at Yz 127 T and the remaining peaks are due to Nal clusters Use reference file NAINEG REF Reference Information Page 150 Q Tof 2 User s Guide index A Acetonitrile 44 Adducts 50 53 70 Acquisition 39 Active inverted magnetron gauge 16 96 Air filter 95 tray 94 Ammonia 44 Ammonium acetate 135 Analog channels 22 Analyser tuning menu 34 Collision 35 Entrance 35 lon energy 35 LM Res and HM Res 34 Multiplier 35 Steering 35 APcl 10 69 Analysis 75 Preparation 29 Tuning 12 75 APcl probe 18 76 113 Checking 71 Filter 113 Fused silica capillary 115 Maintenance 113 Temperature 75 113 Tip heater 114 Atmospheric pressure chemical ionisation See APcl Attenuator 15 Back pressure High 113 123 Low 113 Biopolymers 55 Caesium iodide 55 132 134 136 Calibration 78 Electrospray 55 Camera 63 Capillary 33 52 Charging 98 Cleanable baffle 61 71 98 102 Cleaning materials 126 Cluster ions 53 57 Column 4 6mm LC 46 57 69 Capillary LC 57 Microbore 2 1mm LC 46 57 Cone gas 50 61 Cone gas nozzle 61 107 Contact closure in 22 Conversion dynode 120 Cooling fan 95 Corona 10 Corona discharge pin 18 29 70 98 108 Coupled column chromatography 58 D Data processing 39 Dead time correction 79 Desolvation gas 18 19 75 Desolvation heater 18 Desolvation temp 50 Detector 9 120 Discharge pin See Corona discharge pin Dive
49. atuiss gt il Data Directory CAMASSLYNE DATA Click bd to dismiss this box and all subsequent acquisitions will now be tagged with the newly generated calibration Lock Mass Correction The application of a single point lock mass correction will now correct for subsequent instrument drift and bring masses back to within 5 ppm RMS on the condition that there is no isobaric chemical interference with either lock mass or analyte peaks The lock mass is found under the TOF Spectrum Center menu when QTOF is clicked QTOF Accurate Mass TOF Constants Resolution joo Np Multiplier 0 000 Lock Mass Correction Mass Window 2 000 Lock Mass 520 333 K Cancel ail Calibration and Accurate Mass Page 84 Q Tof 2 User s Guide Centering the spectrum with these parameters will force the peak at 520 to be 520 333 exactly and recalibrate the entire mass spectrum Deadtime Correction Acquire a spectrum of PEG at the higher concentration of 10 nl ml and create a centered spectrum with no lock mass and no correction All parameters set to zero QOTOF Accurate Mass TOF Constants Resolution joo Np Multiplier o 000 Lock Mass Correction Mass Window jo Lock Mass jd 0K Ea etic a Cancel Now go to Tools Make calibration and choose the same peghnh4 reference file Hake new calibration lt Reference material Reference file
50. be accommodated although it is often preferable with electrospray ionisation to split the flow such that 5 50 yl min of eluent enters the mass spectrometer The optional nanoflow interface allows electrospray ionisation to be performed in the flow rate range 5 to 1000 nanolitres per minute For a given sample concentration the ion currents observed in nanoflow are comparable to those seen in normal flow rate electrospray Great sensitivity gains are therefore observed when similar scan parameters are used due to the great reductions in sample consumption Instrument Description Page 10 Q Tof 2 User s Guide Z spray lon Source Quadrupole Hexapole Dynolite Analyser Transfer Lens Point RECENS Hexapole Pusher Detector mcp Collision Cell Detector a a MS1 Quadrupole MS The principal components of the ion optical system are shown here in schematic form Ions generated in the Z spray source are transferred to the quadrupole analyser MS1 via the independently pumped RF lens After leaving the quadrupole analyser the ions flow into the orthogonal time of flight analyser MS2 The ion beam is focused into the pusher by the acceleration focus steer and tube lenses The pusher then pulses a section of the beam towards the reflectron which then reflects ions back to the detector Reflectron EEEN EENEN MS2 TOF MS As ions travel from the pusher to the detector the
51. buliser gas is steady The nitrogen supply pressure should be 7 bar 100 psi 10 Desolvation Temp is not set too high for the liquid flow rate used High temperatures can vapourise solvent within the electrospray probe Should the preceding checks fail to reveal the cause of the problem proceed to the following section Maintenance and Fault Finding Page 136 Q Tof 2 User s Guide High Back Pressure For electrospray a higher than normal back pressure readout on the HPLC pump together with a slowing of the actual solvent flow at the probe tip can imply that there is a blockage in the capillary transfer line or injection loop due to particulate matter from the sample To clear the blockage Remove the probe from the source and increase the solvent flow to 50 ul min to remove the blockage Often injections of neat formic acid help to redissolve any solute which has precipitated out of solution If the blockage cannot be cleared in this fashion Remove the finger tight nut and tubing from the back of the probe If the back pressure remains high Replace the tubing with new tube or first try removing both ends of the tube If the back pressure falls Replace the stainless steel sample tube inside the probe or try reversing the tube to blow out any blockage Reconnect the tubing to the probe The solvent flow can now be readjusted and the probe replaced into the source To check the flow rate from the solve
52. but is increased for higher solvent flow rates Desolvation Temp This sets the temperature of the desolvation gas heater It is usually set to 150 C and increased for higher solvent flow rates Sai Tune DEFAULT ESP File lonMode Gas Ramps Other Stop Window Help S t S S alal ieie 22 Mass Span Gi LM Res Tune Peak 1 57 368 fo aC HM Res Tune Peak 2 Collision Tune Peak 3 Tune Peak 4 lon Energy 19 lt gt ee 4 07e3 Steering Z gt Entrance wog Pre Filter 50 lt Mutipier K Je ee McP SS 571 Source MS MS 2 Acquire OPERATE VIiIsFe2tf3f4 LM Res and HM Res These set the resolving DC on the quadrupoles The two sliders are set to give constant resolution across the mass range When the quadrupoles have been set up settings of 15 on both sliders should give unit resolution at 20 peak height Routine Procedures Page 34 Q Tof 2 User s Guide Collision This sets the collision energy of the ions when they reach the collision cell The cell itself is grounded but the collision energy voltage is simultaneously applied to all the optical elements preceding it i e cone extraction lens source hexapole differential pumping aperture and quadrupole In Q Tof 2 gas is always introduced into the cell affording collisional cooling and consequently higher resolution The collision energy is set to 10eV for MS mode to maximise ion transmission but produce l
53. ce O ring exposed Ensure that the source block heater has been switched off and has cooled before proceeding Observe the Source BlockTemp readback on the tune page f Warning When the source enclosure has been removed the ion block heater is Nanoflow Electrospray Page 60 Q Tof 2 User s Guide Probe Flange Mounting Pillar ee Source Thumb Nuts ZX Source robe Adjustment Flange Thumb Nuts Unscrew the three probe flange mounting pillars using the holes to obtain the necessary leverage If the cone gas nozzle is not in Cone Gas Purge place close the sample cone Nozzle Gas Plug isolation valve Remove the two Da ee screws that secure the sample cone and fit the cone gas nozzle Replace the two screws Connect the cone gas outlet to the cone gas nozzle using the PTFE tubing provided Open the sample cone isolation valve The cone gas flow rate is set at E lated 30 of the total desolvation gas O Ring j flow Ensure that the purge gas is plugged disabled Ensure that the cleanable baffle the exhaust liner and the corona discharge pin blanking plug are fitted Nanoflow Electrospray Page 61 Q Tof 2 User s Guide Fit a viton O ring and the three shorter nanoflow pillars Install the perspex p cover and the en Viton nanoflow end flange __ O Ring securing this with Socket Head Screws socket head screws Do not attempt to refit the moulded cover If not al
54. ce enclosure will run cooler if purge gas is used Warning For health and safety reasons always ensure the exhaust line is vented outside the building or to a fume hood Warning Ensure that a plastic bottle is connected in the exhaust line to collect any condensed solvents Electrospray Page 53 Q Tof 2 User s Guide Removing the Probe To remove the probe from the source proceed as follows On the tune page deselect Operate to put the instrument into standby mode Switch off the liquid flow and disconnect from the probe Deselect API Gas and turn off Nitrogen Disconnect the probe cable from the instrument Disconnect the nebulising gas supply from the instrument Electrospray Page 54 Q Tof 2 User s Guide General Information Care should be taken to ensure that samples are fully dissolved in a suitable solvent Any particulates must be filtered to avoid blockage of the transfer line or the probe s capillary A centrifuge can often be used to separate solid particles from the sample liquid There is usually no benefit in using concentrations greater than 20 pmol l for biopolymers or 10 ng yl for low molecular weight compounds Higher concentrations will not usually improve analytical performance Conversely for biopolymers lower concentrations often yield better electrospray results Higher levels require more frequent source cleaning and risk blocking the transfer capillary Optimisation for low molecular weigh
55. cement The sensitivity of a LC MS analysis can be increased or optimised in a number of ways by alterations to both the LC operation and the MS operation In the LC area some examples include the use of high resolution columns and columns with fully end capped packings For target compound analysis techniques such as trace enrichment coupled column chromatography or phase system switching can have enormous benefits Careful choice of the solvent and solvent additives or modifiers may also prove important Electrospray Page 58 Q Tof 2 User s Guide Overview Nano LC Option O Capillary Option Three axis Manipulator Stop Handle stage Protective Cover The optional nanoflow interface allows electrospray ionisation to be performed in the flow rate range 5 to 1000 nanolitres per minute There are two options for the spraying capillary which can be alternately fitted to the interface e Borosilicate metal coated glass capillary Metal coated glass capillaries allow the lowest flow rates to be obtained although they are used for one sample only and must then be discarded e Nano LC This option is suitable for flow injection analyses or for coupling to nano HPLC and uses a pump to regulate the flow rate down to 100 nl min If a syringe pump is to be used a gas tight syringe is necessary to obtain correct flow rates without leakage A volume of 25ul is recommended Nanoflow Electrospray Page 59
56. components in the sample is small then it may be more efficient to break the experiment into several steps By surveying the mass scale in large e g 20Da intervals and then flagging interesting segments for further study at say 5Da and then Da intervals the experiment time can be significantly reduced The parent scanning facility is automatically available in MassLynx 3 4 in previous versions it may need to be unlocked Unlocking the Parent Scan Facility In this case the MassLynx ini file must be modified to unlock the parent facility Close down all MassLynx windows including the tune page and exit MassLynx In the MassLynx root directory find the MassLynx ini file and double click it to open it up in Notepad Use the Find facility under Search in the top banner to move to the top of the section headed AcquPara Beneath this entry add as the next line the following QTOFParent TRUE Save the file and exit When a user logs into MassLynx the MassLynx ini file is used to create a specific ini file for that user and therefore there will also be a file named user ini in the MassLynx root directory Often users log into MassLynx as Administrators in which case the user ini file will be called Administrator ini For the parent scan to be unlocked this user ini file will need either to be deleted so that it is re created at login or the same changes will need to be made as in the MassLynx ini file NB If neither of these a
57. ction in one second then the limits of the model are being reached If the limits of the model are exceeded no correction is applied the same result will be obtained by centring the data with Resolution and Np Multiplier ser to zero If the limits of the deadtime correction algorithm are exceeded it may be possible to use the C isotope instead e For the best mass accuracy when mass measuring doubly charged ions it is advisable to use a doubly charged lock mass peak Calibration and Accurate Mass Page 89 Q Tof 2 User s Guide e To obtain the true number of ions per peak areas must be selected on the peak centre menu The standard deviation in the determination of the mass strictly z centroid of a triangular shaped peak Gppm due to ion statistics alone is given by the equation below A triangle is assumed to be a close enough approximation to the shape of the mass spectrometer peak for the equation to be valid Oppm 10 AM M 24N gt ppm where AM is the width z of a triangular peak across the base M is the z value of the peak Np is the number of ions per peak Using the above equation we can calculate the number of ions per peak required to give a standard deviation of 5 ppm when measuring a peak at 500 Yz Assuming 10000 FWHM resolution so AM 0 1 Yz width at base twice width at half height then Np 5x10 x 500 0 1 x 24 67 ions per peak Thus standard
58. ctrospray APcI and nanoflow electrospray are given in the relevant chapter of this document Routine Procedures Page 32 Q Tof 2 User s Guide S Tune DEFAULT ESP oi x File lonMode Gas Ramps Other Stop Window Help ha S ct x Bl als ieie 22 Mass Span Gain Capillary Tune Peak 1 Cone Tune Peak 2 Extractor Tune Peak 3 Tune Peak 4 RF Lens 2 d 571 36 2 83e3 x30 Wuhipier lt gt MOP Source Block Temp 0 Desolvation Temp 150 571 Source MS MS 2 Acquire OPERATE MEn gt lg Sl INe The positive ion electrospray ESP source tuning menu is shown Suggested tuning parameters are as follows Capillary This sets the absolute voltage on the electrospray probe or APCI corona needle and is typically adjusted to 3000V Cone This sets the voltage on the sampling cone relative to the extraction lens It is dependent on compound and charge state For multiply charged species this is set to 40 50eV and higher for singly charged species In general higher cone voltages are needed for larger mass ions Extractor This sets the voltage on the extraction lens and is normally set from 0 2V RF Lens This sets the offset voltage on the hexapole and the first differential pumping aperture It is usually set to 1V Routine Procedures Page 33 Q Tof 2 User s Guide Source Block Temp The source block temperature is usually set to 80 C
59. d in the Guide to Data Acquisition Data Acquisition The mechanics of the acquisition of sample data are comprehensively described in the Guide to Data Acquisition Refer to that publication for full details Data Processing The processing of sample data is comprehensively described in the MassLynx NT User s Guide Refer to that publication for full details Routine Procedures Page 40 Q Tof 2 User s Guide Shutdown Procedures Emergency Shutdown In the event of having to shut down the instrument in an emergency proceed as follows Switch off the power at the wall mounted isolation switch es if fitted If not switch the power off at the rear of the instrument and switch off all peripherals A loss of data is likely Disconnect any LC systems to prevent solvent flowing into the source Overnight Shutdown When the instrument is to be left unattended for any length of time for example overnight or at weekends proceed as follows Switch off the LC pumps Set Capillary to OV Undo the finger tight connector on the probe to release the tubing leading from the LC system Before disconnecting the probe it is good practice to temporarily remove the probe and flush it of any salts buffers or acids If APcI is being used reduce APcl Probe Temp to ambient temperature A Caution Leaving the APcI probe hot with no gas or liquid flow will shorten the lifetime of the probe heater Deselect API Gas to turn off t
60. d to run down to 50 speed after which a vent valve automatically admits dry nitrogen Remove the source enclosure and the sample cone as described in the previous section A N When the instrument has vented Remove the two screws which secure the ion block and remove the ion block heater and the ion block Separate the extraction cone and the PTFE insulating ring from the ion block Remove the plug and the PTFE sealing washer Remove the sample cone as described above Maintenance and Fault Finding Page 117 Q Tof 2 User s Guide Leaving the valve stem in place immerse the ion block in an ultrasonic bath containing 50 50 acetonitrile water or 50 50 methanol water followed by 100 methanol Clean the sample cone and the extraction cone using in turn e concentrated formic acid e 50 50 acetonitrile water or 50 50 methanol water e 100 methanol Warning Strong acid causes burns Carry out this procedure in a fume cupboard using protective equipment Dry all components using a flow of nitrogen or place them in a warm oven Maintenance and Fault Finding Page 118 Q Tof 2 User s Guide Removing and Cleaning the RF Lens Assembly View from Rear lon Block Support To remove the RF hexapole transfer lens assembly proceed as follows Remove the ion block as described above Remove the three screws retaining the ion block support and carefully withdraw it together with the su
61. during a LC run e As a switching valve to switch for example between a LC system and a syringe pump containing calibrant This valve is pneumatically operated using the same nitrogen supply as the rest of the instrument The two switches marked Load and Inject enable the user to control the valve when making loop injections at the instrument Instrument Description Page 19 Q Tof 2 User s Guide Rear Panel Connections Collision Gas In Nitrogen In Nitrogen Out O Water In Water Out o ET ee Water Water is used to cool the turbomolecular pumps Nitrogen Gas In The nitrogen supply 100 psi 7 bar should be connected to the Nitrogen Gas In push in connector using 6mm PTFE tubing If necessary this tubing can be connected to 4 inch tubing using standard 1 4 inch fittings nitrogen supply and the instrument The use of other types of plastic tubing will f Caution Use only PTFE tubing or clean metal tubing to connect between the result in chemical contamination of the source Instrument Description Page 20 Q Tof 2 User s Guide Exhausts The exhaust from the rotary pump should be vented to atmosphere outside the laboratory The gas exhaust which also contains solvent vapours should be vented via a separate fume hood industrial vent or cold trap The gas exhaust should be connected using 10mm plastic tubing connected to the push in fitting instrument failure rotary
62. e Active Inverted Magnetron Gauge In particular the quadrupole analyser gauge requires regular maintenance For information on cleaning the active inverted magnetron Penning gauge refer to the Edwards literature supplied with the instrument Gas Ballasting Gas ballasting serves two important purposes Exhaust Gas Ballast e When rotary pumps are used to aes ug pump away solvent vapours the solvent vapour can become a dissolved in the pump oil eb causing an increase in backing line pressure Gas ballasting is a method of purging the oil to remove dissolved contaminants e Oil mist expelled from the Oil a rotary pump exhaust is trapped Indicator in the oil mist filter This oil is returned to the rotary pump during gas ballasting Gas ballasting should be performed routinely on a weekly basis for 30 minutes If the source is used in the APcI or megaflow electrospray modes more frequent gas ballasting is recommended Gas ballasting is performed on the E2M28 pump by rotating the gas ballast valve 5 to 6 turns in a counterclockwise direction It is normal for the rotary pump to make more noise when the gas ballast valve is open A Caution Failure to gas ballast the rotary pump frequently leads to shortened oil lifetime which in turn may shorten rotary pump lifetime Maintenance and Fault Finding Page 110 Q Tof 2 User s Guide Oil Mist Filter The E2M28 rotary pump is fitted with an Edwards EMF20 oil
63. e at the upper end of the mass range used e Do not change transfer lens voltages without re calibrating the instrument Changing Cone will not change the calibration e Always be aware of possible chemical interference problems either on the sample or the lock mass peak e When performing a base calibration using PEG for example better results may be obtained by using a stronger solution and moving the probe off axis to limit the ion current rather than using a lower concentration This has the effect of minimising any possible chemical interference from background ions e Always check the stability of the spray see the instructions for the setting of the probe tip in Maintenance and Fault Finding Short term variations in the spray produce fluctuations in the number of ions per peak per pusher pulse giving rise to errors in the deadtime correction calculations The number of ions per peak per pusher pulse is calculated from the ion current integrated over a period of time thus only giving an average value e To obtain the best deadtime correction only combine scans of a similar intensity either at the top of a chromatographic peak or in the tail of a chromatographic peak This ensures the number of ions per peak per push is calculated correctly e The deadtime correction algorithm can only correct for ion intensities and Pz shifts up to a limit If the ion current approaches approximately 10 000 counts per peak without corre
64. e electronics detector rise time and delays of trigger signals through cables If a data file is acquired from the instrument with no calibration applied then it is assumed that the offset is zero and the gain P is calculated from the instrument geometry Nominal Mass Accuracy The pathlengths should be set up to give at least nominal mass accuracy Nominal mass measurement is achieved on the Q Tof 2 by adjustment of the Lteff factor a term which quantifies the difference between the indicated and actual mass A TOF spectrum of a standard compound is acquired with Lteff set to its default value of 1800 A new value of Lteff can be calculated from the following relation Lteff 18004 Mina mact where Mina indicated m z and Mar actual m z Enter this new value under TDC Parameters all subsequent mass measurements will be nominally correct Calibration and Accurate Mass Page 77 Q Tof 2 User s Guide Calibration With no calibration applied the spectral data in MassLynx is merely a set of mass intensity pairs Mn In based upon instrument geometry The inherent relationship between mass and time shown above makes it prudent to generate higher order calibration coefficients that are applied to the square root of the nominal masses Mn 3 J c A BV CM DM where the terms A B C D are calculated by fitting a polynomial to the acquired mass spectral data Mc is the calibrated displayed mass
65. e heater as described in the preceding section Remove the probe end cover by removing the two screws and the grub screws that retain the LC filter Loosen the filter from the adapter nut Unscrew the adapter nut from the probe Remove and discard the fused silica capillary Using a ceramic capillary cutter cut a new length of 300um o d x 100m i d fused silica capillary about 1 centimetre excess in length Using a GVF 004 ferrule and the adapter nut connect the capillary to the filter ensuring that the capillary passes through the ferrule but stops short of the filter Maintenance and Fault Finding Page 129 Q Tof 2 User s Guide Feed the sample capillary through the probe ensuring that a 0 4mm graphitised vespel ferrule GVF 004 is fitted Using a ceramic capillary cutter cut the capillary at the nebuliser so that between 0 5 and 1 0mm of capillary is protruding from the nebuliser It is important to cut the capillary square This should be examined using a suitable magnifying glass Undo the adapter nut from the probe and withdraw the capillary from the probe Remove 20mm of polyamide coating from the end of the capillary using a flame and clean with a tissue saturated with methanol Carefully re feed the sample capillary through the probe ensuring that the graphitised vespel ferrule is still fitted Using a Rheodyne spanner gently tighten the adapter nut to the probe Replace the probe end cover and retaining scr
66. e the number of discharges and reduce the noise Caution It is strongly recommended that assistance is sought from Micromass if maintenance to the detector system is thought necessary Caution Assistance from Micromass should be sought if due to symptoms such as excessive noise spikes loss of detector gain or abnormal peak shapes maintenance to any of the components within the TOF analyser housing is thought to be necessary Poor Analyser Vacuum Before suspecting a pump fault or vacuum leak see Vacuum System earlier in this chapter it is worth checking the inverted magnetron Penning gauge If this gauge has become dirty it will indicate a poor vacuum or even fail to register at all For information on cleaning the gauge refer to the Edwards literature supplied with the instrument Warning The instrument must be vented and electrically isolated at the supply outlet before removing the instrument s covers to gain access to the active inverted magnetron gauge Note that if the instrument has been vented to atmosphere instead of dry nitrogen it may take one to two days before reaching the vacuum levels obtained prior to venting Maintenance and Fault Finding Page 139 Q Tof 2 User s Guide Cleaning Materials It is important when cleaning internal components to maintain the quality of the surface finish Deep scratches or pits can cause loss of performance Where no specific cleaning procedure is given fine abrasiv
67. ec defaults to 30 usec Entering 0 usec switches the pusher off Increasing the flight time reduces the duty cycle sampling efficiency of the TOF analyser resulting in decreased sensitivity For the best mass accuracy the instrument should be re calibrated if the flight time is changed If Manual Pusher is not selected then the repetition frequency of the pusher pulse is determined automatically according to the highest z requested in the acquisition range as shown in the table below 44 psec lt 1000 62 usec 1001 2000 88 usec 2001 4000 124 usec 4001 8000 176 psec 8001 16000 246 usec 16001 32000 Routine Procedures Page 38 Q Tof 2 User s Guide Other Tune Page Settings TDC Settings To access the TDC time to digital converter settings Select Other TDC settings Signal Centroid Start mv foo First Dif Width Bo Stop mv fso Second Diff Width 2 Min peak height fi Min points in peak fi p Np oo Threshold fo Resolution 10000 Leff e760 Lock Mass jooo Bunching Lock Mass Window fo 00 Cancel Start This is the size of the trigger signal that is necessary to trigger the TDC start the clock The start signal is derived from the pusher voltage itself and a typical value is 800mV This voltage may be different in negative ion mode Stop This is the size of pulse needed to register as being an ion so stopping the clock It is usu
68. ectly With the sprayer assembly removed from the stage Cut approximately 25mm of the Rae red stripe peek tubing and using the plug cap and a Valco nut set a ea ictal ferrule to the correct position on g the tubing 5 Make up 5 Flow At this stage the ferrule is required Only a only to grip the tubing lightly and ooy J should not be too tight Required O Ri mT Cut the peek such that 10mm of a SoN the peek protrudes from the back Red Stripe Peek Tubing ont of the ferrule wl 90m Fused gt o Thread approximately 70mm of Silica the 90 micron o d fused silica ZJ p gt SN through the new fitting z5 MZ aes Nebuliser a gt Ensure that the fused silica is flush Gas 7 ee oJ with the peek sleeve Nano LC S SoN Again using the plug cap tighten Body 5 LANG the nut further to ensure that the b gt sy fused silica is gripped Some force Chamber A may be required to do this Remove the sleeved fused silica from the plug cap and remove the Valco nut Nebulising ay Tip Place an O ring onto the peek tube using tweezers if necessary The O ring is required to seal the region between the ferrule and the end of the thread on the nano LC chamber Thread the sleeved fused silica through the nano LC chamber Rotate the microvolume u
69. ector is used the analog output may be input to MassLynx NT for chromatographic processing The interfacing of 4 6mm columns to the electrospray source can be achieved either by flow splitting or by direct coupling In both cases an elevated source temperature and drying gas flow rate are required In general the best results are obtained by splitting after the column using a zero dead volume tee piece so that 200 300 jl min is transferred to the source A Caution The maximum operating temperature for the source heater is 150 C Do not set Source Block Temp higher than 150 C Conventional reverse phase and normal phase solvent systems are appropriate for LC electrospray Involatile buffers may be used but prolonged periods of operation are not recommended When using involatile buffers the probe should be moved as far away from the sample cone as possible This may reduce sensitivity slightly but will reduce the rate at which involatile material will be deposited on the sample cone Trifluoroacetic acid TFA and triethylamine TEA may be used up to a level of 0 05 If solvents of high aqueous content are to be used then tuning conditions should be appropriate for the solvent composition entering the source Electrospray Page 57 Q Tof 2 User s Guide Higher source temperatures 150 C are also recommended for high aqueous content solvents Tetrahydrofuran THF should not be used with peek tubing LC MS Sensitivity Enhan
70. embedded PC Switch on the host PC Log on to Windows NT and wait for the system to boot up before the Q Tof 2 is switched on Switch on the mains to the mass spectrometer using the two circuit breakers situated on the service panel at the rear of the instrument Log on to Micromass account password analysis Windows NT and MassLynx NT are configured to prevent unauthorised access On the host PC double click on the MassLynx icon in the Windows desktop and display the tune page Routine Procedures Page 25 Q Tof 2 User s Guide Pumping manufacturers recommend that the pump is not started when the oil temperature f Caution To minimise wear to the lubricated components of the rotary pump the is below 12 C Select Vacuum from the menu bar at the top of the tune page Click on Pump The rotary pump and the turbomolecular pumps start simultaneously The Vacuum LED on the front of the instrument shows amber as the system pumps down When the system has reached operating vacuum the Vacuum LED changes to a steady green If the rotary pump oil has been changed or replenished open the gas ballast valve on the rotary pump See the pump manufacturer s literature for details Rotary pumps are normally noticeably louder when running under gas ballast If opened close the gas ballast valve when the rotary pump has run under gas ballast for 30 minutes MCP Detector Conditioning The MCP detector must be conditioned before
71. enables flow rates from 200 jl min to 1 ml min to be accommodated This allows microbore 2 1mm or 4 6mm diameter columns to be interfaced without splitting Changing Between Flow Modes When changing between megaflow and standard electrospray operation it is essential that the correct tubing is used to connect the probe to the sample injector For megaflow operation 16 o d 0 007 i d peek tubing easily identified by its yellow stripe is used This replaces the standard fused silica tube together with the PTFE sleeves Normal Flow Electrospray PTFE Sleeve Fused Silica Tube PTFE Sleeve Probe Injector gt Megaflow Electrospray 1 16 o d 0 007 i d Peek Tube Electrospray Page 46 Q Tof 2 User s Guide Blanking Plug Mounting Contact High Voltage Socket Cleanable Baffle Warning The probe tip is sharp and may be contaminated with A A harmful and toxic substances Always take great care when handling the electrospray probe Ensure that the source is assembled as described in Maintenance and Fault Finding and that the instrument is pumped down and prepared for electrospray operation as described in Routine Procedures Ensure that a supply of nitrogen has been connected to the gas inlet at the rear of the instrument and that the head pressure is between 6 and 7 bar 90 100 psi Ensure that the exhaust liner and the cleanable baffle are fitted to the
72. er MCP Conditioning to access the MCP conditioning program Set Start to 100V Stop to 2400V Duration to 600 minutes and Step to 5 minutes A quick condition may be performed following brief venting after source cleaning for example Set Start to 100V Stop to 2400V Duration to 120 minutes and Step to 1 minute Caution Failure to follow the recommended MCP conditioning procedure can severely reduce detector lifetime Instrument Warm up Switch the instrument into the operate mode by selecting Operate on the MassLynx tune page For the best mass accuracy to be obtained the instrument temperature must be stabilised for a minimum of two hours after switching into operate Leaving the instrument continuously in operate does not shorten the detector lifetime It is recommended that the instrument is left in operate at all times except of course during maintenance procedures in order to reduce mass scale drifts due to temperature changes Switching the instrument out of operate mode overnight is not necessary Using the Instrument The Q Tof 2 is now almost ready to use To complete the start up procedure and prepare for running samples follow the instructions in Start Up Following Overnight Shutdown in the following pages Routine Procedures Page 27 Q Tof 2 User s Guide Start Up Following Overnight Shutdown The instrument will have been left in the operate mode under vacuum It is recommended that the data system
73. es should be used to remove dirt from metal components Recommended abrasives are e 600 and 1200 grade emery paper e Lapping paper produced by 3M After cleaning with abrasives it is necessary to wash all metal components in suitable solvents to remove all traces of grease and oil The recommended procedure is to sonicate the components in a clean beaker of solvent and subsequently to blot them dry with lint free tissue Recommended solvents are e Isopropyl Alcohol IPA e Methanol e Acetone Following re assembly components should be blown with oil free nitrogen to remove dust particles Warning Many of the procedures described in this chapter involve the removal of possibly toxic contaminating deposits using flammable or caustic agents Personnel performing these operations should be aware of the inherent risks and should take the necessary precautions Maintenance and Fault Finding Page 140 Q Tof 2 User s Guide Preventive Maintenance Check List Daily Weekly Monthly x x Avoid venting the instrument when the rotary pump is gas ballasting Do not gas ballast the rotary pump for more than 2 hours under any circumstances For full details of the following procedures consult the relevant sections of this chapter and or refer to the manufacturer s literature Gas ballast the rotary pump for 30 minutes at the end of a day s megaflow or APclI operation It is normal for the rotary pump noise leve
74. ethylamine 57 Trifluoroacetic acid 57 Tuning 32 APcl 72 75 Electrospray 48 Turbomolecular pump 16 95 U UV detector 45 57 Index Q Tof 2 User s Guide Page 153 Q Tof 2 User s Guide Vacuum 16 26 95 Leak 95 Poor 125 Water cooling 20 Index Page 154
75. ews Using a 1 5mm Allen key tighten the grub screw in the probe end cover to clamp the filter Replace the heater and probe tip assembly Maintenance and Fault Finding Page 130 Q Tof 2 User s Guide The Analyser The analyser element of any high performance quadrupole mass spectrometer is of necessity a precisely machined and aligned assembly Q Tof 2 is fitted with a prefilter assembly designed to protect the main analyser by absorbing the majority of any contamination The prefilter is not as mechanically critical as the main rods as it has only RF applied and is therefore not resolving It does however act as a high pass filter and will reject ions of low mass before they enter the main rods Main Analyser Mass Analysed lons Prefilter to the Detector lons from the Source The need to clean the prefilter rods is usually indicated by poor peak shape or loss of resolution in tuning mode although other more likely causes such as contamination of the source should be eliminated first Caution Cleaning the analyser on site is not a task to be undertaken lightly It should be done only when there is clear evidence that the analyser is the source of lack of performance The main rods of the analyser are precision ground as are the ceramics in which they are mounted Under no circumstances should any of the analyser rods be removed from the ceramic mountings It is unlikely that there will be any means on s
76. ews using a 1 5mm Allen key and withdraw the sample cone and cone gas nozzle if fitted from the ion block Remove the extraction tool and separate the sample cone from the cone gas nozzle Place both components in an ultrasonic bath containing 40 40 10 acetonitrile water formic acid or 40 40 10 methanol water formic acid Rinse and sonicate with 50 50 acetonitrile water or methanol water Maintenance and Fault Finding Page 115 Q Tof 2 User s Guide Exhaust Liner Cleanable Baffle Cone Gas Nozzle Extraction Tool Cone Gas Inlet yy Dry the cone and nozzle using nitrogen To minimise down time fit a spare sample cone obtainable from Micromass at this stage If material has built up on the exhaust liner and cleanable baffle Remove the cleanable baffle and the exhaust liner A Caution Do not attempt to remove the baffle without first removing the sample cone Clean these components or obtain replacements Fit the cleaned or the replacement exhaust liner and cleanable baffle to the ion block Refitting the sample cone is a reversal of the removal procedure Maintenance and Fault Finding Page 116 Q Tof 2 User s Guide Removing and Cleaning the Source Block and Extraction Cone On the tune page select Other from the menu bar at the top of the tune page Click on Vent The rotary pump and the turbomolecular pumps switch off The turbomolecular pumps are allowe
77. f 2 User s Guide Table of Contents Q Tof 2 User s Guide Contents Instrument Description Introduction 9 Ionisation Techniques 10 Atmospheric Pressure Chemical Ionisation 10 Electrospray 10 Nanoflow Electrospray 10 Ion Optics 11 Internal Layout 12 Mechanical Components 12 Electronics 14 The Vacuum System 16 Fine Pumping 16 Rotary Pumping 16 Pressure Measurement 16 Vacuum Protection 17 Front Panel Connections 18 Desolvation Gas and Probe Nebuliser Gas 18 High Voltage 18 Heaters 18 Front Panel Controls and Indicators 19 Status Display 19 Flow Control Valves 19 Divert Injection Valve 19 Rear Panel Connections 20 Water 20 Nitrogen Gas In 20 Exhausts 21 Supply Inlet 21 Electronics 21 Rotary Pump 21 Event Out 22 Contact Closure In 22 Analog Channels 22 MassLynx NT Data System 23 Software 23 Routine Procedures Start Up Following a Complete Shutdown 25 Preparation 25 Pumping 26 MCP Detector Conditioning 26 Instrument Warm up 27 Using the Instrument 27 Start Up Following Overnight Shutdown 28 Preparation for Electrospray Operation 28 Table of Contents Q Tof 2 User s Guide Preparation for APcI Operation Transient Pressure Trip Power Failure Nitrogen Supply Tuning Source Tuning Menu Capillary Cone Extractor RF Lens Source Block Temp Desolvation Temp Analyser Tuning Menu LM Res and HM Res Collision Ion Energy Steering Entrance Multiplier MCP MS2 Tuning Menu Transp
78. fo I Peak Purity C All Peaks Decimal Places fo 7 Level High 7 I Scan Base Peak Mass Decimal Places l 0 be m BioLynx J Peak Response Area I Component Label Decimal Places fo I Digest Label I Peak Response Height IV Scan Set Mass Decimal Places fi z Cancel Scan or Time will be available in a later version of MassLynx The TIC display is of little value since this also includes any undissociated precursor ion coming through the gas cell Use the Mass Chromatogram facility under Display in the top banner of the Chromatogram window to display either a single mass e g 86 or range of masses e g 86_177 or a sum of masses e g 70 86 110 120 or the total ion current above the parent mass TIC Above Setmass as shown below Parent lon Scanning Page 100 if Mass Chromatogram x File az14 pa Description m2 nel a File Function fi TOF Parent 50 2000 ES eV x Type TIC Above Setmass Add trace Mass Chromatogram E Fie Mass Chromatogram REET Mass Chromatooron OOOO E 561 Desci Fie az14 Functi s6177 Description m z Cancel e Function 70 86 110 120 Replace trace C New window Q Tof 2 User s Guide D File Edit Display Process Window Tools Help la x S Ala waea w a uz eaaeo Q tre gt 55 TOF Parent ES 86 20 70 653 5 740 57555 85458795 7 TOF Parent ES WFE 86_ 390 5 461 Seq75 5715 6635 7405
79. gonal acceleration cell 9 120 Panels removal 92 PEG See Polyethylene glycol Penning gauge See Active inverted magnetron gauge Peptides 43 56 Pesticides 56 75 Phase system switching 58 Phosphate 55 Phosphor 120 Photomultiplier 9 120 Pirani gauge 16 96 Plasma 10 Pollutants 56 Polyethylene glycol 55 131 135 Polysaccharides 56 Power failure 30 Preamplifier 15 Prefilter 9 37 117 118 Preventive maintenance 127 Probe temperature See APcl probe temperature Proteins 43 56 Proton abstraction 10 Proton transfer 10 Purge gas 50 53 98 Pusher 11 Control 15 R Reciprocating pump 44 57 Reference compound 129 Reflectron 11 120 Reverse phase 57 69 RF generator 14 RF lens 13 98 105 Rotary pump 16 21 95 97 Oil 97 Rubidium iodide 55 132 134 136 Saccharides 56 Sample cone 33 52 98 99 101 Sensitivity LC MS 58 Loss of 124 Shutdown 40 Sodium iodide 55 132 134 136 Software 23 Source 91 98 107 Block 103 Heater 18 Temperature 52 Source tuning menu 33 Spectrum Center menu 80 Split post column 45 57 Start mV 38 Status display 19 Steroids 75 Stop mV 38 Sugar mixture 55 133 Supply inlet 21 Syringe pump 44 57 T Target compound analysis 58 TDC See Time to digital converter TEA See Triethylamine Tetrahydrofuran 58 THF See Tetrahydrofuran Threshold 38 Time to digital converter 11 38 TOF analyser 9 TOF MS profile 80 Trace enrichment 58 Transient pressure trip 30 Tri
80. h a Desolvation Gas flow of approximately 150 litres hour is typical for most samples this flow rate should be tuned for maximum sensitivity while ensuring that the flow rate is not decreased below 100 litres hour Atmospheric Pressure Chemical lonisation Page 75 Q Tof 2 User s Guide Removing the Probe After a session of APcI operation Turn off the LC flow Set APcl Probe Temp to 20 C Deselect Operate to put the instrument in standby mode When the probe temperature falls below 100 C Deselect API Gas and turn off Nitrogen Undo the two thumb nuts and remove the probe from the source Warning Take care when removing the APclI probe There is a risk of burns to the operator St0P Caution Removal of the APcI probe when hot will shorten the life of the probe heater Thumb Nuts If the instrument is not to be used for a long period of time the source temperature should be reduced to 60 C Atmospheric Pressure Chemical lonisation Page 76 Q Tof 2 User s Guide Introduction Extremely accurate mass measurements can be performed with the Q Tof 2 due to the elevated resolution and inherent stability of the calibration law of orthogonal TOF instruments The basic time of flight calibration from mass m to time t is of the form vz Q Pt where the term P represents the resultant gain from the instrument geometry pathlengths and voltages Q is an offset arising from propagation delays through th
81. he supply of nitrogen gas If the instrument is not to be used for a long period of time Reduce Source Block Temp to 60 C It is not necessary to turn the instrument out of the operate mode Complete Shutdown If a power cut is expected or if the instrument is to be moved proceed as follows Switch off the LC pumps On the tune page deselect Operate to put the instrument in standby mode Routine Procedures Page 41 Q Tof 2 User s Guide The tune page indicator changes to red indicating that the instrument is no longer in the operate mode Undo the finger tight connector on the probe to release the tubing leading from the LC system Before disconnecting the probe it is good practice to temporarily remove the probe and flush it of any salts buffers or acids If APclI is being used reduce APcl Probe Temp to ambient temperature Caution Leaving the APcI probe hot with no gas or liquid flow will shorten the lifetime of the probe heater Deselect API Gas to turn off the supply of nitrogen gas Select Other from the menu bar at the top of the tune page Click on Vent The turbomolecular pumps switch off When the turbomolecular pumps have run down to 80 of their normal operating speed the vent valve opens and the instrument is automatically vented to dry nitrogen The rotary pump switches off Exit MassLynx Shut down the host PC Switch off all peripherals Switch off the power to the instrument using the circuit beake
82. ide The following electronics modules are located adjacent to the TOF analyser housing e Pusher unit This produces the high frequency pusher voltage and the MCP voltage e TDC preamplifier attenuator and photomultiplier preamplifier These components condition the output of the detector before the signal travels to the TDC TOF Pusher RF Generator Photomultiplier Preamplifier Attenuator Coaxial Surge Protector TDC Preamplifier Instrument Description Page 15 Q Tof 2 User s Guide Active Inverted Pirani Magnetron Gauge Gauge LL ee ill TOF Analyser Gauge Turbomolecular Pumps Pirani Oil Mist Aut ti 1 utomatic Filter Vent Exh to N pan Rotary xhaust to N Pump Q Tof 2 is equipped with three water cooled turbomolecular pumps providing independent fine pumping of the source hexapole quadrupole and TOF analysers Details of the operation and maintenance of the pumps can be found in the manufacturer s manuals provided 1000000 10001000 Fine Pumping Rotary Pumping Source pumping and turbomolecular pump backing is by a direct drive rotary pump The rotary pump is situated at the front of the instrument Details of the operation and maintenance of the pump can be found in the manufacturer s manual provided Pressure Measurement The backing pressure is monitored by an active Pirani gauge The analyser and TOF pressures a
83. ide Mixture Preparation of Calibration Solutions PEG Ammonium Acetate for Positive Ion Electrospray and APcI PEG Ammonium Acetate for Positive Ion Electrospray Extended Mass Range Sodium Iodide Solution for Positive Ion Electrospray Method 1 Method 2 Sodium Iodide Solution for Negative Ion Electrospray Table of Contents 147 148 149 149 149 150 150 151 151 151 152 153 153 153 154 154 154 154 Q Tof 2 User s Guide Instrument Description The Q Tof 2 hybrid quadrupole time of flight mass spectrometer is available with electrospray ionisation ESI and atmospheric pressure chemical ionisation APcI Q Tof 2 utilises a high performance research grade quadrupole mass analyser incorporating a prefilter assembly to protect the main analyser from contaminating deposits and an orthogonal acceleration time of flight TOF mass spectrometer A hexapole collision cell between the two mass analysers can be used to induce fragmentation to assist in structural investigations Ions emerging from the second mass analyser are detected by the microchannel plate detector and ion counting system A post acceleration photomultiplier detector Dynolite situated after the orthogonal acceleration cell is used to detect the beam passing through the first stage of the instrument for tuning and optimisation A PC computer runs the MassLynx NT software system to control Q Tof 2 and to acquire and process data Instrume
84. ile water or 50 50 Nozzle methanol water A Caution Do not attempt to remove any obstruction by poking This may result in damage to the sample cone Dry the cone using nitrogen If the sample cone is still not clean or if the aperture is partially blocked proceed to the following section Otherwise when the cone is clean and dry Open the isolation valve Replace all removed components following in reverse order the removal procedures Maintenance and Fault Finding Page 114 Q Tof 2 User s Guide Removing and Cleaning the Sample Cone Caution The sample cone is a delicate and expensive component and should be handled with extreme care It is not necessary to vent the instrument to remove the sample cone The source block incorporates an isolation valve for this purpose To remove the sample cone proceed as follows Follow the procedure in the previous section to gain access to the sample cone Using a suitable flat blade screwdriver rotate the valve by 90 into its fully anticlockwise position A small improvement in the analyser vacuum may be observed as a result of this operation The isolation valve is in the closed position when the slot is perpendicular to the direction of flow Disconnect the cone gas inlet line if fitted Take the sample cone extraction tool supplied in the source spares kit and screw it to the flange of the sample cone Remove the two sample cone retaining scr
85. ings M Use Tune Page Settings Collision Energy 2g IF Use Collision Energy Ramp m Retention Window mins Acquiring the Data NB The data in the multi step mode must be acquired from the Sample List If the experiment is launched from the Acquisition Control Panel it will not proceed and no data will be acquired Data may be acquired in single step mode by launching the experiment either from the Acquisition Control Panel or from the Sample List The intensity of these low mass fragments will be enhanced if the RF levels on the gas cell and transport lens are reduced from the normal values 0 3 0 5 to about 0 1 for the precursor scanning experiment Displaying the Data The Precursor Scan The precursor scan data is viewed in the chromatogram window since a precursor scan is really a display of the intensity of a mass or number of masses displayed as a function of the mass transmitted by MS1 In chromatogram set the Peak Annotation Type to Scan Set Mass so that the peaks will be annotated at the top with the mass being transmitted by MS1 Parent lon Scanning Page 99 Q Tof 2 User s Guide If the axis is also set to Scan then in this example scan 100 is equivalent to Yz400 scan 200 equivalent to Yz500 and so on X axis annotation with mass rather than Chromatogram Peak Annotation x m Annotation Type m Annotation Threshold g x Full Scale po I Peak Top Scan C Intensity
86. ions is also available The MassLynx NT User s Guide describes the many facilities of the Micromass software Documentation for the other software is also supplied Instrument Description Page 23 Q Tof 2 User s Guide Instrument Description Page 24 Q Tof 2 User s Guide Routine Procedures Start Up Following a Complete Shutdown Preparation If the instrument has been unused for a lengthy period of time proceed as follows Check the level of oil in the rotary pump sight glass Refill or replenish as necessary as described in the pump manufacturer s literature Connect a supply of dry high purity nitrogen to the connector on the service panel at the rear of the instrument Adjust the outlet pressure to 7 bar 100 psi Connect the water supply to the connections at the rear of the instrument Check that the rotary pump exhaust is connected to a suitable vent Check that the exhaust gas from the instrument is connected to a suitable vent instrument failure rotary pump exhaust could be admitted into the source Caution Do not connect the two exhaust lines together In the event of an chamber producing severe contamination Check that the instrument data system and other peripheral devices LC equipment printer etc are connected to suitable mains supplies Check that the etherlink connection is made between the control PC and the embedded PC Ensure that the VxWorks disk is inserted into the drive of the
87. ite for measuring the assembly to the micron level required If analyser charging effects cannot be resolved by the techniques below it is almost certain that the analyser will have to be returned to Micromass for refurbishment Maintenance and Fault Finding Page 131 Q Tof 2 User s Guide Removing the MS1 and Collision Cell Optical Bench Assembly Vent the system as described at the beginning of this chapter Remove the analyser housing top plate Working inside the MS1 analyser housing proceed as follows A Dismantling Disconnect the two push on connectors which take the analyser RF through to the RF lens at the source end of the analyser Disconnect the three push on connections bringing RF and DC voltages to the gas cell analyser housing right hand side Disconnect the three push on connections bringing RF and DC voltages to the hexapole transfer lens following the gas cell analyser housing right hand side Remove the gas line connection to the gas cell where it enters the gas cell Disconnect the push on DC pole bias connection to the main filter Disconnect the heavy gauge copper RF DC main filter supply from the feedthroughs on the left side of the analyser housing All connections to the ion optical bench main filter assembly gas cell RF lens assembly should now have been removed At the front and rear of the optical bench remove the two 4mm Allen socket screws that secure the bench to the mounting fla
88. ittle or no fragmentation When in the MS MS mode the collision energy is adjusted to give the best fragmentation pattern for the selected parent lon Energy This sets the quadrupole offset DC with respect to the collision energy of the ions travelling between the quadrupoles This should be set between 1 1 8V Steering This adjusts the voltage difference between the top and bottom half plates of the steering focus lens It acts as a y deflector directing the beam into the pusher A setting close to zero should produce an optimum beam Better sensitivity can be achieved however with a voltage positive or negative close to zero e g 1 0 0 5 etc and not more than 2V Entrance This sets the voltage on the pusher entrance and exit and defines the axial speed of the ions through the TOF The theoretical value is 65eV when the ion beam should be central to the detector It should be optimised when looking at a TOF beam not on the first detector It should be possible to correctly tune the instrument using this value Multiplier This sets the photomultiplier voltage and should typically be set to 550V MCP This sets the voltage on the TOF detector The voltage across the MCP itself is limited to 270V less than this value MCP must be conditioned before applying high voltage The TOF analyser is usually operated with this detector set at 2200V Routine Procedures Page 35 Q Tof 2 User s Guide S Tune DEFAULT
89. l to increase during gas ballasting Gas ballast for at least 30 minutes by rotating the gas ballast knob anticlockwise by 5 to 6 turns When gas ballast is complete check the rotary pump oil level and colour Oil that has become noticeably red in colour should be replaced Check the water chiller level and temperature if fitted Check all cooling fans and filters Four Monthly Change the mist element in the oil mist filter Change the oil in the rotary pump Gas ballast lightly for 30 to 60 minutes both before and after changing oil Maintenance and Fault Finding Page 141 Q Tof 2 User s Guide Maintenance and Fault Finding Page 142 Q Tof 2 User s Guide Reference Information Overview The reference files listed in this chapter have all ion intensities set to 100 Actual ion intensities are not of course all 100 but the calibration software does not take account of the ion intensities and this is a convenient way to store the reference files in the required format Most samples can be purchased from the Sigma chemical company To order contact Sigma via the internet or by toll free or collect telephone or fax Internet http www sigma sial com This site contains a list of worldwide Sigma offices many with local toll free numbers Toll free telephone USA amp Canada 800 325 3010 Outside USA amp Canada 1 314 771 5750 call collect Toll free fax USA amp Canada 800 325 5052 Outside U
90. lI interface consists of the standard Z spray source fitted with a corona discharge pin and a heated nebuliser probe Mobile phase from the LC column enters the probe where it is pneumatically converted into an aerosol and is rapidly heated and converted to a vapour gas at the probe tip Hot gas from the probe passes between the sample cone and the corona discharge pin which is typically maintained at 2 5kV Mobile phase molecules rapidly react with ions generated by the corona discharge to produce stable reagents ions Analyte molecules introduced into the mobile phase react with the reagent ions at atmospheric pressure and typically become protonated in positive ion mode or deprotonated in the negative ion mode The sample and reagent ions pass through the sample cone into the ion block prior to being extracted via the extraction cone into the RF lens Atmospheric Pressure Chemical lonisation Page 69 Q Tof 2 User s Guide Changeover between electrospray and APclI operation is simply accomplished by changing the probe and installing the corona discharge pin within the source enclosure For APcI operation the desolvation gas is not heated in the desolvation nozzle However it is important that desolvation gas is used throughout The background spectrum for 50 50 acetonitrile water is dependent upon the settings of Cone and Extractor The main reagent ions for typical sample cone and extraction cone voltages of 40V and 10V respectively
91. lysaccharides Q Tof 2 User s Guide Chromatographic Interfacing Electrospray ionisation can be routinely interfaced to reversed phase and normal phase chromatographic separations Depending on the LC pumping system chromatography column and setup there are some basic options e Microbore and capillary chromatography separations employing 1mm diameter and smaller columns can be interfaced directly to the electrospray probe Typical flow rates for such columns may be in the region of 3 50 yl min It is suggested that a syringe pump is used to deliver these constant low flow rates through a capillary column Alternatively accurate pre column splitting of higher flow rates from reciprocating pumps can be investigated In all cases efficient solvent mixing is necessary for gradient elution separations This is of paramount importance with regard to low flow rates encountered with capillary columns HPLC pump manufacturers recommendations should be heeded e 2 1mm diameter reversed phase columns are gaining popularity for many separations previously addressed by 4 6mm columns Typically flow rates of 200 yl min are used allowing direct coupling to the electrospray source The increased sample flow rate requires increased source temperature and drying gas flow rate A UV detector may be placed in line to the probe provided that the volume of the detector does not significantly reduce the chromatographic resolution Whenever a UV det
92. mist filter which traps oil vapour from the rotary pump exhaust The trapped oil is then returned to the rotary pump during routine gas ballasting The oil mist filter contains two elements the odour element need not be changed but the mist element must be changed every time the rotary pump oil is changed e To change the element follow the instructions in the Edwards manual Rotary Pump Oil The oil in the rotary pump should be maintained at the correct level at all times Check the oil level at weekly intervals topping up if necessary It is important to monitor the condition of the oil regularly Replace the oil when it has changed to a noticeable reddish brown colour or routinely at 4 month intervals 3000 hours operation At the same time replace the oil mist filter s mist element see above Change the oil in the rotary pump as follows Gas ballast lightly for 30 to 60 minutes Vent and shut down the instrument as described in Routine Procedures It will be found easier to drain the oil while the pump is still warm Drain the oil through the drain hole situated near the oil level sight glass Flush the pump then replace the drain plug and refill the pump with the correct grade oil to the correct level Gas ballast lightly for 30 to 60 minutes For further servicing information refer to the manufacturer s manual g Foreline Trap This is used to protect against the chance of pump oil backstreaming into the collision ga
93. nces in the centroided masses of the two centred spectra are less than 1 mDa If this is not the case then repeat the acquisition with less intense peaks either by sample dilution or by de tuning of the electrospray needle Once a satisfactory centered spectrum has been acquired save it in the spectrum history Go to the Control Panel menu select Instrument then Calibrate to obtain the following box Calibration and Accurate Mass Page 81 Q Tof 2 User s Guide Calibrate DEFAULT CAL op x File Edit Process Help m Reference File Last Calibrated x Acctest ref X 09 19 z stop 27 dun 94 Status gt gt Data Directory CAMASSLYNADAT AS Select the reference file to use pehnh4 ref will give the correct masses with the sample prepared as described above From Process select Calibration from file M517 Scanning Calibration Ea Select calibration type Quad TOF Select calibration file Combine scans in data file peglb From fi To fi AM 0 0 0 00 Cm 1 8 DK Cancel Use the Browse option to select the centred spectrum which has been previously saved In the above example box it is from a data file peg06 Once the spectrum has been selected click on OK Calibration and Accurate Mass Page 82 Q Tof 2 User s Guide Calibration DEFAULT CAL olx File Print Edit Display Cancel Default Data file pegO6 Uncalibrated 18 matches
94. nges Caution Before removing the optics from the housing prepare a clean area where it may be placed in preparation for removing and cleaning the prefilter rods Holding the optical bench assembly using two of the clamps that secure the optical elements to the aluminium base plate lift the rear end upwards to clear the vacuum housing and then withdraw the optical bench from the housing Once removed replace the vacuum housing lid to prevent the ingress of dust into the housing and Cleaning the Entrance Prefilter Dismantling and cleaning of the entrance prefilter is a skilled procedure which should be entrusted only to a Micromass engineer Maintenance and Fault Finding Page 132 Q Tof 2 User s Guide Cleaning the MS1 Analyser Assembly A A Caution Under no circumstances should any of the analyser rods be removed from the ceramic mountings Having removed the optical bench assembly as described above remove the two top clamps that secure the main filter including pre and post filter assemblies to the optical bench Roll up a narrow strip of absorbent lint free paper Pass one end through the gap between two adjacent main filter rods and back through the next gap so that the paper is wrapped one half turn around a rod Wet the paper with a solvent such as methanol and move the strip up and down along the analyser rod Remove the strip and use dry nitrogen gas from a cylinder not compressed air to blow out
95. nion in the body such that the ferrule seat is aligned correctly Insert the chamber into the nano LC body and tighten using a pair of spanners Nanoflow Electrospray Page 66 Operation Q Tof 2 User s Guide The capillary can now be checked for flow by connecting the output from a Harvard syringe pump to the other side of the union and setting the flow to I uL min using a micropipette to measure the flow It is recommended that a syringe with a volume of no more than 50 millilitres is used Thread the fused silica through the nebulising tip and screw in the nano LC chamber such that it is screwed in approximately half way Cut the fused silica using a tile cutter and adjust the nebulising tip further such that Imm of fused silica protrudes from the tip Attach the nebulising gas tubing to the sprayer using an O ring and the special screw Attach the sprayer assembly to the stage It may be necessary to alter the position of the thumbscrew underneath the baseplate to attach the sprayer correctly Swing the stage into the interface using the stop and handle For tuning purposes it may be useful to infuse a known sample in 95 water using a Harvard syringe pump Set the liquid flow to about 200 nl min Switch on Gas at the MassLynx tune page Set the pressure of the gas on the regulator to approximately 0 5 bar 7 psi Ensure there are no leaks of gas at the sprayer particularly where the PTFE tubing is connected to it
96. nt Description Page 9 Q Tof 2 User s Guide lonisation Techniques Using the Micromass Z spray atmospheric pressure ionisation API source two techniques are available Atmospheric Pressure Chemical lonisation Atmospheric pressure chemical ionisation APclI generally produces protonated or deprotonated molecular ions from the sample via a proton transfer positive ions or proton abstraction negative ions mechanism The sample is vapourised in a heated nebuliser before emerging into a plasma consisting of solvent ions formed within the atmospheric source by a corona discharge Proton transfer or abstraction then takes place between the solvent ions and the sample Eluent flows up to 2 millilitres minute can be accommodated without splitting the flow Electrospray ionisation ESI takes place as a result of imparting a strong electrical charge to the eluent as it emerges from the nebuliser An aerosol of charged droplets emerges from the nebuliser These undergo a reduction in size by solvent evaporation until they have attained a sufficient charge density to allow sample ions to be ejected from the surface of the droplet ion evaporation A characteristic of ESI spectra is that ions may be singly or multiply charged Since the mass spectrometer filters ions according to their mass to charge ratio 2 compounds of high molecular weight can be determined if multiply charged ions are formed Eluent flows up to 1 ml min can
97. nt delivery system fill a syringe barrel or a graduated glass capillary with the liquid emerging from the probe tip and time a known volume say 10yl Once the rate has been measured and set a note should be made of the back pressure readout on the pump as fluctuation of this reading can indicate problems with the solvent flow For APcI a higher than normal back pressure readout on the HPLC pump can imply that after a long period of use the filter pad requires replacement Maintenance and Fault Finding Page 137 Q Tof 2 User s Guide Loss of Sensitivity As the ion source becomes dirty after prolonged use the performance will degrade Unstable or reduced ion currents are indicators that the source needs cleaning The usual remedy is to clean the source as described earlier in this chapter An increase in the analyser pressure above 4e 6 mbar can also cause loss of sensitivity although the pressure at which this occurs will be sample dependent Incorrect Isotope Distributions Incorrect isotope distributions can be caused by e The TDC Stop mV threshold being set too high Refer to the tune page settings section of Routine Procedures for information regarding the setting of this parameter e A faulty attenuator Attenuators can fail so that they are open circuit no beam or pusher interference peak present or they can fail such that they stop attenuating The latter failure mode gives rise to incorrect isotope
98. nts_of_79 txt 7 Mass 78 950 Save Add Delete New Search Criteria Threshold counts second 5 Window Da 1 Single Mass Summed OK Cancel An alternative way to create the file is to use Notepad and make a text file using the format shown E Parents_of_Immoniums Notepad Of x Eile Edit Search Help The cursor must be at the end of the last text line i e the last character in the file must not be a carriage return If precursors are being sought for more than a single product ion then a new line is added for each using the same format as shown It might be useful to create a Folder in the MassLynx root directory e g Parents in which to place these files Parent lon Scanning Page 97 Q Tof 2 User s Guide Single Step Mode After the MassLynx ini file has been modified log into MassLynx and open up the Scan Function editor This is accessed either by opening up the MS File in the Sample List window or by selecting Set Up Scan which is under the Acquire option in the top banner of the Acquisition Control Panel see Control Panel under the Run command in the Sample List window This Scan Functions window should now appear In the top banner select File and New to open up a new Scan Function file Click on the Parents button to add a Parents function to the editor In the Function 1 Parent Scan window that appears modify the parameters accordingly Scan Functions PA
99. ocating tabs indicated Maintenance and Fault Finding Page 106 Panel 3 Panel 4 Panel 5 Panel 3 covers the RF generator for the quadrupole analyser MS1 It is raised and lowered vertically in the same way as panel 1 with lateral location similarly provided by six pins Panel 4 is attached by four 3mm Allen screws Those marked A in the diagram must be removed completely Those marked B need only be loosened The panel must then be tilted slightly to enable it to be pulled clear of the chassis rail Panel 5 is above the front operator control panel In addition to the Allen screws securing this panel to panel 4 two concealed screws engage with slotted holes in the chassis Once panel 4 has been removed panel 5 may be rotated about the vertical axis z and then pulled forward Q Tof 2 User s Guide Maintenance and Fault Finding Page 107 Q Tof 2 User s Guide Panel 6 Panel 7 Panel 6 covers the embedded PC the rotary pump and the main body of the TOF analyser housing It is held in position by six Allen screws which must only be loosened for the panel to be lifted clearing the locating slots Panel 7 covers some of the electronics systems and the lower air filter tray It is attached in exactly the same way as panel 6 and subsequently the same procedure should be followed for removal and replacement Electronics Maintenance Removal of the left side instrument cover gives access to
100. ort Aperture 2 AccV Focus Tube Lens Offset 1 Offset 2 Pusher TOF Reflectron Prefilter Manual Pusher Other Tune Page Settings Calibration TDC Settings Start Stop Threshold Bunching Lteff Centroid Data Acquisition Data Processing Shutdown Procedures Emergency Shutdown Overnight Shutdown Complete Shutdown Table of Contents 29 30 30 31 32 33 33 33 33 33 34 34 34 34 35 35 oo 35 oo 35 36 36 36 36 36 37 37 oT 37 37 37 37 38 39 39 39 39 39 39 40 40 40 40 40 41 41 41 41 Electrospray Introduction Post column Splitting Megaflow Changing Between Flow Modes Operation Checking the ESI Probe Obtaining an Ion Beam Tuning and Optimisation Probe Position Nebuliser Gas Desolvation Gas Cone Gas Purge Gas Source temperature Capillary Voltage Sample Cone Voltage Extraction Cone Voltage Megaflow Hints Removing the Probe Sample Analysis and Calibration General Information Typical ES Positive Ion Samples Typical ES Negative Ion Samples Chromatographic Interfacing LC MS Sensitivity Enhancement Nanoflow Electrospray Overview Installing the Interface Operation of the Camera System Using the Microscope Glass Capillary Option Installation Nanovial Tip Position Operation Restarting the Spray Nano LC Option Installation Operation Changing Options Q Tof 2 User s Guide 43 45 46 46 47 47 48 49 49 49 49 50 5l 52 52 52 52 53 54 59 55 56 56 57 58
101. page agree with the set values The Corona Discharge Pin If the corona discharge pin becomes dirty or blunt Remove it from the source Clean and sharpen it using 600 grade emery paper If the needle becomes bent or otherwise damaged it should be replaced Maintenance and Fault Finding Page 122 Q Tof 2 User s Guide The Electrospray Probe Overview Warning The probe tip is sharp and may be contaminated with A A A harmful and toxic substances Always take great care when handling the electrospray probe Indications that maintenance is required to the electrospray probe include e An unstable ion beam Nebulising gas may be escaping from the sides of the probe tip Ensure that the probe tip O ring is sealing correctly The probe tip setting may be incorrect Adjust the probe tip setting as described in Electrospray The probe tip may be damaged Replace the probe tip There may be a partial blockage of the sample capillary or the tubing in the solvent flow system Clear the blockage or replace the tubing e Excessive broadening of chromatogram peaks This may be due either to inappropriate chromatography conditions or to large dead volumes in the transfer capillaries between the LC column or probe connection Ensure that all connections at the injector the column the splitting device if used and the probe are made correctly e High LC pump back pressure With no column in line and the liquid flow set to 3
102. plates of the first acceleration region of the Tof Pusher and Grid3 It is used as a fine tuning control to optimise resolution The optimum value for this element may change with pusher frequency The pusher frequency is dependent on mass range when in automatic pusher mode and takes one of six discrete values See pusher rates on Page 38 Offset 2 This determines the voltage difference between the two plates of the second acceleration region of the Tof G3 and puller It is normally set around zero volts and does not need to be adjusted Pusher This sets the amplitude of the pusher pulse and is normally set to 980V TOF This sets the flight tube voltage It is always set to 9 1kV Adjusting this will change the peak position and resolution Reflectron This is set expressed as a percentage of the flight tube voltage and its value is 2150V or about 36 0 Adjusting this will change the peak position and resolution Prefilter This sets the offset voltage on the quadrupole pre and post filters The optimum beam is usually obtained at a setting of 5 7V It is recommended that a record of these values is kept for future reference Routine Procedures Page 37 Q Tof 2 User s Guide Manual Pusher If the Manual Pusher box is selected from the Other sub menu then the repetition frequency of the pusher pulse is determined by the Time entered Time may be set between 30 usec and 255 usec Setting Time at less than 30 ps
103. pport liner and O rings from the pumping block Using a lint free tissue to gently grasp the hexapole carefully withdraw it A Caution Take care not to scratch the internal bore of the pumping block as the hexapole lens assembly is withdrawn Maintenance and Fault Finding Page 119 Q Tof 2 User s Guide Differential Aperture Plate Rod Locating Screws amp Washers Location Recess To clean the hexapole transfer lens proceed as follows Immerse the complete assembly in a suitable solvent 100 methanol and sonicate in an ultrasonic bath Thoroughly dry the assembly using a flow of nitrogen In severe cases Remove clean dry and replace each rod separately one at a time Reassemble the assembly with extreme care checking the assembly against the diagram Maintenance and Fault Finding Page 120 Q Tof 2 User s Guide Reassembling and Checking the Source Feed the hexapole transfer lens into the instrument allowing the recesses in the differential aperture plate to locate onto the two support rails within the analyser assembly Ensure that the assembly is pushed fully in Check the condition of the O rings on the ion block support Replace them if necessary Replace the ion block support pushing it in against the springs of the hexapole assembly Replace the three retaining screws Fit the plug and sealing ring to the ion block Fit the insulating ring and extraction cone Offer the ion block up
104. procedure involves making the following adjustments e Increase Desolvation Gas flow to 500 litres hour e Increase Desolvation Temp to 400 C e Increase Source Block Temp to 150 C e Move the probe further away from the sample cone When changing from electrospray to megaflow operation it is not necessary to adjust any source voltages Caution The maximum operating temperature for the source heater is 150 C Do not set Source Block Temp higher than 150 C Cluster ions are rarely observed with Z spray However solvent droplets may form within the source enclosure if the source and desolvation temperatures are too low Refer to the previous section on operating parameters for typical desolvation gas flow rates Purge gas can be used during megaflow operation to stop the source enclosure from overheating This is also beneficial when the analyte is susceptible to acetonitrile adducting Purge gas is enabled by removing the blanking plug from the outlet situated within the source enclosure If the sample is contained within a dirty matrix the probe may be moved away from the sample cone to extend time between source cleaning operations This may incur a small loss in sensitivity Warning It is normal for the source enclosure the glass tube and parts of the probe mounting flange to get hot during prolonged megaflow operation Care should be taken when handling source components during and immediately after operation The sour
105. pump exhaust could be admitted into the source Caution Do not connect these two exhaust lines together as in the event of an chamber producing severe contamination Supply Inlet The mains power cord should be wired to a 230V mains outlet using a suitable plug or to a transformer For plugs with an integral fuse the fuse should be rated at 13 amps UK only Electronics This circuit breaker switches power to the electronics In the event of the instrument drawing more than the rated current the circuit breaker will trip Rotary Pump This circuit breaker switches power to the rotary and turbomolecular pumps In the event of the pumps drawing more than the rated current it will trip Instrument Description Page 21 Q Tof 2 User s Guide EVENT OUT A s4 our4 CAUTION REFER TO MANUAL BEFORE CONNECTING s3 OUTS TO THESE PORTS S2 OUT 2 S1 OUT 1 CONTACT CLOSURE IN i ve CH1 CH3 ANNALOG CHANNELS Event Out Four outputs Out 1 to Out 4 are provided to allow various peripherals to be connected to the instrument Switches S1 to S4 allow each output to be set to be either a contact closure upper position or a voltage output lower position Out 1 and Out 2 when set to voltage output each have an output of 5 volts The voltage output of both Out 3 and Out 4 is 24 volts During a
106. r Tube Fused Silica Capillary Liner Tube lt Rheodyne Nut amp Ferrule If the stainless steel sample capillary cannot be cleared or if it is contaminated or damaged replace it as follows Remove the probe form the source Disconnect the LC line from the probe and remove the finger tight nut Loosen the grub screw retaining the LC union Remove the two probe end cover retaining screws and remove the probe end cover Unscrew and remove the probe tip Remove the LC union and adapter nut Withdraw and discard the stainless steel sample capillary Remake the LC connection to the LC union Sleeve one end of new sample capillary with the PTFE liner tube Maintenance and Fault Finding Page 125 Q Tof 2 User s Guide Using a GVF 16 ferrule and the adapter nut connect the sample capillary to the LC union ensuring that both the liner tube and sample capillary are fully butted into the LC union Disconnect the LC connection and feed the sample capillary through the probe ensuring that a 0 3mm graphitised vespel ferrule GVF 003 is fitted Using a Rheodyne spanner gently tighten the adapter nut onto the probe Replace the probe tip and adjust so that 0 5mm of sample capillary protrudes from the probe tip Replace the probe end cover and tighten the grub screw to clamp the LC union Maintenance and Fault Finding Page 126 Q Tof 2 User s Guide The APcl Probe Indications that maintenance to the APc
107. r continuous operation The most suitable reciprocating pumps for this purpose are those which are specified to deliver a flow between 1 yl min and 1 ml min A constant flow at such rates is more important than the actual flow rate The injection valve on reciprocating pumps may be replaced by an autosampler for unattended overnight operation e Infusion pump The pump syringe is filled with sample in solution The infusion pump then delivers the contents of the syringe to the source at a constant flow rate This arrangement allows optimisation and analysis while the sample flows to the source at typically 5 30 l min Further samples require the syringe to be removed washed refilled with the next sample and replumbed A 50 50 mixture of acetonitrile and water is a suitable mobile phase for the syringe pump system and the reciprocating pump systems This is appropriate for positive and negative ion operation Positive ion operation may be enhanced by 0 1 to 1 formic acid in the sample solution Negative ion operation may be enhanced by 0 1 to 1 ammonia in the sample solution Acid should not be added in this mode These additives should not be used in the mobile phase for flow injection analysis FIA studies to allow easy change over between positive and negative ion analysis Degassed solvents are recommended for the syringe and reciprocating pumps Degassing can be achieved by sonification or helium sparging The solvents should be
108. re straight and circular in cross section Ensure that the inner stainless steel capillary is coaxial to the outer capillary If the two capillaries are not coaxial it is possible to bend the outer capillary slightly using thumbnail pressure Insert the probe into the source and tighten the two thumb screws Plug the probe high voltage cable into Capillary Corona on the front panel Obtaining an lon Beam If necessary change the ionisation mode using the lon Mode command Using the needle valves on the front panel set the Desolvation Gas flow rate to 300 litres hour and the Cone Gas flow to 50 litres hour Turn on the liquid flow at 10 l min and set Desolvation Temp to 150 C Electrospray Page 48 Q Tof 2 User s Guide Tuning and Optimisation The following parameters after initial tuning should be optimised using a sample representative of the analyte to be studied It will usually be found with the exception of the sample cone voltage that settings will vary little from one analyte to another Probe Position The position of the probe is adjusted using the probe adjustment collar in and out and the adjustment knob i sideways located to the left of the nee probe The two screws can be Adjustment adjusted singly or simultaneously to optimise the beam The position for optimum sensitivity and stability for low flow rate work 10 pl min is shown Cone Gas i 4mm Nozzle A Probe Tip Sideways
109. re done the parent facility will not be unlocked 8 Masslynx ini Notepad OF Xx File Edit Search Help LocateMolWt FALSE LocateAppExact FALSE LocateNum0ne FALSE LocateNumTwo FALSE AcquPara QTOFParent TRUE ReferenceGas amp Reference CollisionGas Collision This is an example of how the MassLynx ini file appears after successful modification Parent lon Scanning Page 92 Q Tof 2 User s Guide Setting up the Mass Transmission of the Quadrupole In the multi step mode of acquisition see next section the data is acquired using quadrupole mass transmission windows of differing widths The widths of these windows are controlled using the information in the massresprofile file in the MassLynx root directory This file should have been created during the instrument installation f massresprofile Notepad ioj x File Edit Search Help The left most number is the transmission window of the quadrupole followed by the LM and HM Resolution settings NB It is important that these numbers are not separated by commas or any character other than a space and that there is not a carriage return following the final number If this file does not exist it must be created The transmission at various resolution settings can be easily determined by using the interactive acquisition mode A section of the mass spectrum containing only background is most useful and the collision energy should be set to that required for M
110. re monitored by active inverted magnetron Penning gauges These gauges act as vacuum switches switching the instrument out of Operate mode if the pressure is too high Pressure readings may be displayed on the MassLynx NT tune page The analyser Penning gauge only comes on when the vacuum display window is open At other times the gauge is off The analyser Pirani gauge is used when the diaply is off though no pressures are shown Instrument Description Page 16 Q Tof 2 User s Guide Vacuum Protection The vacuum system is fully interlocked to provide adequate protection in the event of e a fault in the vacuum system a failure of the power supply a failure of the water supply e a vacuum leak Instrument Description Page 17 Q Tof 2 User s Guide Oooo STANDBY PUMP OPERATE TRIP CAPILLARY CORONA PROBES 7 J NANOFLOW jj INJECTOR D f 0 DESOLVATION GAS NEBULISER GAS O GAS CELL NANOFLOW DESOLVATION GAS CONE GAS O O00 Desolvation Gas and Probe Nebuliser Gas The PTFE gas lines for the Desolvation Gas and probe Nebuliser Gas are connected to the front of the instrument using threaded metal fittings Cone Gas is connected internally High Voltage The electrical connection for the ESI capillary or the APcI corona discharge pin is via the coaxial high voltage connector This socke
111. ready in place attach the microscope or camera brackets using the screw hole and dowels at the top of the bracket Nanoflow End Flange Insert the flexible light guide into the grommet at the base of the perspex cover Set the light source to its brightest Block the Desolvation Gas outlet on the instrument s front panel Close the nebuliser needle valve The cone gas is split from the desolvation gas internally Attach the two cables to the sockets marked Capillary Corona and Probes on the front panel of the instrument Set Source Block Temp to approximately 80 C A Caution The maximum operating temperature for the source heater is 150 C Do not set Source Block Temp higher than 150 C Nanoflow Electrospray Page 62 Q Tof 2 User s Guide Objective Lens Grommet Operation of the Camera System Magnification is controlled by the zoom lens A fine focus can be achieved by rotating the objective lens Using the Microscope Focusing is adjusted by rotating the top of the microscope Nanoflow Electrospray Page 63 Q Tof 2 User s Guide Glass Capillary Option Installation Warning Do not touch the sharp end of the capillary As well as the risk of injury by a sliver of glass the capillary may contain toxic samples Caution The capillaries are extremely fragile and must be handled with great care Always handle using the square end of the capillary The needle may become inoperable
112. rection The data acquisition system for the instrument is a time to digital converter TDC This is an ion counting system which generates a mass spectrum by storing the arrival times of ions in a histogram memory After the arrival and registration of an ion by the TDC there is a minimum time interval before a subsequent ion arrival can be registered This is called the dead time of the TDC and is of the order of 5 nanoseconds At high ion currents some of the ions generated are not registered leading to a shift to lower mass centroids with consequently lower measured areas on reported peaks However the MassLynx software incorporates a correction facility which allows for accurate mass measurements to be achieved over a large range of ion currents and the use of dead time correction is described below Generation of an Instrument Calibration Make up an analyte solution consisting of PEG 300 10 nanolitres millilitre PEG 600 10 nanolitres millilitre in a stock solution of 2mM ammonium acetate in 50 50 acetonitrile water Dilute this by a factor of ten with the stock solution and introduce this to the instrument using a syringe pump operating at 5 microlitres per minute Calibration and Accurate Mass Page 79 Q Tof 2 User s Guide The TOF MS Profile should be set up as below This will give coverage of masses from 150 to 1000 Da albeit with some compromise to sensitivity at the higher masses TOF HS Profile Ea
113. rs on the rear panel of the instrument Switch off power at the wall mounted isolation switch or remove the plug If the instrument is to be switched off for more than one week Drain the oil from the rotary pump according to the manufacturer s instructions Refill the rotary pump with new oil Routine Procedures Page 42 Q Tof 2 User s Guide Introduction __ lt Purge Gas IFoo gt Exhaust Cleanable Exhaust gt Liner lt Cone Gas m Isolation Nebuliser Desolvation Valve Gas Gas gt Analyser Source Enclosure Toph omo Pouar Pumps The ESI interface consists of the standard Z spray source fitted with an electrospray probe See the following chapter for additional information concerning the optional nanoflow interface Mobile phase from the LC column or infusion pump enters through the probe and is pneumatically converted to an electrostatically charged aerosol spray The solvent is evaporated from the spray by means of the desolvation heater The resulting analyte and solvent ions are then drawn through the sample cone aperture into the ion block from where they are then extracted into the analyser The electrospray ionisation technique allows rapid accurate and sensitive analysis of a wide range of analytes from low molecular weight less than 200 Da polar compounds to biopolymers larger than 100 kDa Generally compounds of less
114. rt injection valve 19 Drugs 56 Dye compounds 56 Index Page 151 Q Tof 2 User s Guide Electronics Electrospray Analysis Negative ion Operation Positive ion Preparation Electrospray probe Maintenance Removal Embedded PC Environmental contaminants Event out Exact mass measurement Exhaust Exhaust liner Extraction cone F Fault finding Flow injection analysis Formic acid Fragmentation Gas ballast Glass capillary nanoflow Gradient elution H Hexapole collision cell Hexapole lens See RF lens Infusion pump Injection valve lon evaporation lon mode lon optics lon source See Source Isotope distribution incorrect Index Page 152 61 98 102 33 52 103 91 121 44 59 44 96 127 59 64 57 9 118 LC MS interface 57 Lock mass 78 89 Lteff 39 M Maintenance 91 Manual pusher 37 MassLynx 23 MCP See Microchannel plate detector MCP detector conditioning 26 Megaflow 46 50 53 57 Metabolites 56 Microchannel plate detector 9 120 Microscope 63 Mobile phase 75 MS1 analyser 118 119 MS2 analyser 120 MS2 tuning menu 36 AccV 36 Aperture 2 36 Focus 36 Guard 37 Manual Pusher 37 Prefilter 37 Transport 36 Multiply charged ions 10 Myoglobin 55 131 133 N Nanoflow electrospray 10 59 98 Nano HPLC 59 Nano LC nanoflow option 66 Nebuliser 10 Nebuliser gas 18 19 49 Nitrogen 20 25 31 47 49 Noise 125 Oil mist filter 96 Oligonucleotides 43 56 Organometallics 56 Ortho
115. rush supplied in the spares kit soaked in methanol water Before starting an analysis With the probe out of the instrument connect the nebulising gas supply line Select API Gas and turn on Nitrogen Allow the gas to flow for several seconds to clear any debris from the heater Turn off Nitrogen Insert the probe into the source Maintenance and Fault Finding Page 127 Q Tof 2 User s Guide Select API Gas and turn on Nitrogen Raise APcl Heater gradually starting at 100 C and increasing in 50 C intervals to 650 C over a period of 10 minutes A Caution Do not set APcl Heater to 650 C immediately as this may damage the probe heater This procedure should remove any chemical contamination from the probe tip Replacing the Probe Tip Heater Slotted Grub Screws Probe Tip Assembly Heater pt Remove the probe tip assembly by carefully loosening the two grub screws Disconnect the heater from the probe body by pulling parallel to the axis of the probe Fit a new heater assembly Reconnect the probe tip assembly Maintenance and Fault Finding Page 128 Q Tof 2 User s Guide Replacing the Fused Silica Capillary Fused Silica Capillary Meee oo Sy Coupling 9 Filter D ro O Ring Ferrule LA A Finger tight Nut amp Ferrule PTFE Tube o gt Rheodyne Nut amp Ferrule With the probe removed from the source proceed as follows Remove the probe tip assembly and th
116. s are left flowing Source Thumb Nuts Enclosure Probe Thumb Nuts Adjustment Flange When APcl Probe Temp or Desolvation Temp has cooled below 100 C Deselect API Gas to switch off the nitrogen supply Disconnect both gas lines from the front panel by undoing the knurled nuts Maintenance and Fault Finding Page 113 Q Tof 2 User s Guide Disconnect both electrical connections by pulling back on the plug sleeves to release the plugs from the sockets on the front panel Undo the two knurled thumb nuts that retain the probe and withdraw it from the source Place it carefully to one side Undo the three thumb screws and withdraw the probe adjustment flange and glass tube Place the glass tube end on on a flat surface and place the probe adjustment flange on top of the glass tube Warning When the source enclosure has been removed the source block is exposed Ensure that the source block heater has cooled before proceeding If fitted remove the APcI corona discharge pin The sample cone is now accessible Using a suitable flat blade screwdriver rotate the isolation valve by 90 into its fully anticlockwise position A small improvement in the Isolation analyser vacuum may be observed as a result of this operation The isolation valve is closed when the slot is perpendicular to the direction of flow Carefully wipe the sample cone with a cotton swab or lint free tissue soaked in 50 50 Cone Gas acetonitr
117. s desolvation gas cone gas nanoflow only purge gas if enabled Solvent Flow Rate yl min Desolvation Temp C Desolvation Gas Flow Rate litres hour lt 10 100 to 120 200 to 250 10 to 20 120 to 250 200 to 400 20 to 50 250 to 350 200 to 400 gt 50 350 to 400 500 750 Higher desolvation temperatures give increased sensitivity However increasing the temperature above the range suggested reduces beam stability Increasing the gas flow rate higher than the quoted values leads to unnecessarily high nitrogen consumption A Caution Do not operate the desolvation heater for long periods of time without a gas flow To do so could damage the source Cone Gas The cone gas reduces the intensity of solvent cluster ions and solvent adduct ions The cone gas flow rate should be optimised by increasing until solvent cluster ions and or adduct ions are reduced as much as possible without diminishing the intensity of the ion of interest normally M H Typical cone gas flow rates are in the range 100 to 300 litres per hour Purge Gas Outlet Plugged Electrospray Page 50 Q Tof 2 User s Guide Purge Gas The purge gas is not necessary for most ESI applications It may be useful for megaflow operation where an analyte is susceptible to acetonitrile adducting Purge gas is enabled simply by removing the blanking plug from the outlet situated within the
118. s solenoid and or the turbo pumps The activated alumina should be changed according to the manufacturer s instructions Maintenance and Fault Finding Page 111 Q Tof 2 User s Guide The Source Overview The Z spray source is a robust assembly requiring little maintenance The source consists of three basic parts e The probe adjustment flange e The glass tube e The source flange assembly The probe adjustment flange and the glass tube can be readily removed without venting the instrument to gain access to the source block and sample cone This allows the following operations to be performed e Wiping the sample cone e Removing the sample cone e Fitting or removing the APcI corona discharge pin e Fitting or removing the exhaust liner and cleanable baffle e Fitting or removing the nanoflow electrospray interface e Enabling or disabling the purge gas The sample cone may be cleaned in situ by gentle wiping with a cotton swab or lint tissue soaked with 50 50 acetonitrile water More thorough cleaning of the sample cone may be achieved by removing it from the source This may also be done without venting the instrument by closing the isolation valve located on the ion block Less frequently it may be necessary to clean the ion block the extraction cone and the hexapole lens in which case the instrument must be vented This should only be done when the problem is not rectified by cleaning the sample cone or when ch
119. sample run an event output may be configured to close between acquisitions and is used typically to enable an external device to inject the next sample Contact Closure In In 1 and In 2 inputs are provided to allow an external device to start sample acquisition once the device has performed its function typically sample injection Analog Channels Four analog channel inputs are available for acquiring simultaneous data such as a UV detector output The input differential voltage must not exceed one volt Instrument Description Page 22 Q Tof 2 User s Guide MassLynx NT Data System A PC computer runs the MassLynx NT software system to control Q Tof 2 and to acquire and manipulate data from it A high resolution colour monitor is also supplied Interaction with MassLynx NT is via the mouse and keyboard using menu driven commands Printing file management and other routine procedures are performed using the appropriate Windows NT modules Software The following software packages are supplied with Q Tof 2 e MassLynx NT e Screen Capture a utility for copying user selected areas of any Windows display The selected area can be printed directly or saved as a bitmap file for importing into other Windows NT applications e DataBridge a utility to convert other format data files into MassLynx format e Microsoft Windows NT graphical environment e Mouse configuration A range of optional software modules for different applicat
120. separate experiment In the Q Tof 2 mass spectrometer MS2 is a time of flight mass spectrometer In this configuration since MS2 is no longer mass selective as MSI is scanned or stepped over a range of masses full product spectra can be recorded for any species decomposing in the gas cell In this mode MS2 acquires product mass spectra over a selected mass range e g from M750 2000 MS1 is then stepped over the mass range for which precursors are sought e g from Yz300 1500 in steps of 1Da interval The data set that is produced may be used to construct precursor scans or constant neutral loss scans for any mass within the scan range of MS1 and MS2 with the advantage that multiple precursor scans may be simultaneously displayed from the data obtained in a single experiment If only a single mass is used for the construction of the precursor scan then the sensitivity is in theory substantially about 1 50 lower for Q Tof 2 relative to the triple quadrupole However by using several to many ions to construct the scan this can be recovered to a large extent Under some circumstances the full product spectrum generated in this mode is sufficient for structure interpretation however at the lowest sample levels it may be necessary to return to the appropriate precursor and acquire more data in product mode to improve the quality of the product spectrum Parent lon Scanning Page 91 Q Tof 2 User s Guide When the number of
121. source This is important for optimum electrospray intensity and stability when operating at low flow rates Checking the ESI Probe Connect the electrospray probe to a pulse free pump Solvent should be degassed to prevent beam instabilities caused by bubbles Connect the PTFE tubing of the electrospray probe to Nebuliser Gas on the front panel Secure with the nut provided Electrospray Page 47 Q Tof 2 User s Guide With the probe removed from the source turn on the liquid flow at 10 yl min and check that liquid flow is observed at the tip of the capillary To avoid unwanted capillary action effects do not allow liquid to flow to the probe for long periods without the nitrogen switched on Turn on Nitrogen by selecting API Gas and check that a nebuliser flow of less than 100 litres hour is registered Check that there is gas flow at the probe tip and ensure that there is no significant leakage of nitrogen elsewhere Adjust the probe tip to ensure complete nebulisation of the liquid There should be approximately 0 5mm of sample capillary protruding from the nebulising capillary Sample T The tip of the electrospray probe can influence 2 Capillary the intensity and stability of the ion beam A damaged or incorrectly adjusted probe tip will Nebulising Capillary lead to poor electrospray performance Probe Tip A l Using a magnifying glass ensure that both ERAY inner and outer stainless steel capillaries a
122. source enclosure Purge gas flow rate is a constant fraction 30 of the total desolvation gas flow Electrospray Page 51 Q Tof 2 User s Guide A Source temperature 100 C is typical for 50 50 CH3CN H20 at solvent flow rates up to 50 l min Higher source temperatures up to 150 C are necessary for solvents at higher flow rates and higher water content Caution The maximum operating temperature for the source heater is 150 C Do not set Source Temp higher than 150 C Capillary Voltage Capillary usually optimises at 3 0kV although some samples may tune at values above or below this within the range 2 5 4 0kV for positive electrospray For negative ion operation a lower voltage is necessary typically between 2 0 3 5kV At high flow rates this parameter may optimise at a value as low as 1kV Sample Cone Voltage A Cone setting between 25V and 70V will produce ions for most samples although solvent ions prefer the lower end and proteins the higher end of this range Whenever sample quantity and time permit Cone should be optimised for maximum sensitivity within the range 15V to 150V Increasing Cone will increase ion fragmentation within the source Extraction Cone Voltage Extractor optimises at 0 5V Higher values may induce ion fragmentation of low molecular weight samples Electrospray Page 52 Q Tof 2 User s Guide Megaflow Hints A gt b gt With this high flow rate technique the setup
123. t Scan Options to open up the Parent Scan Options window If a file containing target product ions for which the precursors are being sought has already been created then it can be found using the browse facility IV File D MASSLYN Parents_of_79 txt Mass 78 950 Add Delete New Search Criteria Threshold counts second g Window Da fi Single Mass C Summed OK Cancel If not or if a different set of products is to be specified then a new file can be created using the New and Add facilities Add Modify Step Size m z 147 1 Parent lon Scanning Page 96 Q Tof 2 User s Guide Selecting New will clear the Parent Scan Options window and Add will select the Parent Mass window Enter the mass of the product for which precursors are sought and select OK to add to the list in the Parent Scan Options window When the list is complete a value for the threshold above which the precursor must appear for a window to be flagged for the next stage and a mass tolerance within which the precursor must appear should be entered In single mass mode if any of the masses is detected above the threshold then that segment will be flagged In summed mode the intensities of all the ions are added together and if the sum is above the threshold then that segment will be flagged Select OK and as a final step save the experiment using the File Save As command in the top banner IV File D MASSLYNX Pare
124. t compounds may usually be achieved using a concentration of Ing pl Samples with phosphate buffers and high levels of salts should be avoided Alternatively at the expense of a small drop in sensitivity the probe can be pulled away from the sample cone to minimise the deposit of involatile material on the cone To gain experience in sample analysis it is advisable to start with the qualitative analysis of known standards A good example of a high molecular weight sample is horse heart myoglobin molecular weight 16951 48 which produces a series of multiply charged ions that can be used to calibrate the Yz scale from 800 1600 in either positive ion or negative ion mode Polyethylene glycol mixtures for example 300 600 1000 are low molecular weight samples suitable for calibrating the z scale from approximately 100 to 1200 in positive ion mode A mixture of sugars covers the same range in negative ion mode Alternatively sodium iodide or caesium iodide can be used for calibration Electrospray Page 55 Q Tof 2 User s Guide Typical ES Positive lon Samples Peptides and proteins Small polar compounds Drugs and their metabolites Environmental contaminants e g pesticides pollutants Dye compounds Some organometallics Small saccharides Typical ES Negative lon Samples Electrospray Page 56 Some proteins Some drug metabolites e g glucuronide conjugates Oligonucleotides Some saccharides and po
125. t is labeled Capillary Corona Heaters The electrical connection for the APcI probe or the ESI desolvation heater is via the multi way connector labeled Probes This is removed from the front panel by pulling on the metal sleeve of the plug Both the electrospray desolvation heater and the APcI probe heater use this connector Instrument Description Page 18 Q Tof 2 User s Guide The power for the source block heater is permanently connected As a consequence the source block assembly is usually very hot and should not be touched Front Panel Controls and Indicators Status Display The display on the front panel of the instrument consists of two 3 colour light emitting diodes LEDs The display generated by the Pump LED is dependent on the vacuum status of the instrument The Operate LED depends on both the vacuum status and whether the operate mode has been selected from the Data System Further information is included in Automatic Pumping and Vacuum Protection see Routine Procedures Flow Control Valves The Desolvation Gas and Cone Gas needle valves are five turn valves The flow increases as the valve is turned counterclockwise The Nebuliser Gas valve is a four turn valve Divert Injection Valve The divert injection valve may be used in several ways depending on the plumbing arrangement e As an injection valve with the needle port and sample loop fitted e As a divert valve to switch the flow of solvent
126. tary pump is not maintained the oil may become so contaminated that optimum pumping speed is no longer possible Initially gas ballasting may clean the oil If the oil in the rotary pump has become discoloured then it should be changed according to the pump manufacturer s maintenance manual The turbomolecular pumps switch off if an over temperature is detected This could be due to poor backing vacuum failure of the water supply or a leak in the source or analyser Vacuum Leaks If a leak is suspected the following basic points may help to locate it e Leaks very rarely develop on an instrument that has been fully operational Suspect components that have recently been disturbed Leaks on flanges can usually be cured by further tightening of the flange bolts or by replacing the seal e All seals are made using O rings When refitting flanges pay attention to the condition of O rings Any that are cut or marked may cause a leak The O rings should be clean and free from foreign matter A hair across an O ring is sufficient to prevent the instrument pumping down Maintenance and Fault Finding Page 109 Q Tof 2 User s Guide e Source components that operate at or slightly above atmospheric pressure are not susceptible to vacuum leaks In the unlikely event of a leak on a feedthrough then the unit should be replaced or returned to Micromass for repair Pirani Gauge The Pirani gauge head does not require routine maintenanc
127. the operate mode the system turns off the critical source analyser and detector voltages and the green Operate lamp becomes amber e Acquisition continues though of course no real data are recorded When the vacuum recovers e The amber Pump lamp becomes green e If previously in the operate mode voltages are restored and Operate reverts to green The period during which the trip was operative will appear in a raw total ion chromatogram as a period of reduced baseline noise Further deterioration of the system pressures results in a vacuum fault condition and the system is shut down see below Power Failure In the event of an unexpected failure of the electrical supply the instrument is vented safely If power is unlikely to be restored quickly follow the shutdown procedure described later in this chapter When power is restored follow the startup procedure Should the power fail and then be restored while the instrument is unattended the system will continue to vent and will require to be pumped down in accordance with the start up procedure Routine Procedures Page 30 Q Tof 2 User s Guide Nitrogen Supply Replacement of nitrogen cylinders should be conducted in accordance with the operation handling and storage instructions provided by the local gas supplier Toggle the API gas button to Off to close the nitrogen inlet valve prior to disconnecting the supply Set the nitrogen inlet pressure to 7 bar
128. to be acquired for longer with a separate experiment The Precursor Scan Multi Step Mode In multi step mode the display of the precursor scan data is slightly more complex since there is a data set for each of the different window widths used in the experiment In the Chromatogram top banner select the TIC option under Display to open up the TIC Chromatogram window Parent lon Scanning Page 102 TIC Chromatogram x File az14 OK Function Snes 1 TOF Parent 50 2000 ES OeV Cancel 2 TOF Parent 50 2000 ES Oe File 3 TOF Parent 50 2000 ES Dev l Add trace I BPI Chromatogram C Replace trace C New window Q Tof 2 User s Guide Mass Chromatogram X File az14 OK Description m z Cancel Function 3 TOF Parent 50 2000 ES Oev 7 Type Mass v Add trace Replace trace C New window From this window display all the functions using add mode Then using the Mass Chromatogram facility under Display in the chromatogram top banner replace each trace with the mass es used in the experiment This should give a picture similar to the example shown where a precursor scan of 279 8 was carried out on a protein digest containing some phosphopeptides In this example the phosphopeptides produced M 2H ions at z828 9 and Yz974 5 The parent at z733 produced a product peak at z79 8 but was not in this case phosphorylated E Chromatogram az14
129. to the operator Remove the blanking plug from the discharge pin mounting contact and fit the corona discharge pin ensuring that the tip is in line with the tip of the sample cone Connect the APcI high voltage cable between Capillary Corona and the socket positioned at the bottom left corner of the source flange Replace the glass tube adjustment flange and moulded cover Warning Operating the source without the source enclosure will result in solvent vapour escape and the exposure of hot surfaces and high voltages With the corona discharge pin fitted and the source enclosure in place proceed as follows Insert the APcI probe into the source and tighten up the two thumb screws Routine Procedures Page 29 Q Tof 2 User s Guide A If necessary change the ionisation mode using the lon Mode command Set Source Temp to 150 C Caution The maximum operating temperature for the source heater is 150 C Do not set Source Temp higher than 150 C Do not start the liquid flow until the gas flow and probe heater are switched on with the probe inserted Transient Pressure Trip The transient trip is designed to protect the instrument from potentially damaging pressure surges and operates routinely whenever the pressure rises Should the vacuum gauge s detect a pressure surge above the preset trip level normally set at le 5 mbar by software the following events occur The green Pump lamp becomes amber e If in
130. to the peek ion block support locate the two dowels and push firmly Replace the ion block heater Replace and firmly tighten the two retaining screws taking care not to over tighten the screws On the tune page select Other and click on Pump Replace the PTFE exhaust liner and cleanable baffle if removed Replace the sample cone and if the nanoflow option is to be used the cone gas nozzle on the ion block Reconnect the cone gas supply nanoflow operation only Plug the purge and cone gas outlets and fit the APcI corona discharge pin Fit the source enclosure and the probe adjustment flange Insert the APcI probe and connect the Nebuliser Gas line Select Gas and turn on Nitrogen Fully open the Nebuliser Gas valve Set Desolvation Gas to read back 400 litres hour monitored on the tune page Check for gas leaks using soap solution Reduce Desolvation Gas to 150 litres hour Set Source Block Temp to 150 C and APcl Probe Temp to 20 C Maintenance and Fault Finding Page 121 Q Tof 2 User s Guide A Caution The maximum operating temperature for the source heater is 150 C Do not set Source Block Temp higher than 150 C Select Operate on the tune page With Corona set to zero check that the Cone readback is reading the correct set value Set Corona to 4 0kV Check that the Corona readback is 4 0 kV and that the Cone readback is still reading the same set value Check that all other readbacks on the tune
131. tween two and three times the diameter of the cone orifice as observed through the microscope Manoeuvre the stage so that the microscope or camera can view the capillary tip Using the nanoflow regulator apply pressure to the back of the tip until a drop of liquid is seen On the tune page select APIGas to turn on Nitrogen Select Operate Set Capillary between 600 and 1 0kV Adjust Desolvation Gas flow to 100 litres hour using the knob on the front panel of the instrument An ion beam should now be visible on the tune page Tune the source voltages adjust the gas flow and adjust the three axis manipulator for maximum ion current The ion current may change dramatically with very slight changes of position but the high resolution of the threads in the manipulator allows very fine tuning Restarting the Spray Should the spray stop it is possible to restart it by adjusting the three axis manipulator so that viewed under magnification the capillary tip touches the sample cone and a small piece of the glass hair shears off Set the capillary to zero when doing this It may also be necessary to apply some back pressure to the holder to force a drop of liquid from the capillary Up to 1 4 bar 20 psi can be applied and with this pressure a drop should be visible unless the capillary is blocked Nanoflow Electrospray Page 65 Q Tof 2 User s Guide Nano LC Option From Injector Installation or Column Attached Dir
132. up a new Scan Function file Click on the Parents button to add a Parents function to the editor In the Function 1 Parent Scan window that appears modify the parameters accordingly In the example shown here function will produce a precursor scan using 20Da windows and cover the mass range Yz400 1000 Parent lon Scanning Page 94 Q Tof 2 User s Guide NB The mass range that is set must be an integer multiple of the step width otherwise acquisition will not proceed In this case if the mass range were set to be M7390 1000 this will not divide exactly into an integer number of 20Da windows and the experiment will not run The Collision Energy is set to 30eV and the Cone Voltage is the same as that in the tune page The Spectrum Integration Period is 0 9sec with 0 1sec Inter Spectrum Period to transfer the data to the host PC The experiment will cycle for up to 99 minutes unless terminated interactively E Instrum cfg Notepad oy x Fie Edit Search Help When OK is selected this function will be added to the Scan Function window as shown below Scan Functions Untitled File Function Analog Help MS MSMS Survey F Analog Channels Solvent Delay Time mins 0 00 APcl Probe Temp E Mng 5 10 15 20 25 3 35 40 45 50 55 60 65 70 75 80 85 9 95 1 _ Parents Collision Energy 308V Use Tune Cone Settings ESP Continuum 1P Unused 27 Unused 37 Unused 47 Unused
133. y are separated in mass according to their flight times with ions of the highest mass to charge ratio 2 arriving later The pusher may be operated at repetition frequencies of up to 20 kHz resulting in a full spectrum being recorded by the detector every 50 microseconds Each spectrum is summed in the histogram memory of the time to digital converter until the histogrammed spectrum is transferred to the host PC If the user has requested an acquisition rate of 1 spectrum second each spectrum viewed on the host PC will be the result of summing up to 20 000 individual spectra recorded at the detector Instrument Description Page 11 Q Tof 2 User s Guide Unlike scanning instruments the TOF performs parallel detection of all masses within the spectrum at very high sensitivity and acquisition rates This characteristic is of particular advantage when the instrument is coupled to fast chromatography since each spectrum is representative of the sample composition at that point in time irrespective of how rapidly the sample composition is changing Internal Layout Warning The covers should not be removed without first isolating the instrument at the electricity supply A Caution The internal layout is shown in the following diagrams for information only and does not imply that labelled components are user serviceable Mechanical Components b J J gt Cl Fis SO SLE TOF Analyser

Q-Tof 2 User's Guide, issue 1. 6666526

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