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maXis User Manual

1. The analytical quadrupole consists of three quadrupole segments The middle segment is the resolving part of the mass filter the outer Foc L1 segments optimize the ion transfer efficiency if ee the quadrupole is used as a mass filter The same RF voltage is applied to all segments 3 E 05 mbar The bias voltage can be selected separately for the middle and the outer segments To ow achieve the resolving power the RF voltage of SE the middle element is superimposed with an asymmetric DC voltage For a detailed explanation of the functionality of a quadrupole mass filter please see chapter 4 Figure 2 13 Quadrupole With the Q q stage Figure 2 14 consisting of an analytical quadrupole and a collision cell the hybrid maXis achieves the capability to isolate and fragment parent ions prior to mass analysis with the TOF mass spectrometer 2 18 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 3 4 Collision Cooling Cell Collision Cell Cooling Cell Collision Gas N2 Ar IC1RF IC1EN I FOC2_L1 FOC2_L2 FOC3_L1 pulsed FOC2_L3 FOC3_L3 FOC3 L2 FOC4 Li pulsed FOC4_L3 FOC4 L2 Figure 2 14 Collision Cell Cooling Cell 2 3 4 1 Collision Cell In the collision cell the isolated parent masses can be fragmented by Collision Induced Dissociation CID For this purpose a neutral collision gas typically nitrogen or argon is introduced at about 10
2. Made fo Source i MS MS EN Sample Info l jh Chromatogram Ah Calibration TOF J fie Auto Tune B Auto MS MS Scan Mode 2A Precursor lona Threshold lt oor Abit T MS MS Auto E Absolute 2000 cts Acquisition SILE Precursor lon Lit Relative 0 z gt Fragmentation Exclude H MAM IT Smart Exclusion Width p 0 5 ISUID IY Active F x Collision Cooler GE Z Active Exclusion Add I Active Exclude after 3 Spectra Release after 1 00 min Delete Delete All Set Values Parameter Polarity Group Description GUI Unit Typic Min Max P Precursor lons Precursor lon List Dropdown menu Exclude Range s Width Threshold Absolute Relative Smart Exclusion Active Exclusion Exclude after Spectra 3 0 100 Release after min 1 00 0 00 100 00 Exclude Include 4 The Precursor lon List dropdown menu has the following options Lacheduled Precursor List maxis User Manual Version 1 1 6 13 Appendix Bruker Daltonik GmbH 6 4 1 4 Smart View MS MS Tab gt Auto MS MS gt Preference Mode l SA Source E MS MS E Sample Info le Chromatogram Eh Calibration TOF aie Auto Tune E Auto MS MS TREES Prefered Mass List Charge State i o E width lz 05 Preferred Range 2 A d Bu Fragmentation Exclude Singly MAM Import SCID eat olisi Sot P EE Coll
3. Heated drying gas N2 flowing in the opposite direction to the stream of droplets enters the spray chamber and is used to aid volatilization thus ionization and to carry away any uncharged material The desolvation assembly section 2 15 delivers the pressurized drying gas and guides it past the spray shield into the spray chamber at temperatures ranging from 120 C to 365 C and flowing at a rate of between 1 and 12 l min lons are attracted by the electrical field strength between the spray chamber ground potential and the negatively biased metal coated glass capillary the inlet to the vacuum system A potential difference of 400 V between the spray shield and the tip of the glass capillary acts as a further ion pull into the vacuum system All flows temperatures and bias voltages are adjusted and controlled automatically by the data system please refer to the micrOTOF contol manual The waste pipe of the spray chamber used to pump away solvents gas and sample molecules is connected to the rough pump The door of the spray chamber can be opened for maintenance purposes On opening this an interlock switch isolates all high voltages to the spray shield and capillary cap Functionally the interface consists of the following components Spray chamber Nebulizer gas Spray shield Capillary cap Drying gas Desolvation unit with o Glass capillary o Dry gas heater 2 12 maxXis User Manual Version 1 1 Bru
4. In GC MS electron capture often makes negative ionization the most sensitive operation mode In ESI electron capture is not a common ionization mechanism Negative ionization is generally less sensitive than positive ionization in ESI It is also possible to switch from positive to negative polarity during a scan of a peak Fast Polarity Switching and to switch between positive and negative polarity in different segments of a scan 3 2 2 4 Formation of adduct ions Neutral molecules that do not readily dissociate and do not protonate in the presence of the strong electric fields can sometimes be ionized through adduct formation Sugars can be adducted through the addition of a low concentration 50 micromolar solution of an alkaline metal such as sodium acetate or potassium acetate Urea can be ionized in the same manner maxis User Manual Version 1 1 3 9 Understanding API and APCI Electrospray Bruker Daltonik GmbH 3 2 2 5 Solvents ESI requires polar solvents Non polar solvents however can often be used successfully if a polar modifier is added For example toluene a non polar solvent modified with 15 isopropyl alcohol can be used as a solvent for the ESI analysis of fullerenes in negative ion mode The following table includes examples of other solvents that can be used for normal phase chromatography when modifiers are added For positive ionization mixtures of acetonitrile water methanol water and isopropyl alcohol
5. e Ease of operation such as eliminating a post column Tee maxis User Manual Version 1 1 3 13 Understanding API and APCI Electrospray Bruker Daltonik GmbH 3 3 2 APCI Solvents Mobile phases for APCI LC MS is preferably an aqueous organic solvent combination with 2 mMol 20 mMol of volatile organic buffer The following solvents are typical APCI mobile phase solvents and buffers High concentrations of acetonitrile ACN should be avoided and it s use has been shown to quickly carbonize the corona needle which can lead to reduced total ion current Common Solvents Common Buffers Methanol Acetic Acid Propanol Formic Acid Butanol Heptafluoro Butyric Acid Acetonitrile Ammonium Acetate Acetone Ammonium Formate and Acetate CHCI3 Ammonium Hydroxide Toluene Triethylamine Ethanol Tetraethylammonium Hydroxide lsopropanol Tetrabutylammonium Hydroxide Water CH2CIl3 CCI4 Benzene Hydrocarbons such as Hexane Cyclohexane When performing APCI standard buffers such as phosphate borate and sulfate buffers are non volatile and form ion pairs in solution To maximize APCI sensitivity use buffers that are volatile and do not form ion pairs Adjust the pH with buffers formic acid acetic acid and ammonium hydroxide or Triethylamine Typical pH for positive ion is neutral to pH 2 and for negative mode typical pH is neutral to pH 10 For ion pair separations use additives such as Heptafluoro butyric acid or Tetraethylammonium hydroxide or
6. 100 z Timing pee d Timing d 50 E 50 oe 50 oe 50 Sr Flush Flow Hate 30 0 DI a Collision Gaz Set Values Parameter Polarity Group Description GUI Unit Typic Max I M P lon Cooler RF Start End Timing Start Timing End Collision Energy Start End Timing Start Timing End Collision Gas Flow Rate 6 30 maXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 2 10 Expert View Sample Info Tab ER Made ie Source Zi MS MS EI sample Into La Chromatagram ih Calibration TOF ie Instrument Tune Data Fle spt AA Sample Parameter Analysis Name Sample Hame PretigCounter Manual DOSEN Pretix Counter SR Acq ooo e Comment Gubdrechonm 2 2 a k No SubDirectory gt Fath D data z There are no values to set in the Sample Info page 6 4 2 11 Expert View Chromatogram Tab E Mode Teh Source i MS MS Sample Into Ai Chromatogram EI Calibration TOF aft Instrument Tune A Moe Pesa jas Add Change Delete Delete All Reset Type Base Peak Chromatogram sl Masses W Enable Color Fed Filter A Width P 0 5 Polarity Both Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P Masses maXis User Manual Version 1 1 6 31 Appendix 6 4 2 12 Expert View Calibration Tab Bruker Daltonik GmbH ES Made SA Source MS MS By Sample Info Chromatogra
7. 2 14 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components the spray shield and the capillary cap focuses the ions directly onto the entrance of the glass capillary 2 3 1 4 Drying gas The drying gas usually nitrogen is used to completely evaporate the solvent in the small droplets before they enter the capillary The drying gas streams through the opening in the spray shield against against the flow of the charged droplets in the spray chamber see Figure 2 9 The gas is typically heated to between 100 C and 350 C at a flow rate of between 1 l min and 12 l min Flow and temperature are controlled by the data system and have to be adapted for each application While the drying gas assists in the desolvation process it does not thermally decompose the analytes 2 3 1 5 Desolvation Unit Basically the desolvation unit Figure 2 11 includes the drying gas heater the guidance of the heated drying gas the electrical connectors for the ESI high voltages and the glass capillary Heater ae Vacuum stage The analyte ions are transferred oA through the glass capillary from Ee SE the spray chamber into the first stage of the vacuum system The inner diameter and the length of the capillary determines the gas flow and so the pressure EES Figure 2 11 Desolvation unit The second function of the glass capillary is to isolate the high voltages at the entrance to the capillary see above fr
8. 3 2 1 2 Nebulization Nebulization aerosol generation begins when the sample solution enters the spray chamber through a grounded needle see Figure 3 1 For high flow electrospray nebulizing gas enters the spray chamber concentrically through a tube that surrounds the needle The combination of strong shear forces generated by the nebulizing gas and the strong electrostatic field 2 kV to 6 kV in the spray chamber draws out the sample solution and breaks it into droplets As the droplets disperse ions of one polarity are preferentially attracted to the droplet surface by the electrostatic field As a result the sample is simultaneously charged and dispersed into a fine spray of charged droplets hence the name electrospray Because the sample solution is not heated when the aerosol is created ESI ionization does not thermally decompose most analytes The charged droplets contain analyte solvent and both positive and negative ions The type of ions formed depends on the composition of the liquid sprayed If for example the solution contains the sample in acetic acid with a positive potential on the needle the predominant positive ions will be HOT and positively charged molecular analyte ions MH 3 4 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 2 1 3 Desolvation Before the ions can be mass analyzed solvent must be removed to yield a bare M H ion where n 1 2 A c
9. Rheude Richling Roberts 2 23 maxXis User Manual Version 1 1 6 25 6 14 2 14 3 4 3 19 2 22 5 33 3 17 3 17 Rollgen Roscher Rule S Safety Safety symbols Sample Info Tab Expert View Sample Info Tab Smart View Sample inlets Schematic of the maXis Schneider Schreier Schwab SEM Shut down options SILE Expert View SILE Smart View Silgoner Site preparation Specification solution chemistry Importance of Solvents APCI Source Tab Expert View Source Tab Smart View Sources Sources Optional Spare Parts maxXis Spray Chamber cleaning Startin Support Syringe pump T Table of Changes Table of Contents Text conventions Thompson Thomson Thorpe TOF assembly TOF Assembly TOF Tab Expert View TOF Extraction orthogonal Transfer Expert View U Understanding AC Understanding API Electrospray and APCI Unpacking 3 17 2 21 3 18 3 19 3 20 1 3 6 31 6 20 6 3 3 19 3 19 3 19 2 22 5 7 6 27 6 16 Index Bruker Daltonik GmbH V VW van der Greef 3 20 Wachs 3 17 Ventilation air filter 1 4 Waste 2 12 Ventilation Filters Replacement 5 34 Weight and dimensions 2 3 Venting 1 2 When to Use AC 3 13 Vestal 3 17 Whitehouse 3 17 3 18 Voltages hazardous 5 5 Wong 3 17 3 18 Voyksner 3 18 3 19 Y Yamashita 3 18 1 4 maxXis User Manual Version 1 1
10. a W Defaut Uuscdrupcoke pam eee ha Mass 300 00 mz ec 000 mis Start Cancel Accept Clear Set Values Group Description GUI Unit Typic Mass Range from to RampRange from to Quadrupole Mass Isolation Width 0 00 0 00 Results Current 1 0 maXis User Manual Version 1 1 Max 300 00 300 0 300 0 Parameter Polarity I M P 20 00 3000 00 6 33 Appendix Bruker Daltonik GmbH 6 4 2 15 Expert View instrument Tune Tab gt Transfer 2 Made ie Source i MS MS EN Sample Info all Chromatagram Jh Calibration TOF air Instrument Tune Haa Transfer Multipole Focusi Quadrupole Focus Collision Cell Focus Ton Cooler Focus4 TOF EEA UH C C C E IO GS Bias 34 0 y L3 Bias 30 0 W LZ Bas 2OOY LS Bes UlLbN L la LS Pl Oe CH O O O S ol LiL Lal Ea LiL GLE Ls Lap mil Focus Focu 2 Foti 2 ge us MME op vy a a0 oo y us 40 o0 v us 50 oo y 00 oo y LIE 35 0 UU y Lie 20 5 DU Ww LIE 13 0 OO vy LS SH UI y L 1 0 00 y L2 20 0 D w L2 50 0 DI yY 2 DU DU y Di 1100 0 y 0 rit L3 39 0 00 y al 25 0 DI yw L3 DUU DI oy 3 20 0 oo y Mass 55 00 m z e O 00 mz No values can be set in the Instrument Tune gt Transfer page 6 4 2 16 Expert View instrument Tune Tab gt TOF ER Made ie gt Source Zi MS MS fey Sample Into all Chramatagram i Calibration TOF air Instrument Tune hie
11. kinetic E RF otential E Figure 4 11 Collisional Excitation maxXis User Manual Version 1 1 4 13 Understanding maxis Basic Principles Bruker Daltonik GmbH The hexapole in the collision cell acts as an ion guide or two dimensional ion trap keeping the mother ions as well as the fragment ions together and close to the multipole axis Thus the ions are extracted very efficiently and injected into the cooling cell 4 6 Cooling Cell The cooling cell is an additional pressure stage which further reduces pressure in the orthogonal acceleration stage and extends the cooling and focusing range Due to the influx from the collision cell there is still a reasonable amount of collision gas molecules inside the cooling cell Without applying additional collision energy analyte ions continue to collide with collision gas molecules but the energies are too low to induce fragmentation Instead the multiple low energy impacts reduce the translational energy of the ions they get cooled down and hence are well focused along the multipole axis before entering the orthogonal acceleration stage 4 7 TOF assembly Orthogonal Extraction Acceleration lon Beam Region Stage Transfer and focus lenses Figure 4 12 Schematic of the TOF assembly 414 maXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles 4 7 1 Orthogonal TOF Injection The lens system situated between the cooling cel
12. mbar A hexapole is used to guide and focus the parent ions and the fragment ions To maintain the high vacuum conditions in vacuum stage 4 the hexapole is enclosed in a chamber the collision cell with small apertures at the entrance and exit A lens is needed to focus the ion beam on the small entrance aperture in front of the collision cell To obtain optimal fragmentation efficiency the collision energy can be adjusted by increasing all DC voltages in front of the collision cell ion transfer stage and quadrupole mass filter up to 200 eV Due to the high pressure inside the collision cell and the effective potential generated by the hexapole RF field the ions cool down lose their energy and can be focused very tightly onto the axis of the collision cell maXis User Manual Version 1 1 2 19 Identifying System Components Bruker Daltonik GmbH 2 3 5 Cooling Cell The cooling cell is an additional pressure stage with a multipole ion guide It reduces pressure in the orthogonal acceleration stage and extends the cooling and focusing range The cooling cell ends with a gate lens and a transfer lens During the fragmentation of parent ions the gate and lens voltages are set to block ion transmission to the TOF stage This facilitates the efficient accumulation of fragment ions After an adjustable time slot the voltage is set to transfer the accumulated ions into the TOF stage The TransferTime defines the beginning of the time slot and
13. Reference Leder 3 17 3 4 1 Reference articles for El stu cnesrensgecdenspcandelinceiieasand ida telnctieUeiaddaternaeeats 3 17 3 4 2 Reference articles for ACTA 3 19 Understanding maXis Basic Principles ccccccseesseeeseeeesseeeeeeesseeseeeeseeeeseeeenseesseneees 4 1 4 1 maxis as an API MS MS instrument ee ccec cee eeeeeeeeeeesaeeeeeaeeeeeeseeeeeeeaaeeeeeas 4 4 Bie e Ee 4 4 AA RF lon Guides closed repulsive wall 4 7 4 4 Quadrupole Mass Spectrometer OM 4 7 AD CONSON TEE 4 12 AG CONG C BEE 4 14 i maXis User Manual Version 1 1 Bruker Daltonik GmbH At WOR assombra 4 14 4 7 1 Orthogonal TOF TT 4 15 4 7 2 Orthogonal TOF ug Lee EE 4 16 9 NEE NEE 5 1 51 Chemical al 5 2 92 Bl lggical el 5 3 597 Mook Temporalil EE 5 4 94 Razardous DEE ee Eeer Ee 5 5 99 lee ege ee Ee 5 6 96 Elek Un Un Le bt CERN 5 7 5 6 1 EE He US EES Ee EE 5 7 5 6 2 Removing the Nebulizer uk REENEN ENEE ENEE EEE NA 5 9 5 6 3 Fl shing the NeDUIZ EE 5 10 5 6 4 Replacing the Nebulizer Needle bk 5 11 5 6 5 Reinstalling the hNebultzer kk 5 13 5 6 6 Removing the Glass Capillary cccccccccseeceeceeeeeeeeeeeeseseeeseeeeeesaeeseesaaeeees 5 14 5 6 7 Cleaning the Spray Chamber 5 15 5 6 8 Maintenance of Funnel and Multipole Cartdoe 5 17 5 6 8 1 Dis assembling and Cleaning Multipole Cartridge and Funnel 5 18 5 6 8 2 Re Assembling Multipole Cartridge Lens Block and Funnels 5 24 5 6 8
14. Rheude and M Dole Molecular Beams of Macroions Il J Chem Phys 1970 52 4977 4986 maxXis User Manual Version 1 1 3 17 12 13 14 15 16 17 18 19 20 21 22 23 Understanding API and APCI Electrospray Bruker Daltonik GmbH Mann M Electrospray Its Potential and Limitations as an lonization Method for Biomolecules Organic Mass Spectrometry 1990 25 575 587 Mann M C K Meng and J B Fenn Interpreting Mass Spectra of Multiply Charged lons Anal Chem 1989 61 1702 1708 Mann M C K Meng and J B Fenn Of protons or proteins Z Phys D Atoms Molecules and Clusters 1988 10 361 368 Rollgen F W E Bramer Weger and L Butfering Field ion Emission liquid solutions lon Evaporation against Electrohydrodynamic Disintegration Journal de Physique Colloque C6 November 1987 11 48 253 256 Thompson B A and J V Iribarne Field Induced ion evaporation from liquid surfaces at atmospheric pressure J Chem Phys 1979 71 4451 4463 Voyksner R D Electrospray LC MS can it be used to determine lower molecular weight molecules Nature 1992 356 86 87 Voyksner R D and T Pack Investigation of Collisional Activation Decomposition Process and Spectra in the Transport Region of an Electrospray Single Quadrupole Mass Spectrometer Rapid Comm in Mass Spectrometry 1991 263 269 Whitehouse C M R N Dreyer M Yamashita and J B Fenn Electrospray Interface for Liq
15. cartridges or lenses see Maintenance section 5 6 8 5 6 maXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 6 Maintaining the maXis 5 6 1 Vent the Instrument Applying the Shud button opens a dialog to set the instrument in a defined mode Make one of these three choices Figure 5 1 Shutdown Options CG Standb To bring system into Standby mode tandby e g to increase detector lifetime overnight or over weekend C Shutdown Went Vacuum Cancel Figure 5 1 Shut down options for the instrument If you want to vent the instrument click Vent Vacuum to select this mode Figure 5 2 To zech off all vollages and to went vacuum spiten dearer f Vent Vacuum EE EE Ke Figure 5 2 Click the Vent Vacuum option maxis User Manual Version 1 1 5 Maintenance Bruker Daltonik GmbH A confirmation dialog is displayed as shown in Figure 5 3 micrOTOF control AN Do vou really wank to vert the mass spectrometer Figure 5 3 Confirmation dialog Click on Yes to vent the instrument 5 8 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 6 2 Removing the Nebulizer When required When removing the nebulizer for visual inspection Tools Required e Gloves latex 200622 Parts Requires e None Preparation e Ensure work surfaces are clean and dust free Caution Sharps and needle hazard The nebulizer tip can puncture latex gloves and skin Avoid
16. Abrasive Cleaning When required Abrasive cleaning of the spray shield or capillary cap will be necessary if significant discoloration or deposits cannot be removed by polishing Tools required Sand paper 8000 grit Cloths clean lint free 45485 Gloves latex 200622 Isopropyl alcohol 99 5 reagent grade or better 58477 Water reagent grade or better 49145 maxis User Manual Version 1 1 5 31 Maintenance Bruker Daltonik GmbH Parts required None Preparation Mix a solution of 50 isopropyl alcohol and 50 water for cleaning All work surfaces should be clean and dust fee 9 32 CAUTION Because the spray shield and capillary cap are made of stainless steel they can safely be abraded However these are the only parts that should be cleaned in this way Many other metal parts such as the spray chamber may look similar to stainless steel but are made of much softer metals or are plated with materials that will be damaged by abrasive cleaning WARNING The spray chamber operates at high temperatures Let it cool down to ambient temperature before proceeding Shut down the maXis section 5 6 1 Open the spray chamber Remove the spray shield Remove the capillary cap Place the sandpaper grit side up on the workbench Move the flat surface of the spray shield over the surface of the sandpaper in a figure of 8 Only the large flat surface needs to be cleaned in this way unless
17. Auto Tune hie Optimize H Transfer Jl TOF Repetition Rae lt 2 Flight Tube BO k FlightTube s8600 y oo vy Puse ARADDBBBSSS_ Fee Phe bee mpm mA Push 1560 0 V iis V Decelerator 1554 8 V np V Pull m vi oo wv Reflector n v on vw Corector Detector Fill a l gees OO wm Extract enn V oo V TOF 2560 0 oo V Lenz 6200 0 V oo V No values can be set in the Instrument Tune gt TOF page 6 34 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 5 Patents Key Word glass capillary DE 195 15271 C2 GB2300295B US 5 736 740 A 25 Apollo II lon DE 195 23 859 C2 GB 2 302 985B US 5572 035 A Funnel Source gridless orthogonal GB 2 361 353 B US 6 717 132 B2 accelerator ultrastable DE 101 09917 B4 GB 2 375 654B US 6 723 983 B2 electronics digital threshold WE GB 2 385 982B US 6 836 742 B2 DE 101 58 924 B4 GB2386751B US 6 903 332 B2 focus signal processing DE 10206173 B4 GB 2 390 936 B US 6 870 156 B2 enabeling TIP Apollo II lon GB 2 402 261 B US 7 064 321 B2 Funnel Source high precision multipole rod GB 2 416 915 A systems L ve e oe reflector detector maxis User Manual Version 1 1 6 35 Bruker Daltonik GmbH 7 INDEX A Abrasive cleaning Achieving Gas Phase Conditions Acquisition Expert View Acquisition Smart View Adjusting the Nebulizer Needle Allen Alpendurada Analyte delivery APC
18. Bruker Daltonik GmbH 1 3 2 Operating Precautions To protect yourself from harm and to prevent system malfunction observe the following guidelines Before using the instrument read all of the warnings explained at the beginning of this manual e Wear appropriate protective clothing including safety glasses and gloves when preparing samples and solutions for use with this instrument e Follow the correct safety procedure and the manufacturer s recommendations when using solvents Read and follow precautions as detailed on the Material Safety Data Sheet MSDS obtainable from the supplier e Clean the exterior surfaces of the instrument with a soft cloth dampened with a mild detergent and water solution Do not use abrasive cleaners or solvents e Exercise caution when moving as the maXis mass spectrometer as it weighs 345 kg 760 lbs Wear appropriate clothing and use appropriate equipment when carrying or moving the instrument Caution Do not restrict the ventilation air intake or the exhaust both located at the rear of the instrument TO ensure proper operation check the ventilation air filter every three months The ventilation filter is situated at the rear of the instrument and must be replaced if it becomes clogged Only use Bruker filter 216264 1 4 maxXis User Manual Version 1 1 Bruker Daltonik GmbH General 1 3 3 Safety Safety considerations consist of the following sections Before installing or oper
19. Daltonik GmbH General 1 4 Facility and Electrical Requirements The facility must provide Table 1 3 Power supply data North America 208 VAC 10 dual phase voltage 230 VAC 10 single phase voltage 240 VAC 6 single phase voltage e The instrument comes with a 3 m long IEC320 line cord and a mains plug suitable for use in your country e The maXis mass spectrometer requires approximately 3 5m of floor space including space for ventilation and access The surface on which the maxis stands must be designed to safely support the full 345 kg 760 Ibs instrument weight e To ensure proper ventilation and access to the connections and the main switch maintain at least 500 mm 20 in of free space on the left hand side 1000 mm 40 in in front and 100 mm 4 in behind the maxis Warning The main electrical supply must provide adequate grounding The system has an exhaust port to accommodate venting This port is located at the rear of the instrument Individual facilities may have safety guidelines which require the exhaust gasses and particles to be treated in a particular way It is the responsibility of each user to comply with the requirements of their respective facility maxXis User Manual Version 1 1 1 7 General Bruker Daltonik GmbH 1 5 Unpacking Installation and First Setup A packing list is created for each order and is placed in the crate with the equipment Note The warranty does NOT c
20. Figure 3 1 Electrospray ionization flow of drying gas N2 and analyte 3 2 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 2 How ESI works The process of electrospray ionization ESI API and APCI can be summarized in four steps e Formation of ions e Nebulization e Desolvation e lon evaporation Several different aspects concerning ESI have to be considered e Importance of solution chemistry e Positive ion analysis e Negative ion analysis e Formation of adduct ions e Solvents e Buffers maxis User Manual Version 1 1 3 3 Understanding API and APCI Electrospray Bruker Daltonik GmbH 3 2 1 Process of Electrospray lonization The process of electrospray ionization ESI API and APCI can be summarized in four steps 3 2 1 1 Formation of ions lon formation in API electrospray occurs through more than one mechanism If the chemistry of analyte solvents and buffers is correct ions can be generated in solution before nebulization When possible and done properly this results in high analyte ion abundance and good API electrospray sensitivity Preformed ions are not a requirement for ESI Analytes that do not ionize in solution can still be analyzed The process of nebulization desolvation and ion evaporation creates a strong electrical charge on the surface of the spray droplets This can induce ionization in analyte molecules at the surface of the droplets
21. GmbH 26 REME EE Edel EE 2 31 2 6 1 Initiating Remote Gervice 2 32 Zh E e gen Ee le 2 36 E EN e WE ee 2 37 ZT AMe2 PAP lel SOU C EE 2 38 ZI Aso Rule Sp ayo EE 2 40 ZA NA GAP PU SOUR E amie A ieee ct ese deseidccteatebieeieela te 2 41 2 1 5 Capillary Electrophoresis CEA 2 42 ZA CHEN eege ee EE EE ee 2 43 2 7 1 7 Off line NAnOElectrospray cccccccceccceeseeeeeeeeeeeeeseeeesseeeeeesseeeeeeaeeeeesaees 2 44 2 7 1 8 On line NanoElectrospray cccccccseecceeceeeeeeeeeeeeeaeeeeeeeeeeeeesaeeeeeeaeeeessaess 2 45 Understanding API and APCI Electrospray ccccccesseseseeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeeseeeeeeennes 3 1 3 1 Atmospheric Pressure Interface API ccccccssseeeceesseecceseeeceeseeecseseesseaseeessaaess 3 2 SE MOWE ET e EE 3 3 3 2 1 Process of Electrospray lonization cccceccceeeeeeeeeeeeeeeaeeeeeeeeeeeeeeeeeesaaeeeeens 3 4 OZ Nel Forman OT Lee EE 3 4 222 INGDUNZ ATION EE 3 4 Ser BESOVA aiacasiet ee 3 5 S20 HEEN EE ee e EE 3 7 3 2 2 Different ASpectS Ol Bol EE 3 8 3 2 2 1 Importance of solution chemtsirv 3 8 3422 EE IHN a a 3 8 3229 Negative lomanalySiS ania dics eeaouscalondiginstsancnewand nalenesauseetentanatannes 3 9 3224 Formation Ree e rer A E 3 9 E NEE el EE 3 10 32260 EE 3 11 Bao OW SARGI WORKS EE 3 13 3 3 1 When to Use APC EE 3 13 3 3 2 PAP leede 3 14 3 3 3 Achieving Gas Phase Conditions ccccccccceccseeeeecseeeeeseeeeeeseeeeeesaaeseeeanens 3 15 3 4
22. MAINTENANCE This section gives users guidance on regular maintenance that is required to ensure consistent instrument operation CONTENTS Subject Page Number D1 Chemical E 5 2 9 22 Biological le EE 5 3 99 el ele Keele 5 4 94 Mazardo s V ONA GCS aesae ceiice nent riadarsrieneeienada emt diatalenedencandiewadies 5 5 5 5 Maintenance Schedule sassa a a eed 5 6 960 Jee 5 7 5 6 1 Vent ME INSrUme Maesen a N 5 7 5 6 2 Removing the Ee EE 5 9 5 6 3 FIUSAING he Ee IEN 5 10 5 6 4 Replacing the Nebulizer Needle cccccccssseceseseceesseeeseseeseeeeeeseeeneneeens 5 11 5 6 5 Reinstalling the EES ene 5 13 5 6 6 Removing the Glass Capillary EE 5 14 5 6 7 Cleaning the Spray Chamber egene 5 15 5 6 8 Maintenance of Funnel and Multipole Cartmdoe 5 17 5 6 8 1 Dis assembling and Cleaning Multipole Cartridge and Funnel 5 18 5 6 8 2 Re Assembling Multipole Cartridge Lens Block and Funnels 5 24 5 6 8 3 Re fitting the Multipole Cartridge to hemaiis 5 27 5 6 9 Adjusting the ESI Nebulizer Needle n nnnnannnnonnnneannnennnnnennnnsnnennnnensnreesereenne 5 30 5 6 10 EELER ee 5 31 5 6 11 Replacing the Nitrogen Gas Filter ce cecccccseeeeeeseeeeeeeeeeeeesaeeeesaeaeeesaaes 5 33 maXis User Manual Version 1 1 5 1 Maintenance Bruker Daltonik GmbH Caution Operators may be exposed to the following during maintenance access e Chemical Residues section 5 1 e Biological Residu
23. MS MS gt Fragmentation 00 na00nnnnaannna 6 17 6 4 1 8 Smart View MS MS TabzMHM 6 17 6 4 1 9 Smart View MS MS Table 6 18 maxXis User Manual Version 1 1 vil 7 viii Bruker Daltonik GmbH 6 4 1 10 Smart View MS MS Tab gt Collision CGooler 6 19 6 4 1 11 Smart View Sample Info Tab 6 20 6 4 1 12 Smart View Chromatogram Tab 6 20 6 4 1 13 Smart View Calibration TOF Tab 6 21 6 4 1 14 Smart View Auto Tune Tab 6 21 6 4 1 15 Expert View Values and Hanges 6 22 6 4 2 Expert View Mode Tab 6 22 6 4 2 1 Expert View Source Tab 6 23 6 4 2 2 Expert View MS MS Tab gt Auto MM 6 24 6 4 2 3 Expert View MS MS Tab gt Auto MS MS gt Preference a nonneennnnnnennnnnn 6 25 6 4 2 4 Expert View MS MS Tab gt Auto MS MS gt Acquisition cccccceeeeees 6 26 6 4 2 5 Expert View MS MS Tab gt Auto MM GIE 6 27 6 4 2 6 Expert View MS MS Tab gt Auto MS MS gt Fragmentation n oaannnnaannaan 6 28 6 4 2 7 Expert View MS MS TabzMHM 6 28 6 4 2 8 Expert View MS MS TabzlGcCh 6 29 6 4 2 9 Expert View MS MS Tab CGolleon tCooler 6 30 6 4 2 10 Expert View Sample Info Tab 6 31 6 4 2 11 Expert View Chromatogram Tab 6 31 6 4 2 12 Expert View Calibration Tab 6 32 6 4 2 13 Expert View Instrument Tune Tab gt Auto Tune 6 32 6 4 2 14 Expert View Instrument Tune Tab Cptpmte 6 33 6 4 2 15 Expert View Instrument Tune Tab Transfer 6 34 6 4 2 16 Expert Vie
24. MS Scan Mode _ Parent Condition Preference MS MS MRM e aaan L MS MSCMMY Uso isol Test Cal Energy 150D Ere Aca Fac Te SILE F Altemate Colision Energy 92200 1000 500 0 0 1 0 1 Fragmentation Tune Collision Energy ean Strategy Fragments ll Collision Cooler Number 3 x Range from 0 0 ey to 200 0 e 1522 00 15 00 70 0 0 0 1 0 2 zi Import New Delete Delete All Ur Down Set Values Parameter Polarity Group Description GUI Unit Typic i Max I M P Tune Collision Energy Number Sigs vi Range from 0 0 200 0 Range to 0 0 200 maxXis User Manual Version 1 1 6 17 Appendix Bruker Daltonik GmbH 6 4 1 9 Smart View MS MS Tab gt ISCID 2 Mode feo Source i MS MS Ej Sample Info j Chromatogram a Calibration TOF j Auto Tune E Auto MS MS be Preference Scan Mode IT MS MS M5 ISCID MS Settings S SCID i Collision A Cooler ISCID oo Energy us ey MS MS ISCID Settings ISCID Soen 5 0 eW Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P MS Settings ISCID Energy eV MS MS Settings ISCID Settings ISCID Energy eV 6 18 maXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 1 10 Smart View MS MS Tab gt Collision Cooler E Mode gt Source Fe MS MS EN Sample Infa 2 Chromatogram ih Calibration TOF aie Auto Tune GC Auto
25. Si Source Pai MS MS By Sample Info te Chromatogram cd Calibration TOF ile Instrument Tune B Auto MS MS Scan Mode pa Precursor lons Threshold e IT MS MS Auto a v Absolute 2000 cts Precursor lon ist aea T be a Exclude ha 5 Ir EE 205 gt Smart Evchueon z Jh Active z x d SS Active Exclusion Add h Active Exclude after E Spectra Release after 1 00 mir Delete Set Values Parameter Polarity Group Description GUI Unit Typic Min Max P Precursor lons Precursor lon List Dropdown menu Exclude Range s Width Absolute Relative Smart Exclusion Active Exclusion Exclude after Spectra 3 0 Release after min 1 00 0 00 100 00 ISS Include T The Precursor lon List dropdown menu has the following options Lacheduled Precursor List 6 24 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 2 3 Expert View MS MS Tab gt Auto MS MS gt Preference Mode gt Source Ze MS MS ay Sample Info aie Chromatagram Z Calibration TOF ie Instrument Tune Preferred Mass List ______ Charge State width p 0 5 sl Preferred Range d 2 Exclude Singly Import Sort Precursors by Intensity v Active Exclusion Strict active Exclusion Add Delete Delete oi Set Values Parameter Polarity Group Description GUI Unit
26. Tetrabutylammonium 3 14 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 3 3 Achieving Gas Phase Conditions In APCI the probe temperature is the most important parameter to achieve good sensitivity and minimal decomposition Many compounds do ionize at high vaporizer temperatures For example compare the response of Vitamin D3 compound 7 and Furosemide compound 9 where the vaporizer temperature was lowered from 400 C to 200 C At 400 C significant response for these compounds was observed Figure 3 5 At 200 C low response for these compounds was observed Figure 3 6 Detected Compounds in Figure 3 5 and Figure 3 6 1 Penicillin G 2 Cloxacillin 3 Tetracycline 4 Sulfamethazine 5 Sulfamethizole 6 Amino Chlorobenzamide T Vitamin D3 8 Methylene Blue 9 Furosemide 10 Spectinomycin 11 Gentamicin 12 Streptonycin 13 Disperse Orange 13 14 Basic Yellow 2 15 Basic Violet 10 16 Disperse Blue 3 maXis User Manual Version 1 1 3 15 Understanding API and APCI Electrospray Bruker Daltonik GmbH Figure 3 5 Vaporizer temperature at 400 C with significant response of compound 7 and compound 9 72 34 5678 910 1 12131415 16 Figure 3 6 Vaporizer temperature at 200 C with low response of compound 7 and compound 9 3 16 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 4 Reference articles 3 4 1 Reference articles
27. Typic Min Max P Preferred Mass List Charge State Preferred range Exclude Singly Sort Precursors Active Exclusion maxXis User Manual Version 1 1 6 25 Appendix Bruker Daltonik GmbH 6 4 2 4 Expert View MS MS Tab gt Auto MS MS gt Acquisition 2 Mode p Source Et MS MS ae Sample Info le Chromatogram Ben Calibration TOF sie Instrument Tune E Auto MS MS Preference Precursor Acquisition Control Intensity Summation e Se F tati ragmentation Ms ISCID i Collision A Cooler MS MS V Low 10000 cts 2000 V Total Cycle Time Perea 4 zer High 1000000 cts S000 x Absolute Threshold 2000 cts Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P Intensity Low cts Summation Low X Intensity High cts Intensity Summation 6 26 maXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 2 5 Expert View MS MS Tab gt Auto MS MS gt sSILE r ES 1 5 S S z E Mode Source iT MS MS E Sample Info Chromatogram Z Calibration TOF shir Instrument Tune E Auto MS MS Advanced MS M 5 Auto Preference l SILE H AcQuisition E Fragmentation Within Top Mas no Delta blaszs of labels Charge Range P ecm 2 1 3 SCID T 6 0201 2 1 3 i Collision Cooler Add Change Delete Delete All Intensity Ratio Set Values Group Description GUI Unit Typic Advance
28. a solvent bath and clean them with an ultrasonic cleaner maxis User Manual Version 1 1 5 15 Maintenance Bruker Daltonik GmbH Note If contamination or discoloration of the spray shield and capillary cap cannot be removed by polishing the use of abrasives may be necessary see section5 6 10 e Reinstall the capillary cap and spray shield e Wipe all other accessible surfaces Pay special attention to the bottom of the spray chamber near the drain hose and to areas that are discolored e Close the spray chamber e Reinstall the Electrospray nebulizer 5 16 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 6 8 Maintenance of Funnel and Multipole Cartridge When required e As necessary Tools Required e Torx Screwdriver e Allen Key Parts required e Cloths clean lint free 45485 e Gloves latex 200622 e Isopropyl alcohol 99 5 reagent grade or better 58477 e Water reagent grade or better 49145 Preparation e All work surfaces to be clean and dust free CAUTION The funnels and the multipole in the cartridge are very sensitive parts Be careful to avoid damaging them maxXis User Manual Version 1 1 5 17 Maintenance Bruker Daltonik GmbH 5 6 8 1 Dis assembling and Cleaning Multipole Cartridge and Funnel 1 Vent Vacuum System In the micrOTOFcontrol software click on Shutdown select Vent vacuum and click OK fe Vent Vacuum To satch off
29. all voltage and to went vacuum system eg fortonophcs caplan cleaning Figure 5 5 Shutdown dialog Click on YES in the confirmation dialog Do you really want to vent the mass spectrometer mcr OF control Figure 5 6 Confirmation dialog NOTE Please wait until system is vented This takes approximately 5 minutes 5 18 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 2 Remove lon Source Disconnect the tubing from the Nebulizer and remove the Spray Chamber by unclipping the toggle clamp on the right hand side swinging the chamber to 90 and lifting it off its pivot pins Figure 5 7 lon source open maxXis User Manual Version 1 1 5 19 Maintenance Bruker Daltonik GmbH 3 Remove Desolvation Unit H lt lt wf BE Pull out desolvation unit Figure 5 8 Disconnect cables and tubing unscrew the four fixing screws 4 Remove the cartridge containing the funnels and the multipole Multipole Cartridge oe a Locate the multipole b Hook your fingers inside c Ease the cartridge out of cartridge the metal Grab Handle the instrument and and pull to break the transfer it to the bench double seal 5 Reassemble the Desolvation Unit to protect the vacuum system from contamination 5 20 maXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 6 Remove the Grab Handle Neoprene Ring a Remove the neoprene ring
30. as reaction chamber The kinetic energy of the injected ions is at least partially converted into internal energy of the ions giving rise to fragmentation if this internal excitation exceeds the dissociation energy of the molecular ions The fragmentation induced by gas collisions is Known as collision induced dissociation CID The reaction products i e the fragments are analyzed in the second MS stage Therefore the ions are extracted from the collision cell and injected into the TOF analyzer The fragment spectrum gives structural information as well as some energetic information on the isolated molecules from the sample In MS mode the quadrupole is used as an ion guide RF only mode not isolating an arbitrary mass but transmitting a broad mass range The collision energy is set very low in order to keep the internal excitation low and to avoid fragmentation 4 2 lon Guides The maXis uses several types of ion guides Funnels and multipoles are used to guide ions from the capillary exit to the analyzer passing through several vacuum stages An ion guide acts like a tube for charged particles keeping the ions together but allowing the neutral gas and solvent molecules to escape from the ion path Hence the ions are 440 maXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles brought into the analyzer with high transmission efficiency but the neutral molecules are removed from the system by
31. for ESI 1 10 11 Allen M H and M L Vestal Design and Performance of a Novel Electrospray Interface J Am Soc Mass Spectrom 1992 3 18 26 Blades A T M G Ikonomou and P Kebarle Mechanism of Electrospray Mass Spectrometry Electrospray as an Electrolysis Cell Anal Chem 1991 63 2109 2114 Carr S A M E Hemling M F Bean and G D Roberts Integration of Mass Spectrometry and Analytical Biotechnology Anal Chem 1991 63 2802 2824 Covey T R A P Bruins and J D Henion Comparison of Thermospray and lon Spray Mass Spectrometry in an Atmospheric Pressure lon Source Organic Mass Spectrometry 1988 23 178 186 Fenn J B M Mann C K Meng and S F Wong Electrospray ionization principles and practices Mass Spectrometry Reviews 1990 9 37 70 Fenn J B M Mann C K Meng S F Wong and C M Whitehouse Electrospray lonization for Mass Spectrometry of Large Biomolecules Science 1989 246 64 71 Hodgson J Electrophoresis in Thin Air Bio Technology 1992 10 399 401 Huang E C T Wachs J Conboy and J D Henion Atmospheric Pressure lonization Mass Spectrometry Anal Chem 1990 62 713 722 Ikonomou M G A T Blades and P Kebarle Electrospray lon Spray A comparison of Mechanisms and Performance Anal Chem 1991 63 1989 1998 Iribarne J V and B A Thomson On the evaporation of small ions from charged droplets J Chem Phys 1976 64 2237 2294 Mack L L P Kralik A
32. optimize chromatography and those that do not hinder the electrospray process can be added before the separation Buffers that interfere with the separation must be added post column For most positive ion analysis of polar materials such as amino acids peptides and proteins the pH of the solution should be adjusted to a pH of 2 5 The addition of acetic acid at 0 1 to 0 2 is a good starting point For positive ion analysis of pharmaceuticals a solution of 0 015 formic acid serves the same purpose and may have less chemical noise and smell than acetic acid Some pharmaceutical compounds can be analyzed successfully in a neutral mobile phase For example benzodiazepines and opiates can be analyzed with a traditional mobile phase of acetonitrile and water Buffers such as sodium acetate or potassium acetate alkali metals can be used to form adducts with the analytes that would otherwise not ionize in solution Sugars and urea are two examples of chemicals that form sodium adducts that can be analyzed in positive ion mode Other buffers such as ammonium acetate and ammonium formate are sometimes added to prevent undesired adduction of the analyte with sodium or potassium ions from endogenous sources Buffers can be used to optimize chromatography The addition of 50 micromolar ammonium acetate or ammonium formate is often used to increase chromatographic resolution of basic nitrogen containing compounds on reversed phase silica columns
33. the Pre Pulse Storage Time defines the end of the time slot Both are referenced to the next TOF pulse and limit the transferred mass range A higher us value for Transfer Time will give a higher upper limit of transferred m z A lower us value for Pre Pulse Storage Time will reduce the lower limit of transferred m z The transfer lens works together with the entrance lens of the orthogonal accelerator to generate a suitable parallel beam shape inside the acceleration stage 2 20 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 3 6 TOF Assembly Dual Stage Reflector TOF Spectrometer Cooling Cell _ x SS 1 ICIEN I FOC4 L5 loo 1g a FOC4_L5 FOC4 L FOC4_L4 FOC4_L1 pulsed Orthorgonal Accelerator Detector FOC4 L2 1 E 07 mbar Figure 2 15 Schematic of the TOF assembly The layout of the TOF assembly is shown in Figure 2 15 The main components of the TOF assembly are e Orthogonal acceleration stage section 2 3 6 1 e Reflector section 2 3 6 4 e Detector section 2 3 6 5 maxXis User Manual Version 1 1 2 21 Identifying System Components Bruker Daltonik GmbH In ESI TOF applications the orthogonal acceleration stage replaces the ion source This stage does not create ions but simply deflects and transfers incoming ions to the reflector by the use of pulsed voltages During pulser off time when electrodes of the acceleration stage are
34. the pumping system X e Ps LP 3 aw A IX Y LPN p PAZ V Ka X N SOREN ATEN AAT RAAT d NS f Figure 4 3 lon Guide principle The ions cannot escape from the ion guide Hence they are guided over a distance with high efficiency The repulsive force in the ion guide keeping the ions focused on the center line arises from the interaction of the ions with the inhomogeneous RF field Due to the inhomogeneity of the RF field visualized by the electric flux lines the initial motion of the ions towards the ion guide couples with the RF oscillation The ion is pushed up and down or back and forth tangentially to the flux lines of the oscillating electric field Due to the curvature of the flux lines there is always a component of the force pushing the ions towards the weaker field Hence an ion moving towards the electric field will be decelerated and if the repulsive force of the RF field is strong enough reflected maXis User Manual Version 1 1 4 O1 Understanding maxis Basic Principles Bruker Daltonik GmbH This behavior of ions in an inhomogeneous RF field is described as the Effective Potential or Pseudopotential or as the Ponderomotive Force The effective Potential can be calculated by V e Eo 4mw and is a function of the local field strength the ion mass and charge and the RF frequency The initial energy of the ion is transferred into RF oscillation and back into translational motion Thus the m
35. touching the nebulizer tip Warning Burn hazard The tip of the nebulizer may be very hot Let it to cool down Warning Chemical or Biohazard Solvents and sample material deposits can be toxic Take precautions appropriate to the hazard Read the Material Data Safety Sheets MSDS supplied with chemicals e Shut off the flow of LC solvent e Shut off the flow of nebulizing gas e Disconnect the LC tubing and nebulizing gas tubing from the nebulizer e Turn the nebulizer counterclockwise and disengage it from the retaining screws e Carefully lift the nebulizer out of the spray chamber maxis User Manual Version 1 1 5 9 Maintenance Bruker Daltonik GmbH 5 6 3 Flushing the Nebulizer After a series of measurements it is recommended that the nebulizer tubing and valves are flushed out with e Isopropyl alcohol reagent grade or better 58477 and e Water reagent grade or better 49145 Flushing Procedure e Remove the nebulizer e Mixa solution of 50 isopropyl alcohol and 50 water e Use a syringe and a hose to pump this mixture through the nebulizer several times e Clean the tip of the Nebulizer in an ultrasonic bath Note This applies to both Electrospray and APCI nebulizers 5 10 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 6 4 Replacing the Nebulizer Needle A clean and undamaged needle is essential to achieve good electrospray conditions Flush the needle before an
36. valve with loop port 3 from HPLC port 4 to nebulizer TIV C port 1 calibrant from VIN o ge ke Ax syringe pump a4 Ee d a port 6 to waste Figure 6 2 Sample flow through the divert valve with loop Divert valve in source position e green HPLC to yellow nebulizer e blue calibrant via loop to gray waste gt loop is filled with calibrant Divert valve in waste position e green HPLC via loop to yellow nebulizer gt calibrant from loop is injected to source e blue calibrant to gray waste Conclusion e constant flow irrespective of valve position e loop must be filled during runtime of the LC analysis e filling time of loop should be optimized with flow rate of syringe e calibration is undertaken by post processing software this is not a feature of micrOTOF control maxis User Manual Version 1 1 6 7 Appendix Bruker Daltonik GmbH 6 3 2 Example 2 Sample flow through the divert valve with loop port 3 from HPLC port 2 to nebulizer port 5 calibrant from syringe pump port 6 to waste Figure 6 3 Sample flow through the divert valve with loop Divert valve in waste position e green HPLC to yellow nebulizer e blue calibrant via loop to gray waste loop is filled with calibrant Divert valve in source position e green HPLC via loop to yellow nebulizer calibrant from loop is injected to source e blue calibrant to gra
37. with a superfine capillary It replaces the ESlI nebulizer and also requires a pressurized nitrogen gas feed to function Figure 2 32 The ESI nano Sprayer Nebulizer Nano HPLC or Syringe Pump ESI nano Sprayer ESI Zone ma i Se Capillary Kat fm N Drying Gas Spray Chamber Waste Figure 2 33 Schematic of ESI nano Sprayer 2 40 maXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 7 1 4 APPI Source The APPI source Atmospheric Pressure Photon lonization can also be connected to the instrument For further information see the user manual for the APPIl source The Bruker APPI Atmospheric Pressure Photon lonization source Figure 2 35 and Figure 2 34 is best used for the analysis of solved samples which do not ionize well with ESI or APCI The nebulization process is similar to that in the APCI Figure 2 35 APPI source with UV lamp for source and also occurs in a heated ionization vaporizer tube For gas phase solvent ion ionization the APPl source uses a UV lamp instead of a discharge corona needle The high 272 ge energy UV radiation ionizes the gas Nebulizer gas inlet Np phase solvent molecules These ener solvent lons convert sample Spray needle sheathed molecules into sample ions by means with nebulizer gas of a charge transfer High wattage vaporizer Spray shield 63 6 ky Heated drying gas Mz Glass capillary inners 0 5 0 6 mm Ca
38. with b Remove the Grab Handle by unscrewing tweezers the three Torx T10 screws 7 Disconnect Funnel 1wiring a The four wires connecting Funnel 1must b Use narrow nosed pliers to ease the be disconnected from their sockets in the connectors from the sockets transfer cartridge 8 Unscrew Funnel 1 c Funnel 1 is now a Four Torx T10 screws b Remove these screws secure the Funnel 1 to Funnel 1 then pulls ready for cleaning the transfer cartridge straight out maxXis User Manual Version 1 1 5 21 Maintenance Bruker Daltonik GmbH 9 Cleaning Funnel 1 The complete funnel can be washed with acid free organic solvents in an ultrasonic bath 10 Removal of Funnel 2 a Disconnect the orange b The F2 Funnel is secured c Remove these screws violet yellow and blue to the transfer cartridge and Funnel F2 can be wires from the pins at the by four Torx T8 screws pulled out Funnel F2 is lens end of the cartridge deep inside the recess now ready for cleaning 11 Cleaning Funnel 2 The complete funnel can be washed with acid free organic solvents in an ultrasonic bath 12 Remove Lens Block EH a EH G Green Yellow Se a Disconnect the green b Remove the red wire c Caution There is a and yellow Lens Block using a pair of tweezers compressed spring wires from the transfer Then remove the two T6 located behind the lens cartridge Torx screws Fig c block Hold the block in place wh
39. 2005 WebEx Communica tions Inc Siren 8 internet 7 Figure 2 23 The Bruker Support Session webpage 2 32 maXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components Note The http connection changes to a https connection coded with 128 bit to provide the highest possible level of security gt Bruker Daltonik GmbH Enterprise Site Windows Internet Explorer fel KE p Datei Bearbeiten Ansicht Favoriten Extras X v 4 zz X ev Wikiped electron volts E me Seite Of Extras RW 7 Ie https bdal webex com mw0304l mywebex default do siteurl bdal amp service 9 non print degree sym term Synonyms Fro W Electronvolt Wikiped e Bruker Daltonik G gt e Registerbrowsen we d BB 7 Inform Home Navigator Contact w Get Support Pre Session Form In order to provide a higher quality of service we ask that you fill in the following information b Provide Support denotes a required field gt Assistance Support Session Number First name Last name Email address Company powered i Aa mea BALTENIES Copyright 2008 WebEx Communications Inc Privacy Terms of Service Request information about WebEx services Internet 100 Figure 2 24 Enter the required information 4 Enter the Support Session Numb
40. 3 Re fitting the Multipole Cartridge to hemais 5 27 5 6 9 Adjusting the ESI Nebulizer Needle cccccssscccceeeeeceseeescseeeecssseeeseaes 5 30 5610 Abrasive CIE Ann EE 5 31 5 6 11 Replacing the Nitrogen Gas Elter 5 33 5 6 12 Replacing the Ventilation Filters cc ccceececeeeeeeeeeeeeeeeeseeeesaeeeseeeeeseeeeeas 5 34 6 AAD DOI GI iecdcscsvecitaacectiiedecs ionann an eaaa oaaae a Saaana ea aai 6 1 Se NN E ele Pars E 6 1 G2 SCHEMAaAlC Of IME E EE 6 3 6 3 Divert Valve Connection Examples ccccccccceececeeseeceeeeese cece sesseeeessaeeeseeeeeseeeees 6 6 6 3 1 Example 1 Sample flow through the divert valve with l00p n001nnn01nn001000n 6 7 6 3 2 Example 2 Sample flow through the divert valve with lOO cccceeeeeeee 6 8 6 3 3 Example 3 Sample flow through the divert valve without Joop 6 9 6 4 Values and Ranges in micrOTOFcontrol nnneaanneneannenenennennnnsrnnrnsnrnnsrnrrnsnrresrnrrnn 6 10 6 4 1 Smart View Values and HRanges 6 11 6 4 1 1 Smart View Mode Tab pacts seuss eege ege Ee 6 11 6 4 1 2 Smart View Source TaD EE 6 12 6 4 1 3 Smart View MS MS Tab gt Auto MM 6 13 6 4 1 4 Smart View MS MS Tab gt Auto MS MS gt Preference nnannnnnannnnennnnnn 6 14 6 4 1 5 Smart View MS MS Tab gt Auto MS MS gt Acquisition 00noaannnannnaannnaanna 6 15 6 4 1 6 Smart View MS MS Tab gt Auto MM GIE 6 16 6 4 1 7 Smart View MS MS Tab gt Auto
41. BRUKER maxis User Manual Bruker Daltonics Version 1 1 October 2008 Copyright Copyright 2008 Bruker Daltonik GmbH All Rights Reserved Reproduction adaptation or translation without prior written permission is prohibited except as allowed under the copyright laws Document History First edition September 2006 Printed in Germany Warranty The information contained in this document is subject to change without notice Bruker Daltonik GmbH makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose Bruker Daltonik GmbH is not liable for errors contained herein or for incidental or consequential damages in connection with the furnishing performance or use of this material Bruker Daltonik GmbH assumes no responsibility for the use or reliability of its software on equipment that is not furnished by Bruker Daltonik GmbH The names of actual companies and products mentioned herein may be the trademarks of their respective owners Interference Immunity The maXis is an electrical equipment for measurement control and laboratory use where the electromagnetic environment is kept under control That means in such an environment transmitting devices such as mobile phones should not be used in immediate vicinity EN 61326 A1 1998 Appendix B WARNING Connecting an instr
42. DC 2 16 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components voltages connected to the first and last plate of the funnel direct the ions towards the funnel exit using an adjustable DC gradient The wide opening of the funnel 1 entrance collects nearly all the entering ions without the need for a strong focusing electrostatic field For this reason the funnel configuration has a high transmission efficiency especially regarding fragile analyte ions The small inner diameter of the funnel plates at the funnel 1 exit ensures a well defined ion beam near the axis of funnel 1 Uncharged particles like drying gas will be pumped away through the gaps between the funnel plates To avoid contamination at the funnel 1 exit and the following ion optics the funnel axis is offset from the capillary axis Small droplets entering this stage will hit the outer funnel plates while the offset axis configuration does not reduce the ion transmission The first and second funnel stages are separated by a DC plate This is F1 base The diameter of the orifice restricts the gas flow into the next stage The funnel 2 stage is connected to the intermediate stage of a triple stage turbo pump Figure 2 2 The operating pressure is 3x10 mbar By increasing the DC potentials of funnel 1 the ions will be accelerated into the funnel 2 stage This fact can be utilized to activate In Source Collision Induced Dissociation ISCID 2 3 2 2
43. E 3 14 3 3 3 Achieving Gas Phase Conditions ccccccecccccceeeeeeceeeeeeseeeeeesaeeeeesaaeeeeeaaees 3 15 34 Reference nde 3 17 3 4 1 Reference articles for EG 3 17 3 4 2 Reference articles for ACTA 3 19 maXis User Manual Version 1 1 3 1 Understanding API and APCI Electrospray Bruker Daltonik GmbH 3 1 Atmospheric Pressure Interface API A liquid chromatograph mass spectrometer LC MS interface must perform three fundamental processes e Aerosol generation e lonization e Solvent removal In APl electrospray the aerosol generation nebulization is a result of pressurized nebulizing gas combined with a strong electrical field The strong electric field also aids in ionization Solvent is stripped away by an inert warm gas All three of these processes occur at atmospheric pressure outside the vacuum region of the mass spectrometer in a specially designed spray chamber The desolvated ions are directed into the low pressure region of the source through a sampling orifice the capillary Skimmers an ion guide and exit lens transport and focus the ions into a beam while the nebulizing and drying gases are pumped away The ions are thus transferred into the mass spectrometer for mass analysis This chapter is an introduction to the processes that occur in the ESI and APCI For more information about ESI and APCI refer to the list of journal articles at the end of this chapter Heater Vacuum stage
44. I Optional Sources Solvents APCI reference articles APCI source Apffel API API electrospray ionization ESI APLI APLI configuration APLI Schematic APLI Source APPI APPI Source Atmospheric Pressure Interface Atmospheric Pressure Interface API Auto MS MS Expert View Auto MS MS Smart View Auto Tune Expert View Auto Tune Tab Smart View B Barcelo Barcelo Barnes Basic principles maXis Bean Betham Biological Residues Blades Boyd Bramer Weger Brewer Bruins Bruker Support Session Buffers Butfering 5 31 3 15 6 26 6 15 5 30 3 17 3 19 2 34 2 37 2 37 3 14 3 19 2 37 3 18 2 12 3 1 4 4 2 12 2 38 2 39 2 38 2 38 2 41 2 41 2 12 3 2 6 24 6 13 6 32 6 21 3 19 3 19 3 19 4 1 3 17 3 20 5 3 maXis User Manual Version 1 1 C Calibration TOF Tab Smart View Calibration Tab Expert View Capillary Electrophoresis CE Carr Castillo CE CE Optional Sources Chemical Residues Chemical Residues Chromatogram Tab Expert View Chromatogram Tab Smart View Index 6 21 6 32 2 42 3 17 2 42 Cleaning Funnel and Multipole Cartridge 5 17 Cleaning the Spray Chamber Collision Cooler Smart View Collision Cell Collision Cooler Expert View Conboy controlling the divert valve Cooling Cell Copyright Covey D Desolvation Desolvation process Desolvation unit Desolvation Unit removal Detector Detectors D
45. MS MS Ge Preference Collision Sweeping IT Active Mode lon Cooler REAR ADD Ellison Energy Stark End Start End 400 0 Mee 200 0 Yop 100 Z 100 Timing l NN Fb E boot I Timing l NN E bb boot I pj 5 x f BS x f Bx Flush Flow Rate 30 0 0 0 A Collision Gaz Set Values Parameter Polarity Group Description GUI Unit Typic i Max I M P lon Cooler RF Start End Timing Start Timing End Collision Energy Start End Timing Start Timing End Collision Gas Flow Rate maXis User Manual Version 1 1 6 19 Appendix Bruker Daltonik GmbH 6 4 1 11 Smart View Sample Info Tab H Model t Source MS MS BaP Sample Info st Chromatogram A Calibration TOF fe Auto Tune Data Fle gt t AAA Sample Parameter Anales Name lt 2 Sample Name Prefiy Counter Manual No Sampl Bref Counter SD Acq onon o Comment Subdirector Hi _A pas 2 E No SubDirectory gt sl Path 2 De data There are no values to set in the Sample Info page 6 4 1 12 Smart View Chromatogram Tab ES Made RE Source i MS MS K i Samplelnio 2 Chromatogram EI Calibrate hie Instrument Tune G i Service Add Change Delete All Reset Type Base Peak Chromatogram sl Masses MW Enable Color es Green Filter LA width P 0 5 Polarity Both Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P Masses 6 20 maXis U
46. Mark as Calibration Segment Set Values Parameter Polarity Group Description GUI Unit Typic i Max P Include Profile Spectra Mode Threshold Segment parameters Mark as Calibration segment Focus Active Processing Absolute Threshold Peak Summation Width Mode is set using the radio buttons Always Threshold and Off 6 22 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 2 1 Expert View Source Tab Mode Source i MS MS fa Sample Info 2 amp Chromatogram 2 Calibration TOF fe Instrument Tune Source Transfer End Plate Offset Gi v foe eee Funnel 1 RF 300 0 pp Capillary 4000 0 A Gel 00 ei Multipole RF 200 Vpp Nebulizer 04 Ba 00 Bar Ke 40 eV LowMass 55 00 m z SE 40 an OO imin Collision Cel Dry Temp v 180 C D La Ger 100 e CollsionRF 500 0 vo lon Cooler lon Cooler RF 400 0 Vpp 1295 ys Ae 1 0 us Transfer Time Set Values Parameter Polarity Group Description GUI i Max I M P Source End Plate Offset Capillary Nebulizer Dry Gas Dry Temp Transfer Funnel 1 RF ISCID Energy Multipole RF Quadrupole lon Energy eV 4 0 0 200 0 Low Mass m z 300 00 20 00 3000 00 Collision Cell Collision Energy Collision RF lon Cooler lon Cooler RF Transfer Time Pre Pulse Storage maXis User Manual Version 1 1 6 23 Appendix Bruker Daltonik GmbH 6 4 2 2 Expert View MS MS Tab gt Auto MS MS Em Mode
47. Multipole The subsequent multipole stage is connected to the first turbo stage of the triple stage turbo pump The operating pressure is 3x104 mbar In this stage a multipole is used to transport and focus the ions The applied RF voltage generates a radially increasing effective potential so that the ions are focused onto the multipole axis The multipole stage ends with a gate lens and a focusing lens To avoid crosstalk and to minimize delay time between MS and MS MS spectra the ion transmission has to be blocked between two spectra Therefore the gate lens is set to a high block voltage During ion collection the gate lens voltage is adjusted to maximize ion transmission The focusing lens provides a suitable beam shape for transferring the ions into the analytical quadrupole maxXis User Manual Version 1 1 2 17 Identifying System Components Bruker Daltonik GmbH 2 3 3 Quadrupole The analytical quadrupole is located in the fourth pumping stage of the vacuum system The second turbo stage of the triple stage turbo pump reduces the pressure down to Quadrupole approximately 3x10 mbar The analytical quadrupole is the first mass d COEY analyzer in the maXis It is used as a mass filter to isolate a certain ion mass or a defined mass range The isolation width is adjustable from 0 1 to 300 Dalton For MS analysis the resolving power of the quadrupole can be switched off In this case the quadrupole works as an additional ion guide
48. NV Ke A fi NV NV d A a spit Fleeg Tube Pump l di Rough Pump Route of the lons through the maXis maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles E Figure 4 2 maXis schematic showing the path of the ions through the Quadrupole Collision Cooling Cell and the TOF Spectrometer maxis User Manual Version 1 1 4 3 Understanding maxis Basic Principles Bruker Daltonik GmbH 4 1 maXis as an API MS MS instrument In API techniques like ESI and APCI ions are formed at atmospheric pressure However mass analysis of individual molecules can only be performed in high vacuum Hence the ions are to be introduced into the mass analyzer passing several pressure stages The ion guides in the transfer system allow for an efficient ion transfer to the analyzer while the neutral gas molecules are removed by the pumping system MS MS is an indirect method of obtaining structural information Characteristic compounds are isolated by the 17 MS stage since it is almost impossible to get direct information on the structure of complex but low abundance molecules This isolation is performed in the mass resolving Quadrupole Mass Spectrometer which only transmits a narrow mass range when it is operated in mass selective mode In order to obtain structural information on this isolated compound it is forced to react In the maXis the isolated ions are injected into the collision cell which serves
49. This improves the peak shape thereby enhancing signal and improving sensitivity The final solution solvent analyte should be neutral to acidic for good positive ionization Buffers or other additives used to optimize chromatography can sometimes interfere with the ionization process For example TFA is almost always used for the chromatography of peptides and proteins TFA enhances the chromatographic resolution but may actually suppress ion formation Post separation addition of a weaker acid such as propionic acid can effectively counteract the TFA ion suppression problem 23 maxXis User Manual Version 1 1 3 11 Understanding API and APCI Electrospray Bruker Daltonik GmbH When performing ESI standard buffers such as phosphate borate and sulfate buffers are non volatile and form ion pairs in solution To maximize ESI sensitivity use buffers that are volatile and do not form ion pairs Adjust the pH with buffers formic acid acetic acid and ammonium hydroxide or triethylamine Typical pH for positive ion is neutral to pH 2 and for negative mode typical pH is neutral to pH 10 For ion pair separations use additives such as heptafluoro butyric acid or tetraethylammonium hydroxide or tetrabutylammonium hydroxide 3 12 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 3 How APCI works What is the difference between ESI and APCI APCI is a gas phase chemical ionization mechanism ve
50. WARNING The spray chamber operates at very high temperatures Let it cool down before proceeding e Vent the maXis see section 5 6 1 e Open the spray chamber e Remove the spray shield e Remove the capillary cap from the end of the capillary e Carefully pull the glass capillary straight out of the desolvation assembly CAUTION Pull the capillary straight out along its long axis The capillary is made of glass and can break it during handling 5 14 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 6 7 Cleaning the Spray Chamber When Required It is recommended that the spray chamber is cleaned after each series of measurements to avoid a carry over of sample material between analyses Tools required e None Parts required e Cloths clean lint free 45485 e Gloves latex 200622 e Isopropyl alcohol 99 5 reagent grade or better 58477 e Water reagent grade or better 49145 Preparation e All work surfaces to be clean and dust free Procedure e Mixa solution of 50 isopropyl alcohol and 50 water WARNING The spray chamber operates at high temperatures Let it cool down to ambient temperature before continue working e Shut down the instrument section 5 6 1 e Remove the Nebulizer section 5 6 2 e Open the spray chamber e Dampen a clean cloth with the mixture of isopropyl alcohol and water e Remove spray shield and capillary cap e Put both parts into
51. XIS Basic Principles Meng micrOTOFcontrol Mode page Mode Tab Expert View Mode Tab Smart View Molina MRM Expert View MRM Smart View MS MS Multimode Multipole Cartridge maintenance Multipole Cartridge re assembly N Nebulization Nebulizer Negative ion analysis Niessen Nitrogen Gas Filter Replacement Non polar solvents O Off line NanoElectrospray On line NanoElectrospray Operating environment Operating Precautions 2 16 2 12 3 17 3 18 6 29 6 18 3 4 2 13 3 9 3 20 5 33 3 10 2 44 2 45 1 2 1 4 maXis User Manual Version 1 1 Bruker Daltonik GmbH Optimize Expert View Optional Sources APCI APLI APPI CE ESI nano Sprayer Multimode Off line NanoElectrospray On line NanoElectrospray Orthogonal Acceleration Orthogonal TOF Extraction Orthogonal TOF Injection P Pack PC Configuration Pegg Peripheral Interface Pin assignment polar solvents Positive ion analysis Power Preference Expert View Preference Smart View Principle of the ESI process Process of Electrospray lonization Puig Pulser Q Q q stage Quadrupole Mass Spectrometer R Reference articles reference articles ESI reference articles AC Reflector Reinstalling the Nebulizer Remote Service Remote service capability Removing the Glass Capillary Removing the Nebulizer Replacing the Nebulizer Needle Replacing the Nitrogen Filter Replacing the Ventilation Filters Reynolds
52. agnostics can be carried out and software or firmware updates can also be implemented The service process also becomes more efficient as after remote diagnosis the service engineer can arrive on site with the appropriate spare part Prerequisite To implement Remote Service the customer must have Internet access on the maXis Control PC Remote Service http bdal webex com Daltonics Service Customer Hotline Figure 2 22 Operating principle of the remote service maxis User Manual Version 1 1 2 31 Identifying System Components Bruker Daltonik GmbH 2 6 1 Initiating Remote Service To initiate Remote Service 1 Call Bruker Service on 49 421 2205 450 to obtain an authorized Support Session Number 2 Enter http odal webex com in the browser address bar and the Bruker Support Session window appears Figure 2 23 3 Click on the Join button on the Support Session page and a Pre Session Form appears Figure 2 24 Z Bruker Daltonik GmbH Enterprise Site Microsoft Internet Explorer Datel Bearbeiten Ansicht Favoriten Extras Ja Zurick gt Q A GE Ruhen Favoriten Meden G Ey SG GI sl Adresse https bdal webex comjbdal mywebex defaukt php Rnd2357 0 0057494402980593495 Y Wechseln zu Links BEE LS Support Center Support Session New User ession Join LA i Start a support session EK 3 a support session OO ge K sy BRUKER d Copyright
53. agram cd Calibration TOF aie Auto Tune Spectra Acquisition Focus External Control IY Save Spectra W Active Configure Include Profile Spectra f Always C Threshold 1000000 Off Segment Parameter Mark as Calibration Segment Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P Include Profile Spectra Mode Threshold Segment parameter Mark as Calibration Segment Active Mode is set using the radio buttons Always Threshold and Off maxXis User Manual Version 1 1 6 11 Appendix Bruker Daltonik GmbH 6 4 1 2 Smart View Source Tab Ri Mode Source Pe MS MS Sample Info ail Chramatogram a Calibration TOF ae Auto Tune Source Smart Parameter Settings End Plate Offset 500 Wy Target Mass Range Capillary 4000 Y from DO ms to 1800 mez Nebulizer D4 Bar E r l ISCID Dr Gas 4 0 min D Ee DI ey Mubpole HE 300 0 Yop Dry Temps 180 E Collision Cell Collision RF 500 0 pp lon Cooler lon Cooler RF 400 0 Vop Set Values Parameter Polarity Group Description GUI Unit Min Max I M P Source End Plate Offset Capillary Nebulizer Dry Gas Dry Temp Transfer ISCID Energy Multipole RF Collision Cell Collision RF lon Cooler 6 12 maXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 1 3 Smart View MS MS Tab gt Auto MS MS
54. as collisions translational energy of the ions is converted into internal vibrational excitation If the internal energy overcomes the dissociation energy the ion may dissociate into fragments In general a complex ion may dissociate in different reaction channels requiring appropriate dissociation energies The injection energy and thus the internal excitation can be chosen arbitrarily allowing also for higher energetic dissociation channels Hence the fragment spectrum is not only a function of molecular structure but it is also a function of internal energy and thus of injection energy and the collision gas B B B AA 7 E gt E2 A C A C A Cc 7 S Ge Ka B B a P ER Z N c A C E lt E1 Figure 4 9 Fragmentation Structure and Energetics An maxis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles The conversion of translational energy into internal energy is correlated with momentum transfer The amount of translational energy to be converted into internal excitation of the molecules is not only a function of the kinetic energy itself and thus of the injection voltage and the ion s charge but it is also a function of the ion s mass as well as the collision partners mass The conversion efficiency increases with the collision gas molecular mass m and can be estimated as AE E 4m m gas molecule 8 m W ion m Figure 4 10 Energy Transfer Momentum Transfer
55. ating the maXis mass spectrometer read the following information concerning hazards and potential hazards Ensure that anyone involved with installation and operation of the instrument is knowledgeable in both general safety practices for the laboratory and safety practices for the maXis mass spectrometer Seek advice from your safety engineer industrial hygienist environmental engineer or safety manager before installing and using the instrument Position the maXis mass spectrometer in a clean area that is free of dust smoke vibration and corrosive fumes out of direct sunlight and away from heating units cooling units and ducts Verify that there is an adequate and stable power source for all system components Verify that the power cord is the correct one for your laboratory and that it meets the national safety agency guidelines for the particular country of use Warning DO NOT attempt to make adjustments replacements or repairs to this instrument Only a Bruker Daltonics Service Representative or similarly trained and authorized person should be permitted to service the instrument Warning When it is likely that the electrical protection of the maXis mass spectrometer has been impaired 1 Power off the maXis mass spectrometer 2 Disconnect the line cord from the electrical outlet 3 Secure the instrument against any unauthorized operation maXis User Manual Version 1 1 1 5 General Bruker Daltonik GmbH Warn
56. ation polarity switching for the determination of selected pesticides Rapid Commun Mass Spectrom 1997 11 117 123 Castillo M Alpendurada M F and Barcelo D Characterization of Organic Pollutants in Industrial Effluents Using Liquid Chromatography Atmospheric Pressure Chemical lonization Mass Spectrometry J Mass Spectrom 1997 32 1100 1110 Herderich M Richling E Roscher R Schneider C Schwab W Humpf H U and Schreier P Application of Atmospheric Pressure lonization HPLC MS MS for the Analysis of Natural Products Chromatographia 1997 45 127 132 Puig D Barcelo D Silgoner and Grasserbauer M Comparison of Three Different Liquid Chromatography Mass Spectrometry Interfacing Techniques for the Determination of Priority Phenolic Compounds in Water J Mass Spectrom 1996 31 1297 1307 Bruins A P Atmospheric pressure ionization mass spectrometry I Instrumentation and ionization techniques Trends Anal Chem 1994 13 Nr 1 37 43 Bruins A P Atmospheric pressure ionization mass spectrometry II Applications in pharmacy biochemistry and general chemistry Trends Anal Chem 1994 13 Nr 13 81 90 Voyksner R D Atmospheric Pressure lonization LC MS New Solutions for Environmental Analysis Environ Sci Technol 1994 28 Nr 3 118A 127A maxis User Manual Version 1 1 3 19 Understanding API and APCI Electrospray Bruker Daltonik GmbH 10 Betham R A and Boyd R K Mass Spectrom
57. can be found in one spectrum The APCI mode can be switched off making the ESI function available by itself maXis User Manual Version 1 1 Identifying System Components Figure 2 37 The multimode source Nebulizer Mai MM ES Zone Thermal container Figure 2 38 Multimode schematic diagram 2 43 Identifying System Components Bruker Daltonik GmbH 2 7 1 7 Off line NanoElectrospray When only very small sample quantities are available the Off line NanoElectrospray ion source can be used for the determination of analytes in sample volumes as low as 1 ul 2ul The electrical high voltage gradient at the tip of the fine metal coated glass capillary needle acts as its own sample delivery system resulting in flows of approximately 30 nl min and analysis times of up to 40 min The Bruker Off line NanoElectrospray ion source Figure 2 39 and Figure 2 40 is an Esl source specially Figure 2 39 Off line NanoElectrospray ion designed to handle extremely small source sample volumes typically 0 5 to 1 ul without LC coupling In this case the sample is introduced manually Removable N inlet needle halder Using a pipette a droplet lt 1ul of Cap dissolved analyte is introduced into a A Gasdiverter hollow needle tapered at one end 7 The needle holder is then mounted inside the source directly in front of the glass capillary Heated drying gas N The potential difference between the needle ti
58. cts ions exiting from the capillary and focuses them onto an orifice leading to the next vacuum stage Furthermore the ions can be pushed gently towards the funnel exit by an axial DC gradient closing the structure around an axis extending the structure A KA Multipole E eTe Gi R ee SE Dipole Le SZ axis parallel Wi repulsive ote drun field San y extending the structure GE repulsive wall axis perpendicular Stacked lon Figure 4 5 Getting the structure for the funnels from theory 4 4 Quadrupole Mass Spectrometer Q MS maxXis User Manual Version 1 1 4 7 Understanding maxis Basic Principles Bruker Daltonik GmbH As discussed in chapter 4 2 lon Guides a multipolar RF field creates a potential well for charged particles In a quadrupole this field is quadratic allowing for harmonic oscillations This means the oscillation frequency depends not on oscillation amplitude but only on mass RF frequency RF amplitude and field dimensions An RF only quadrupole is suitable as an ion guide The RF effective potential is always repulsive pushing the ions towards the ions guide axis However the pseudopotential V acts on q m and thus depends also on mass Applying a DC voltage to the opposite rod sets also creates quadratic potential but this potential is only focusing repulsive U in one dimension while it is attractive defocusing U in the other dimension perpendicular to th
59. d MS MS Auto Within Top 1 0 01 0 0001 Tolerance Delta Mass Max no of labels Charge Range Pattern match Cross Correlation Intensity Ratio Heavy Light gt or lt Heavy Light gt and lt maXis User Manual Version 1 1 Tolerance 0 20 mz Pattern Match Cross Correlation 0 60 em Check Charge Consistency Do MS MS the Largest Peak e C Heawy Ligt gt 1 20 o cl O80 f Heavy Light gt 005 and lt 20 00 Parameter Polarity Max I M P 1000 10 00 100 0000 20 10 6 27 Appendix Bruker Daltonik GmbH 6 4 2 6 Expert View MS MS Tab gt Auto MS MS gt Fragmentation 2 Mode Si Source ZE MS MS faf Sample Info wile Chromatogram amp Calibration TOF 1 fe Instrument Tune E Auto MS MS Isolation Fragmentation List a me Lies b Coll Energy Craget J ren 500 00 500 00 500 00 1000 00 Collision Cooler 1000 00 1000 00 2000 00 2000 00 2000 00 New Delete Delete All Fallback o Charge State WI i E oon nm e Ww N Kg Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P Isolation Fragmentation List Fallback Charge State z 6 4 2 7 Expert View MS MS Tab gt MRM 2 Mode Si Source MS MS E Sample Info wil Chromatogram Z Calibration TOF 1 dr Instrument Tune El Auto MS MS Scan Mode Parent Condition i Preference MS MS MRM 8 A D MSMS MAM sie leat Wi Col Energ
60. d after each analysis Flushing helps to keep the needle clean and reduces the frequency of needle replacements When required e When the needle is visibly bent or damaged e When the spray is not symmetrical with the needle assembly e When the needle is blocked Common symptoms are increased LC backpressure or off axis spraying or dripping from the nebulizer The needle must be replaced when data shows excessive noise or the current signal is unstable Tools required e Adjustment fixture 20207 e Gloves latex 200622 e Wrench 3 mm open end 222971 e Wrench 8 mm 32169 Parts required e Nebulizer needle ES shipping kit 27281 Preparation e All working surfaces should be clean and dust free Procedure Remove the nebulizer from the spray chamber CAUTION Be very careful when inserting the needle The tapered end of the needle must pass through restrictions in the nebulizer shaft The end of the needle can be damaged if it is forced maxXis User Manual Version 1 1 5 11 Maintenance Bruker Daltonik GmbH e Install the nebulizer in the adjustment fixture e Loosen the locked nut next to the zero dead volume ZDV union e Remove the union from the nebulizer e Pull the needle and ferrule out of the nebulizer e Push a new ferrule large end first onto the blunt end of a new needle The tapered end of the ferrule should be level with the blunt end of the needle e Very carefully push the tapere
61. d end of the needle into the nebulizer until it appears at the tip of the nebulizer e Reinstall the union e Tighten the lock nut against the union e Adjust the Electrospray needle position before reinstalling the nebulizer in the spray chamber Figure 5 4 Mounting the Nebulizer needle 5 12 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 6 5 Reinstalling the Nebulizer Make sure the nebulizer needle is correctly adjusted Make sure the nebulizer cover is open CAUTION Be careful not to bump the tip of the needle while inserting the nebulizer The tip of the needle is easily damaged CAUTION Do not over tighten the LC fitting This can crush the tubing or creating a restriction e Slowly and carefully insert the nebulizer into the spray chamber e Reconnect the nebulizing gas tubing to the nebulizer e Finish inserting the nebulizer into the spray chamber e Turn the nebulizer clockwise to lock it into place e Reconnect the LC tubing to the zero dead volume union e Close the nebulizer cover maxXis User Manual Version 1 1 5 13 Maintenance Bruker Daltonik GmbH 5 6 6 Removing the Glass Capillary When required Removing the capillary is necessary for cleaning and replacement Tools required Required tools e Gloves latex 200622 Parts required e Glass capillary 500um Part No 27329 Preparation e All working surfaces to be clean and dust free Procedure
62. d in the annular groove Even a small displacement of the O ring can result in it being damaged Figure 5 9 Desolvation unit showing the Figure 5 10 Desolvation unit O ring correctly fitted with O ring displaced from groove 5 28 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Figure 5 11 Connect cables and tubing insert and tighten down 4 fixing screws d P e e A n we j i uy s t se J kb gy y d g y K P A A Ge H e i l Ke N e RS Ei KE Figure 5 12 Replace the spray chamber 7 Pump vacuum system Maintenance Slide the desolvation unit into position and connect the cables and tubing see Figure 5 11 Insert the four fixing screws and tighten them securely Replace the spray chamber by sliding it onto the hinge pins in the open position see Figure 5 12 Close the chamber and lock it in place using the toggle clamp In the micrOTOF control software click on Standby A confirmation dialog will appear asking Do you really want to Click YES and the vacuum pumps will start to evacuate the system maxXis User Manual Version 1 1 5 29 Maintenance Bruker Daltonik GmbH 5 6 9 Adjusting the ESI Nebulizer Needle Note These instructions are for the standard ESI source The ESI nano Sprayer is adjusted differently see ESI nano Sprayer User Manual 253701 When required Adjusting the nebulizer needle is necessarily after replacem
63. dronium ions present Solutions containing weak acids such as formic acetic or propionic acid generally work best Strong acids such as trifluoroacetic acid TFA and hydrochloric acid work poorly because the strong acid anion pairs with the analyte cations reducing analyte ion abundance 3 8 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray Analytes which have basic sites on the molecule such as basic nitrogen functions usually show high sensitivity in slightly acidic solutions pH lt 7 Those which have no basic nitrogen functions generally show a lower response in positive ion mode Hydrocarbons have a very low response in positive ion mode 3 2 2 3 Negative ion analysis Analytes that are rather acidic are generally analyzed in negative ion mode The sample molecule acid loses a proton and transfers it to a base pH gt 7 in solution and becomes negatively charged Therefore for high sensitivity negative ion analysis it is important to have a base in solution Ammonia and other volatile bases yield best results MII E lt gt MW HA HE For negative ionization analytes with functional groups that deprotonate readily such as carboxylic or sulfonic acids show the best sensitivity Analytes that are polar but contain no acid groups show less sensitivity Charge exchange is another mechanism that can occur in negative ion mode It results in an M ion instead of an M HI ion
64. e axis The static potential acts only on the ion s charge q Resulting Potential reduced Resonance Frequency gt 0 Non Capture Heavy lons gt x Rod Set Resulting Potential increased Resonance Frequency gt Yfouad Parametric Excitation Light lons gt y Rod Set Figure 4 6 Resulting pseudo potential 48 maXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles Consequently the resulting potential is also quadratic if an RF and a DC potential are applied to the quadrupole at the same time In one dimension the RF pseudopotential V and the DC U act against each other The resulting potential V U may also become negative As long as the effect of the pseudopotential dominates over the attractive DC potential the ions will still pass through the quadrupole If the static potential overcomes the pseudopotential the ions will hit the rods with the attractive DC potential Since the pseudopotential decreases with increasing mass the heavier ions will be lost first Figure 4 7 shows this on the left side Since the resulting potential has also to overcome the thermal energy of the particle the transmission fades away very softly for the heavy masses In the other dimension both potentials are repulsive Hence the effects of the pseudopotential and the DC potential support each other The resulting potential V U provides a well for the fundamental oscillation of the ions Since the
65. e out and pull upwards latches 5 34 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance Pull the old filter material from the keeper tabs and dispose of it e Push the new filter material into place ensuring that it is located behind the keeper tabs e Replace the grille by first locating the three tabs along the lower edge into the slots in the instrument housing Pivot the grille inwards to engage the latches The latches may need to be pushed down to engage properly with the instrument housing maxis User Manual Version 1 1 5 35 Bruker Daltonik GmbH 6 APPENDIX 6 1 List of maXis Spare Parts Description Carbon Filter Air Filter Pads 2 pieces necessary Lubricant reservoir for Turbo Pump Desolvation Unit Spray shield Capillary Cap Contact spring Gold plated Glass Capillary 500um ESl Source without Nebulizer Nebulizer Nebulizer Needle ES shipping kit APCl Source Nebulizer AC Nebulizer needle AC APCI Corona needle APPI Source Rough pump Varian DS602 Oil Inland 45 for Rough Pump Exhaust Filter Oil exhaust replacement cartridge maxXis User Manual Version 1 1 Part Number 219454 260994 19565 216221 210036 216156 73046 27329 218063 20210 27281 21568 24623 13032 72569 212978 218818 20221 218820 226181 Appendix 6 1 Appendix Description Tools 3 mm wrench 8 mm wrench Torx T 25 Magnifier Nebulizer Ad
66. eeeeeeeceessneeeeeeeeeeoeensseeeeeeeeooenneeeeseeeonesneeeeees 2 1 SEENEN 2 3 2 2 Sample input AEVICES cccccccccsscccssecccsseeceseeecceececcuaeeeaeeesaueceeaseeeeaseeseueeencuaeesaeeess 2 6 2 2 1 al a E ORY Co 2 E E A one E AA AE A E A OR Re 2 6 2 2 2 BV FFU SNA EE 2 2 2 3 Divert Valve INtroduction ccccccsscccsseeeceeececeseeeseseeeeeeeesseeeseeessaeeensueeenees 2 9 2 3 Route through the TOF Mass Spectrometer nnnnennnnnnnnennnnnesnnnnrnnnesrrrrnrnrnrsrnrrnn 2 11 2 3 1 PD ONO SOURCE EE 2 12 ZW VINCE ZS at hese deene 2 13 Zee HNO CMOS Gly arb Steet atten a a tisethcatuan Sida 2 14 2 3 1 3 Spray shield and capillary Cap 2 14 2 E GG EE 2 15 Ziel ISSO tee UN EE 2 15 2 3 2 On R EIDEN LE 2 16 2 3 2 1 Double Stage lon Funpnel 2 16 ZO 2 2 MUIPO EE 2 17 2 3 3 Eelere 2 18 2 3 4 Collision Cooling Cell EE 2 19 ZA ACOMSION CG tee ee EE ee batts 2 19 2 3 9 Cooling Celli EE 2 20 2 3 6 WOPSASSOMDIY EE 2 21 2 3 6 1 Orthogonal Acceleration Pulser c ce ccccceeeeeeseeeeeeseeeeeesaeeeesneeeeeeeaees 2 22 2 91002 HIN ee ET 2 22 2 3 6 3 Determination of the m z Hanoi 2 23 2 3 6 4 Dual Stage Reflector EE 2 23 Eet Ee 2 24 24 External ell COINS spe ees aces eget a nace aces ee eee eae ee 2 25 2 4 1 EEN 2 26 2 4 2 Peripheral Interface External start for data acquisition cccceeeeeeeeeeees 2 2 20 cs Orn ele Le DE 2 30 maxis User Manual Version 1 1 V 3 VI Bruker Daltonik
67. een the subject of many scientific investigations yet different theories still exist regarding the specific physical process The ion evaporation process described below is the model accepted by Fenn and others 6 In the ion evaporation model sometimes referred to as ion desorption ions are emitted directly from the charged droplets into the gas phase As solvent evaporates from the droplets in the presence of the strong electric field the surface of the droplet becomes highly charged When the field created by the ions at the surface of the droplet exceeds the surface tension bare analyte ions are emitted directly from the droplet Figure 3 4 This model was first described by Iribarne and Thomson 10 EVAPORATION 8 m m mp MULTIPLY CHARGED ION aN F ing 8 D Ce Be ka W ei Foi GL T ay DROPLET Figure 3 4 lon evaporation mechanism within the ESI chamber e analyte The hydration energy of the sample in a solvent dictates the ease of desorption of ions into the gas phase In general the more hydrophobic less hydration a sample is in a solvent yet still soluble in that solvent the better ions can be desorbed into the gas phase maxis User Manual Version 1 1 3 Understanding API and APCI Electrospray Bruker Daltonik GmbH 3 2 2 Different Aspects of ESI Several different aspects of the ESI process should be considered 3 2 2 1 Importance of solution chemistry Solution chemistry plays an important r
68. ent or if operating performance indicates that the needle is not be correctly adjusted Tools Required e Adjustment fixture 20207 e Gloves latex 200622 e Magnifier 20206 e Wrench 3 mm open end 2229771 e Wrench 8 mm 32169 e Wrench 1 2 inch x 9 16 inch open end Parts Required e Nebulizer Needle ES shipping kit 27281 Preparation All working surfaces to be clean and dust free Procedure Remove the nebulizer from the spray chamber see5 6 2 CAUTION Be careful to avoid knocking the tip of the nebulizer against anything Any slight damage can have a large negative effect on system performance Note The needle adjustment detailed here works very well for a wide range of LC flows If you intend to work exclusively with flows above 0 5 ml min you can achieve even better performance by adjusting the needle so that it is level with the tip of the nebulizer 5 30 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance Adjustment fixture Place the nebulizer in the adjustment fixture Loosen the needle holder locknut Position the magnifier so you can view the tip of the nebulizer Adjust the needle holder until the needle extends just slightly less than 1 2 its own diameter beyond the tip of the nebulizer Tighten the locknut and re check the position of the needle Remove the nebulizer from the adjustment fixture Reinstall the nebulizer in the spray chamber 5 6 10
69. er obtained in step 1 and the other required information 5 Click on the Submit button and follow the instructions to successfully connect the remote service to your maXis maxis User Manual Version 1 1 2 33 Identifying System Components Bruker Daltonik GmbH Analyte Delivery Pipette Nanoflow LC Capillary Syringe Electrophoresis Pump CE MS5 Sprayer x NanoMate ESI Off line On line Nano Nano Electroeprau ESCH Source Interface maxis Delivery methods 051 Ian Seu 9 Dale 05 Nov 2008 Figure 2 25 Analyte delivery and source interface devices 2 34 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components Devices ei E HPLC U HPLC GasChromatograph System Standard Standard ESI nano ESI APCI Sprayer Sprayer Sprayer H Transfer Line Multimode AFFI APCI APCI APLI Devices Spray Chambers API Not available forall Bruker ESI MS maxis User Manual Version 1 1 2 35 Identifying System Components Bruker Daltonik GmbH 2 7 Optional Sources The mass spectrometer is of a modular design allowing for the easy interchange of ion sources Each ion source has been designed to meet the particular needs of different applications The diagram Figure 2 25 on the facing page illustrates various possible configurations available at this time Available sources include APCI source section 2 8 1 1 APLI section 2 8 1 2 Apollo ESI source sec
70. es additional nebulizing gas is not required to aid dispersion As for the ion sources described previously heated drying gas is introduced into the spray chamber maXis User Manual Version 1 1 Identifying System Components Figure 2 42 Capillary frorsource Nano Lt On line NanoElectrospray ion Needle holder Insulating sleeve Cap _ Gas diverter Heated drying gas N Glass capillary innere 0 5 0 6 mm Spray needle tip Spray chamber Figure 2 41 Schematic of an On line Nanospray Source 2 45 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 UNDERSTANDING API AND APCI ELECTROSPRAY This chapter provides an introduction to the processes that occur in APl electrospray and to the type of data that can be obtained CONTENTS Subject Page Number 3 1 Atmospheric Pressure Interface API cccccccssseecceseeeccseeeceeeeecsegseeessaseeessaaees 3 2 SR el Ke EE 3 3 3 2 1 Process of Electrospray lonization ccceccceseeeeeeeeeeeeeeaeeeeesaeeeeeeseeeeesaaeeeeens 3 4 SN Eat Lee ei Lee EE 3 4 EN 2 UE ee DEE 3 4 OZ Aed ee EE 3 5 O21 WION EVADORAUON eege eege leede 3 7 3 2 2 Different Aspects of EE 3 8 3 2 2 1 Importance of solution chemtsirv 3 8 322 2 Postivelion analysis sosea a a 3 8 3 2 2 3 Negative Tel 3 9 3 2 2 4 Formation of adduct ons 3 9 Se Een EE 3 10 22 00 TUMORS EE 3 11 29 HOW Ree 3 13 3 3 1 WHET USE APC le Tiritu aaa a a a a 3 13 3 3 2 APC e E
71. es section 5 2 e High Temperatures section 5 3 e Hazardous Voltages section 5 4 5 1 Chemical Residues The API Electrospray interface does not ionize all of the sample and solvent The majority of sample and solvent passes through the interface without being ionized The vacuum pumps of the maXis pump away the unionized sample and solvent The exhaust from these pumps can contain traces of samples and solvents Vent all pump exhaust outside or into a fume hood Comply with your local laws and regulations WARNING The exhaust fumes from the vacuum system and spray chamber will contain trace amounts of the chemicals being analyzed Health hazards include chemical toxicity of solvents samples buffers and pump fluid vapor as well as potentially bionazardous aerosols of biological samples Vent all exhausts outside the building where they cannot be re circulated by the environmental control systems Do not vent the exhaust into your laboratory See the warning labels on the instrument WARNING When replacing pump fluid use protective gloves and safety glasses Avoid contact with the fluid 5 2 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance WARNING Fluid drained from the spray chamber is composed of solvent and sample from your analyses The fluid in the mechanical and diffusion pumps collects traces of the samples and solvents In addition non nebulized solvent and sample accumulate at the bott
72. etry in Trace Analysis J Am Soc Mass Spectrom 1998 643 648 11 Henion J Brewer E and Rule G Sample Preparation for LC MS n Analyzing Biological amp Environmental Samples Anal Chem 1998 70 650A 656A 12 Harrison A The Gas Phase Basicities and Proton Affinities of Amino Acids and Peptides Mass Spectom Rev 1997 16 201 217 13 Niessen W M A van der Greef J Interfacing A General Overview Liquid Chromatography Mass Spectrometry Principles and Applications 1992 pages 81 115 Marcel Dekker New York 3 20 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles 4 UNDERSTANDING maXis BASIC PRINCIPLES CONTENTS Subject Page Number 4 1 maxis as an API MS MS instrument 0 cece cece ce eeeeeeeeeeeeeeeeeeesaeeeeesaeeeeeesaeeeeas 4 4 d SE e 1 6 EE 4 4 4 3 RF lon Guides closed repulsive wall 4 7 4 4 Quadrupole Mass Spectrometer CM 4 7 AS COOC TEE 4 12 7414 Camm 510 e Le Ee EE 4 14 AS LEE 4 14 4 7 1 Orthogonal TOF ITT 4 15 4 7 2 Orthogonal TOF Extrachon 4 16 maxis User Manual Version 1 1 4 1 Understanding maxis Basic Principles Source Funnel 1 A fare Petes oe Drp al Piiira HEPA Pa DOL Zgenp Iw vu H CaP LM F ii Ms d L Ve d Row rF KA dei Figure 4 1 Transfer Funnel 2 BEY W 0 3 mbar Bruker Daltonik GmbH Multocke IDEY FSE L Tpi PECH La FOX LZ 3 EHH mbar AO O Sw d a X L fy A Lt Lt Fl i
73. flector and detector The link between pulser fill time and TOF pulse time allows an ion loss of about 5 2 3 6 2 HV Focus Lens The HV Focus Lens is part of the orthogonal acceleration stage Due to the long flight path of the maxis it is necessary to focus the ionbeam with great precision to ensure a high ion yield at the detector The HV Focus Lens is a lens system that focuses the ion beam during the acceleration phase to reduce beam divergence and optimize utilization of the detector surface 2 22 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 3 6 3 Determination of the m z Ratio Charged ions are not detected by their mass alone but by their mass to charge ratio m z m z is used to scale the x axis of mass spectra The charge state of an ion has influence on its behavior in the mass analyzer lons with n charges are detected at a 1 n mass scale e g mass 1000 amu with two charges is detected at m z 500 This is true for all types of MS Isotopic peaks of n times charged ions are at 1 n amu distance This allows an easy identification of the charge state from isotopically resolved spectra which is of high importance for ESI spectra Mass determination m z takes place in the drift region of the TOF section by a precise time measurement of the drift time after acceleration of the ions in the orthogonal acceleration stage and their impact on the detector An electro static field accele
74. g position and hence the local potential the ions get different energies lons starting closer to the repeller plate left get more energy but have a longer flight path Due to their higher kinetic energy they catch up with the ions starting more to the right with less energy as well as a shorter flight path in a first order space maXis User Manual Version 1 1 4 17 Understanding maxis Basic Principles Bruker Daltonik GmbH focus at 1 2 x After the space focus the ions drift apart again now with the faster ions in front The reflector will compensate for this difference points of stop and return potential energy F l extra path extra time for fast ions Figure 4 16 Focusing of ions in the reflector In the reflector the ions are retarded stopped and finally reaccelerated towards the detector lons with higher kinetic energy fly deeper into the reflector and spend more time in the retarding field This effect is used to compensate the shorter flight time of the faster ions in the field free flight tube The compensation is optimized when the ions spend the same amount of time in both the flight tube and the reflector In terms of distance the field free flight path should be twice as long as the reflector This is true for standard single stage reflectors In maXis enhanced dual stage reflection technology is used see 2 3 6 4 4 18 maXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5
75. ight hand side the ions couple with the RF field Due to the resonant excitation this edge is sharp and its nearly linear because the resulting field grows linearly with the DC voltage applied to the quadrupole The mass selective quadrupole in the maXis is located between two short segments of RF only quadrupoles These segments significantly improve the acceptance behavior and the transmission efficiency of the mass selective quadrupole because the resolving DC heavily distorts the beam profile maxXis User Manual Version 1 1 4 11 Understanding maxis Basic Principles Bruker Daltonik GmbH The operation of a mass selective quadrupole can by summarized as follows i The effective potential RF focuses the ions ii The DC potential focuses one dimension but defocuses the other dimension iii Heavy ions will hit the attractive rods due to the dominant DC attraction iv Light ions will hit the repulsive rods due to parametric excitation v lons are transmitted if the RF is dominant but does not excite fundamental oscillation vi Quadrupolar field is two dimensional Hence injection and ejection are to be considered 4 5 Collision Cell The collision cell provides a reaction chamber for indirect structural analysis The ions isolated in the quadrupole are injected with some arbitrary energy into the collision cell The molecular ions collide with the gas atoms or molecules if N serves as collision gas Due to the g
76. ile loosening the Screws 5 22 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance d The lens can be a tight fit e The Lens Block is now on the end of the ready for cleaning cartridge and may need to be prised off 13 Remove Multipole a Remove the multipole b Push the multipole out of c The multipole is now connector block by the cartridge ready for cleaning unscrewing two Torx T10 Screws 14 Cleaning of Funnel 1 Funnel 2 the Multipole and Lens block It is recommended that all parts are cleaned with a brush and solvent before using the ultrasonic cleaner NOTE Do not use acidic solvents to clean any part of the product or its components maxis User Manual Version 1 1 5 23 Maintenance Bruker Daltonik GmbH After manual cleaning funnel 1 funnel 2 the Multipole and the Lens block must be cleaned in an ultrasonic cleaner with appropriate solvents 5 6 8 2 Re Assembling Multipole Cartridge Lens Block and Funnels 1 Reassembling the Multipole The multipole must be oriented correctly in the multipole cartridge The multipole molding has a keyway detail shown in Figure a below This keyway must be aligned with the pin inside the multipole cartridge as shown in Figure b below a The Multipole showing D c With the Multipole in Koceeseng b Position of the location place replace the pin in the bore of the Multipole connector and cartridge tighten the two Torx T10 Screw
77. ing The maXis mass spectrometer uses very high voltages Under normal operation the instrument requires NO user access to the inner components of the instrument NEVER operate the maXis mass spectrometer with the protective cover removed as this exposes the user to risk of severe electrical shock Caution Use only fuses with the required current and voltage ratings and of the specified type for replacement Caution Use the instrument according to the instructions provided in this manual If abused the built in instrument protection may be impaired putting the operator at risk of serious injury Caution Connect the instrument to an AC line power outlet that has a protective ground connection To ensure satisfactory and safe operation of the instrument it is essential that the protective ground conductor the green yellow lead of the line power cord is connected to true electrical ground Any interruption of the protective ground conductor inside or outside the instrument or disconnection of the protective ground terminal can impair the built in instrument protection Gs P 1 3 4 Environmental Conditions The maXis mass spectrometer is designed for indoor use and functions correctly under the following ambient conditions Table 1 2 Environmental Conditions Operating Conditions Temperature 13 to 35 C 55 to 95 F Relative Humidity 15 85 non condensing 30 C 1 6 maxXis User Manual Version 1 1 Bruker
78. ision d Cooler Ac EE by Intensity Delete Active Exclusion D Strict Active Exclusion Delete all Set Values Parameter Polarity Group Description GUI Unit Typic Min Max P Preferred Mass List Charge State Preferred range Exclude Singly Sort Precursors Active Exclusion 6 14 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 1 5 Smart View MS MS Tab gt Auto MS MS gt Acquisition El Made gt Source Fa MS MS Ei Sample Info l se Chromatogram Z Calibration TOF J l sie Auto Tune E Auto MS MS 5 Freference Precursor Acquisition Control Fragmentation Intensity Summation e M5 SCID 5000 i Collision Cooler MS MS Low 10000 cts SU vu Total Cycle Time Range d SEC High 1000000 cts SU x Abszolute Threshold 2000 cls Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P Intensity Low cts Summation Low X Intensity High cts Intensity Summation maxXis User Manual Version 1 1 6 15 Appendix Bruker Daltonik GmbH 6 4 1 6 Smart View MS MS Tab gt Auto MS MS gt sSILE ES Made BS Source E MS MS EN Sample Info a Chromatograrn Ah Calibration TOF sie Auto Tune Advanced MS MS Auta El Auto MS MS Pattern Match Preference B SILE Within Top 100 loss a Max no Tolerance 0 20 mz Correlation 0 60 o ILE Dela Mass of labels Charge Ra
79. ithin angle brackets e g lt ENTER gt maxXis User Manual Version 1 1 1 1 General Bruker Daltonik GmbH 1 2 Site Preparation Specification Before starting the installation of the instrument the site must be properly prepared Please refer to the Site Preparation Specification document that is sent to all customers prior to the shipment of the instrument It contains information regarding the device requirements such as operating environment gas supply power exhaust venting grounding etc This document has to be verified and returned to Bruker with the customer s signature before a service representative will start the installation 1 2 maXis User Manual Version 1 1 Bruker Daltonik GmbH General 1 3 Safety Safety considerations for the maXis spectrometer include e maXis Safety Symbols section 1 3 1 e Operating Precautions section 1 3 2 e Electrical Safety section 1 3 3 1 3 1 Safety Symbols The following symbols may be found on or near various components of the mass spectrometer Table 1 1 Safety Symbols Den A Indicates that a terminal either receives or delivers alternating current or voltage Indicates that a protective grounding terminal must be connected to earth ground before any other electrical connections are made to the instrument Indicates the ON position of the main power switch O Indicates the OFF position of the main power switch maXis User Manual Version 1 1 1 3 General
80. its source e Purge the filter for 5 minutes at the normal pressure e Turn off the flow of nitrogen gas at its source e Connect the pipe from the outlet of the gas conditioner to the maXis e Turn on the gas flow at its source e Dispose of the old filter in accordance with the instructions on the Material Data Safety Sheet MSDS maxis User Manual Version 1 1 5 33 Maintenance Bruker Daltonik GmbH 5 6 12 Replacing the Ventilation Filters When required Replacing the ventilation filters is necessary when they become clogged with dust and they prevent the free flow of ventilating air The life of a filter will depend on the environment in which the instrument operates For this reason it is important to check the filters on a monthly basis Tools requires e No tools required Parts required e Replacement filter x2 260994 Preparation e Have the replacement filters ready to install Operating the instrument without ventilation filters can cause the performance of the instrument to deteriorate Procedure e Remove the ventilation grilles on both sides of the instrument base see Figure 5 13 The grilles each have two latches which should be pushed down Figure 5 14 e Pivot the grille as shown in Figure 5 15and pull the grille upwards to release the three tabs on the lower edge of the grille Figure 5 13 Position of Figure 5 14 Push latches Figure 5 15 Pivot grille ventilation grille and down to release grill
81. ive coe Figure 2 21 Configure dialog for external devices maxXis User Manual Version 1 1 2 29 Identifying System Components Bruker Daltonik GmbH 2 5 PC Configuration The mass spectrometer is controlled by micrOTOFcontrol software running on a PC which also acquires data and saves it to disk In addition the dual processor system makes rapid database queries possible On delivery the system is likely to have the following configuration e Dual IBM compatible processors two hard disks e 21 inch monitor resolution 1280 x 1024 True Color CD ROM R W CD drive 3 5 Floppy drive e Digitizer PCl card e Two LAN cards Intranet LC system e Laser Printer e Microsoft Windows 2000 SP 4 or Microsoft Windows XP SP 2 operating systems e Control and application software micrOTOFcontrol DataAnalysis Note Due to the variety of computer hardware Bruker Daltonik GmbH cannot support third party computers for instrument control If you need a new acquisition computer please contact a Bruker representative in your area 2 30 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 6 Remote Service To optimize operating time the maXis is equipped with a remote service capability Figure 2 22 This feature allows for troubleshooting via the internet Thus problems can often be solved efficiently with the customer PC being fully controlled by the Daltonics Service Hotline Di
82. ivert Valve Divert valve connection example 1 Divert valve connection example 2 Divert valve connection example 3 Dole double stage ion funnel Dreyer Drying gas Dual Stage Reflector E Electrical Safety Electrospay electrospray ionization Environmental Conditions ESI 1 5 2 14 2 12 1 6 2 12 1 1 Index ESI nano Sprayer ESI Nebulizer Needle adjustment ESI reference articles ESI Different Aspects of External Connections External devices External Sart Stop function Extraction Phase F Fenn Fill Phase Fischer Flushing the Nebulizer Formation of adduct ions Formation of ions Fragmentation Expert View Fragmentation Smart View Funnel maintenance Funnels re assembling Fussell G Gas supply GC MS Glass Capillary removal Goodley Grasserbauer Grounding H Harrison Hazardous Voltages Hemling Henion Herderich High Temperatures Hodgson How APCI works How ESI works HPLC system Huang Humpf HV Focus Lens I Identifying System Components Ikonomou lon evaporation lon Guides lon Source removal 1 2 3 17 5 10 6 28 6 17 5 17 5 24 3 19 3 9 5 14 3 18 3 19 1 2 5 19 Bruker Daltonik GmbH lon Transfer stage ionization Iribarne ISCID Expert View ISCID Smart View K Kebarle Kralik Kuhlmann L Lacorte LED Display Lens Block re assembly M m z ratio m z Ratio Mack Maintenance Maintenance Schedule Mann MA
83. justment fixture Syringe Pump 6 2 Bruker Daltonik GmbH Part Number 222971 32169 21 352 20206 20207 46866 maxXis User Manual Version 1 1 Bruker Daltonik GmbH 6 2 Schematic of the maXis E maxXis User Manual Version 1 1 Appendix 6 3 Appendix Bruker Daltonik GmbH SOUrCE Transfer Funnel 1 Funnel 2 Mulpeocle 1 Metokner Gan Ory Gm Piiira MBPA Plow DP Temp KNIT SEN KEN H FCO A L iparba PET LJ POH L A meer d 3mba 3 E mbar Seit Flow Tie Pum d KN L i Rough Purnp L 4 i a WA dei 6 4 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix maxis User Manual Version 1 1 6 5 Appendix 6 3 Bruker Daltonik GmbH Divert Valve Connection Examples micrOTOFcontrol allows the eluent either to be directed into the ion source or to the waste via the divert valve The divert valve is used to direct the solved sample either via the nebulizer into the source or to the waste The selected flow path is controlled in micrOTOFcontrol see Figure 6 1 6 3 1 lon Polarity Deet Make Scan bode Pene S Mass Range From KO tol 3000 miz Rolling Average Summation Pon 2 wf eer Apply T Link Edit M Al Segments Figure 6 1 Divert valve settings dialog in micrOTOF control maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix Example 1 Sample flow through the divert
84. ker Daltonik GmbH Identifying System Components Sample Me buliz er inlet grounded Nebulizer gas inlet hh pressure controlled Spray needle sheathed with nebulizer gas Spray shield CG 3 6 ky 3 Heated drying gas M F i Glass capillary inners 0 5 mm N Capillary cap GA kV Te Waste Spray chamber Figure 2 9 Schematic of an APCI interface 2 3 1 1 Nebulizer To achieve reasonable sensitivity in the mass analysis of liquid samples the solved sample must first be sprayed into very fine droplets which can be easily evaporated prior to entering the vacuum system This is best achieved with the use of a pneumatic nebulizer which routinely produces droplets within a controlled range The nebulizer see Figure 2 9 receives the solution of sample and solvent from a syringe pump or liquid chromatograph The solution passes through a very fine needle The needle is mounted inside a tube that transports pressurized nebulizer gas usually nitrogen At the end of the tubes the two streams interact in such a way that the solution is dispersed into small droplets The nebulizing gas is important for the production of a good spray and a steady ion stream The operator can manually adjust the position extension of the needle although this is not normally necessary The pressure of the nebulizing gas is controlled by the user through the data system to optimize the spray The presence of the electrospray can easily be checked
85. l and the TOF assembly effectively holds the ions in the cooling cell The ions are injected into the TOF by setting the lens voltage to a voltage below the cooling cell bias Now the ion beam can overcome the lens potential and can pass through the electrostatic focusing lenses and then into the extraction region of the TOF This ion beam is not really as thin as the very thin line shown in Figure 4 12 it has a radial dimension Orthogonal Extraction There are 2 operational states for the orthogonal accelerator i The Fill Phase injection The Cooling Cell Exit lens voltage is dropped down to allow the ions to fill the extraction volume The TOF acceleration voltages are switched off ii The Extraction Phase The TOF acceleration voltages i e Repeller push and Extractor pull are switched on to push the ions out of the extraction volume into the flight tube Extraction pr Extractor j Ba Repeller Cooling Cell SE Exit Lens Figure 4 13 lon beam injection and extraction in the orthogonal accelerator maxis User Manual Version 1 1 4 15 Understanding maxis Basic Principles Bruker Daltonik GmbH The injection velocity and the extraction velocity are added vectorially Hence the ions leave the accelerator at an angle arctan V Uext Uinj which is independent of the ions mass The pulsed injection of the ions from the cooling cell into the accelerator gives rise to a time of flight separati
86. m 23 Calibration TOF LA Instrument Tune Reference List Bet eli sees Zooming P 1Uz sl Calibration Mode me a E Enhanced Quadrate z Li LiCOOH 1 53 029114 Calibrate e LILICOUH 2 117 0427 72 e LILICOOH 3 163 056430 Accept Lance e LiLICOOH 4 215 0700849 Calibration tatuz Asa AA e LILICOOH 5 26r U8arAr Fit Previous e LILICOOH 6 319 097405 StdDev O40 O40 porn e LILICOOH 371 111063 LiiLICOOH 8 423 124722 x Groe WT zem GER lear a Po f Properties There are no values to set in the Calibration page 6 4 2 13 Expert View instrument Tune Tab gt Auto Tune Es Made ie gt Source oa MS MS EN Sample Info Ai Chramatagram Jh Calibration TOF air Instrument Tune aie Auto Tune Task Feu List l Digitizer he TOF Detector Most abundant Mass B220 mis Fi Clear Shark anc Accept There are no values to set in the Instrument Tune gt Auto Tune page 6 32 maxXis User Manual Version 1 1 Bruker Daltonik GmbH 6 4 2 14 Appendix Expert View instrument Tune Tab gt Optimize E Made ie Source SC MS MS fey Sample Info jh Chromatagram h Calibration TOF sfx Instrument Tune aie Auto Tune sir Optimize E Transfer TOF List Results User Optimize List fe ntensity 3 e C Resolution 3 3e Faameter A a aa Previous V Current gad V Focus 1 Lens 2 sl Message List Mass Range pA A from 5o md to 1800 mez Ramp Range from 50 0 to
87. m flow rate of approximately 100 ul min 2 8 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 2 0 Divert Valve Introduction The divert valve allows the sample to bypass the ion source preventing contamination of the ion source and the vacuum system Selecting To Source lets the sample pass through the valve to enter the source default selecting To Waste switches the valve so that the sample flows directly into a drain bottle useful for a large solvent peak and a small compound peak to direct the solvent peak to waste or to reduce memory effects after using samples which may contaminate the source Another application is to use the standard 20ul sample loop to inject a calibrant after a measurement for example A detailed explanation of the divert valve can be found in Appendix 6 3 micrOTOFcontrol allows eluent to be directed either into the ion source Scan Mode or to waste via the divert SE valve MS MSMS ISCID ll MS MSMS ISCID ll lon Polarity Divert Valve 3 lon Polarity Divert Valve to Source Mass Honger Mass Honger From AL tol 3000 ms From AL ol 3000 ms Rolling Average Summation Rolling Average Summation On 2 8 93990 x M On 2 E g990 x IT Link Edit M Al Segments F Link Edit M Al Segments Figure 2 5 Divert sample Figure 2 6 Divert sample to source in dialog to waste in dialog maXis U
88. maintained at ground potential the incoming ion beam is guided directly to the conversion dynode of the SEM Secondary Electron Multiplier Figure 2 15 This set up is used for monitoring ions and can be used for troubleshooting or tuning the ESI System This detector is not used to acquire spectra 2 3 6 1 Orthogonal Acceleration Pulser In the maXis the orthogonal acceleration stage represents the ion source normally operating in pulsed mode This assembly consists of an array of electrodes mounted on top of one another Excluding the base electrode all the others assembled towards the reflector are shaped like slot diaphragms This region is used to accelerate ions towards the reflector Orthogonal acceleration on the maxXis is a two stage process If the acceleration electrodes are at ground potential the incoming flow fills this region with ions which continue straight ahead to the SEM dynode lons that have passed out of the pulsing region are not available for TOF analysis Before ions leave the pulsing region appropriate voltages are applied to the acceleration electrodes The ion package in the pulsing region is now forced to pass through slits of the electrodes towards the reflector This fill cut off and acceleration process can be repeated up to 20 000 times second Before the continuous flowing ion beam has re filled the pulsing region to be sampled again and accelerated the previous ion package has just reached the re
89. maxXis User Manual Version 1 1 2 5 Identifying System Components Bruker Daltonik GmbH 2 2 Sample input devices Samples can be introduced into APl electrospray ionization via some basic delivery systems which differentiate themselves principally by the liquid flow rates for which they are designed e Liquid chromatographic system 10 ul min 1000 l min max 5000 l min e Syringe pump 0 3 ul min 10 ul min alone and 100 ul min 1000 ul min with LC pump max 5000 ul min e Off line NanoElectrospray see section 2 8 1 7 optional sources approximately 30 nl min e On line NanoElectrospray see chapter 2 8 1 8 optional sources flow rates 100 nl min 400 nl min e Multimode Source e Divert valve introduction directs the sample either to the source or via the bypass to waste 2 2 1 HPLC system Due to the widespread use of liquid chromatography the LC system is the most common form of sample delivery for the instrument The electrospray ionization is optimized to accept flow rates up to 1 ml min and with the APCI option flow rates up to 1 5 ml min are possible The nebulization process for both of these ion sources is assisted with nebulizing gas and countercurrent drying gas The LC system can be operated in several modes in conjunction with the instrument Normal modes include standard LC analysis analysis without LC separation flow injection analysis FIA and combined flow with the low flow syringe pump The LC S
90. ne NAnOElectrospray 2 2 00 ecceccseecceceeeeeeeeeeeeeaeeeeeeseeeeeesaeeeeeeaeeeeeaeess 2 44 2 7 1 8 On line NanoElectrospray cccccccceeceeeseeeeeeeeeeeesseeeeeeseaeeeesaeeseeeaeeeeesaess 2 45 maxXis User Manual Version 1 1 Bruker Daltonik GmbH 2 1 Overview Identifying System Components The Bruker maXis is a Hybrid Quadrupole Atmospheric Pressure lonization orthogonal accelerated Time Of Flight mass spectrometer It is a space saving reflector instrument configured with the Bruker Apollo ion source an analytical quadrupole and a vertically arranged ion flight tube that contains the orthogonal acceleration stage the reflector and a detector The PC mounted digitizer is able to attain a sample rate up to 2 GS sec Figure 2 1 illustrates the dimensions of the instrument maxXis User Manual Version 1 1 Figure 2 1 maXis weight and dimensions 2 3 Identifying System Components Bruker Daltonik GmbH Figure 2 2 shows the maxXis in a typical LC MS MS arrangement For details about the liquid chromatographic system or the syringe pump see the manual supplied with those delivery systems Figure 2 2 Example of an LC MS system arrangement 2 4 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components It is a space saving instrument which includes the Apollo II Electrospray lon Source a quadrupole MS MS stage a vertically arranged Time of Flight mass spectrometer a vac
91. net www bdal de maxXis User Manual Version 1 1 lil Bruker Daltonik GmbH Safety Symbols NOTE This symbol is placed on the product where it is necessary for you to refer to the manual in order to understand a hazard WARNING This symbol is placed on the product within the area where hazardous voltage is present or shock hazard can occur Only trained service persons should perform work in this area WARNING This symbol is placed on the product within the area where hot parts and surfaces are present Allow the product to cool before performing work in this area WARNING This symbol is placed on the product within the area where biohazards are present Handle these areas with the respective care Warning The source chamber may not be opened until the sample flow has stopped Health Risk Fire danger Contamination of the Environment and Air maxXis User Manual Version 1 1 Bruker Daltonik GmbH Table of Contents Bs AG QING RA so esem cee sentence cate cecal te tances asaietees vidlat et sem aanciae tana snwadiatetewaceesteanaustacssedextaetuertentcose 1 1 a TEX ee ONS EE 1 1 1 2 Site Preparation Gpecfcaton 1 2 E EE 1 3 1 3 1 Safe en ele 1 3 1 3 2 Operating Precautions eessen sees eege ed RSR 1 4 1 3 3 Eeer 1 5 1 3 4 Environmental Conditions 1 6 1 4 Facility and Electrical Heourements 1 7 1 5 Unpacking Installation and First Gen 1 8 2 Identifying System Components ccccceessee
92. nge a all E p20 E i E T GE 6 0201 Z 1 3 Add Do MS MS the Largest Peak sl Change Intensity Ratio Ata Delete Heavy z Light gt 120 o 0 80 Delete All Ge Heavy d Light gt 0 05 and lt 20 00 Set Values Parameter Polarity Group Description GUI Unit Typic i Max I M P Advanced MS MS Auto Within Top 100 1000 Tolerance m z 0 20 10 00 Delta Mass 6 0201 100 0000 Max no of labels Charge Range Pattern match Cross Correlation Intensity Ratio Heavy Light gt or lt Heavy Light gt and lt 6 16 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 1 7 Smart View MS MS Tab gt Auto MS MS gt Fragmentation 2J Mode Si Source E MS MS EH Sample Info ae Chromatogram Z i Calibration TOF he Auto Tune El Auto MS MS Isolation Fragmentation List e Die Lien io wan Col Energy Charge State Import 500 00 Fragmentation 500 00 500 00 1000 00 Collision Cooler 1000 00 1000 00 2000 00 2000 00 2000 00 t New Delete Delete All Fallback a Charge State E GA N GA N w fo oon mom e O N he Set Values Parameter Polarity Group Description GUI Unit Typic Min Max I M P Isolation Fragmentation List Fallback Charge State z 6 4 1 8 Smart View MS MS Tab gt MRM E Mode gt Source Pai MS MS KN Sample Info i Chromatogram Eh Calibration TOF J ahr Auto Tune E Auto MS
93. ole in enhancing sensitivity for both positive and negative electrospray ionization Many compounds can be analyzed as neutral molecules in a neutral environment Other compounds however can be analyzed with much greater sensitivity if the chemical environment is one that favors ion formation When an analyte is dissolved in an acidic or basic polar solvent such as an acid or base it can either ionize or take on a strong dipole moment For analytes that ionize ESI is generally simple and highly sensitive Provided no other ion ion interactions interfere ions are already present in the solution before spraying These ions are easily evaporated from the droplets in the spray and result in a high analyte ion abundance Analytes that form strong dipole moments but do not ionize can still be analyzed The ionization process is driven by the strong electrostatic fields in the spray chamber These fields induce a charge on the spray droplets This charge can induce ionization in analyte molecules at the surface of the droplets These analytes can also be ionized chemically by adduction using special chemicals 3 2 2 2 Positive ion analysis Analytes that are rather basic in character are generally analyzed in positive ion mode The sample molecule base picks up a proton from the more acidic solvent solution MI HA lt gt M H A For very polar analytes the process is in equilibrium lonization is enhanced by increasing the number of hy
94. olled Spray needle sheathed with nebulizer gas High wattage vaporizer Spray shield 3 6 kV Glass capillary innere 0 5 0 6 mm Capillary cap 4 kV Spray chamber Corona discharge needle HV Figure 2 27 Schematic of an APCl interface 2 3 Identifying System Components Bruker Daltonik GmbH 2 7 1 2 APLI Source The APLI source Atmospheric Pressure Laser Ionization Figure 2 28 and Figure 2 29 can also be connected to the instrument For further information see the user manual for the APLI source Figure 2 28 APLI lon Source Figure 2 29 APLI lon Source with GC transfer line corona needle GC separation capillary stainless steel capillary resistively heated to 320 C glass tube GC Oven APLI Source 7 power supply 5V 20A SN Figure 2 30 APLI Schematic diagram 2 38 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components APLI lon Source Nass Spectrometer Laser Gas Chromatograph Figure 2 31 An APLI configuration An APLI source allows for coupling maXis to a Gas Chromatograph and a laser source as shown in Figure 2 31 maxXis User Manual Version 1 1 2 39 Identifying System Components Bruker Daltonik GmbH 2 7 1 3 ESI nano Sprayer The ESI nano Sprayer or nebulizer is a spray technique specially developed for coupling with capillary LC at very low flow rates similar to the On line NanoElectrospray The ESI nano Sprayer utilizes a nebulizer
95. om the low voltages needed at the end of the capillary for the subsequent ion optics see following In the drying gas heater pressurized nitrogen is heated up to a pre defined temperature the drying gas streams Through a heat chamber and around the capillary from the rear of the spray shield maxis User Manual Version 1 1 2 15 Identifying System Components Bruker Daltonik GmbH 2 3 2 lon Transfer stage FARF FOC1_L3 I Il k ee Ti ul Au FOC1_L1 pulsed FOC1_L3 FOC1 L2 3 mbar 0 3 mbar 3 E 04 mbar 30m h 30 Us 250 I s Figure 2 12 Double Stage lon Funnel and Multipole 2 3 2 1 Double Stage lon Funnel The ion transfer stage Figure 2 12 contains the first three of the five vacuum stages in the maXis mass spectrometer The glass capillary transmits analyte ions drying gas and a small amount of solvent into the vacuum system The first stage is pumped by a 28m roughing pump which reduces the pressure to approximately 3 mbar The aim of the ion transfer region is to separate analyte ions from drying gas and solvent and to transfer these ions with minimal losses to the quadrupole stage which requires a pressure lower than 3x10 mbar The first two vacuum stages of the ion transfer contain funnel ion guides These are stacked ring ion guides with the inner profile of a funnel The applied RF voltage generates an effective potential that confines the ion beam inside the funnel Two
96. om of the spray chamber Connect the drain at the bottom of the spray chamber to a closed container Handle and dispose of all fluid with care appropriate to its chemical and or biological content Handle all used pump fluid as hazardous waste Dispose of used pump fluid as specified by your local laws and regulations Also refer to the Material Safety Data Sheets MSDS obtainable from the supplier 5 2 Biological Residues The NanoSpray interface does not ionize all of the sample and solvent Some sample and solvent passes through the interface without being ionized The vacuum pumps of the maXis are designed to pump away the unionized sample and solvent The exhaust from these pumps can contain traces of samples and solvents Vent all pump exhaust outside or into a fume hood Comply with your local regulations and laws WARNING Fluid drained from the spray chamber is composed of solvent and sample from your analyses The fluid in the mechanical and diffusion pumps collects traces of the samples and solvents In addition non nebulized solvent and sample accumulate at the bottom of the spray chamber Connect the drain at the bottom of the spray chamber to a closed container Handle and dispose of all fluid with care appropriate to its biohazardous and biological content Handle all used pump fluid as hazardous waste Dispose of used pump fluid as specified by your local laws and regulations WARNING The needle in the NanoSpray sou
97. on in the incident ion beam The injection energy Cooling Cell Bias is converted into kinetic energy 1 2 m v Hence the ions velocity and their arrival time in the extraction volume are dependent on their mass This has to be considered for the timing transfer time pre pulse storage 4 7 2 Orthogonal TOF Extraction When the extraction region of the TOF is filled with the ion beam bunch the acceleration voltage is switched on pushing the ions through the accelerator unit into the flight tube where the ions move uniformly During the acceleration the ions closer to the repeller plate will get more energy than those farther away Figure 4 14 Acceleration of ions 4160 maXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles a q m E v V 2 U q m total Time of Flight tota d 2x VEm 2 q U effective Flight Path dere Eerst VL 2 g U m TOF Principle In the accelerator the ions are accelerated by the electric field acting on their charge Hence they get a kinetic energy E 7 m v2 which equals their potential energy OU U is the local potential at the starting position In the field free drift the ions fly uniformly until they hit the detector acceleration fi d free drift vV AV V AV V AY d DAT je d DAT Potential Energy q U Flight Path X 1 2x Figure 4 15 Start and space shift of ions with the same mass Depending on their startin
98. otion of the ion acts like a potential barrier The ion energy in the pseudopotential equals the mean kinetic energy in the RF oscillation Kinetic Energy Figure 4 4 Injection RF Motion 10 20 30 40 50 60 Time of Flight us The translational energy of the ion is converted into RF oscillation and back into translational motion Thus the motion of the ion in the RF field acts like a potential barrier reflecting the ion The ion energy in the pseudopotential equals the mean kinetic energy in the RF oscillation maXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles 4 3 RF lon Guides closed repulsive wall The inhomogeneous field can be extended by adding further electrodes forming a repulsive line or if we consider rod electrodes a repulsive wall This wall may be converted into a tube by wrapping it around an axis parallel to the rods ending up with a multipole with 4 quadrupole 6 hexapole or more rods The repulsive wall might also be wrapped around an axis perpendicular to the electrodes ending up with a stack of rings A variant of this Stacked Ring lon Guide is the lon Funnel in which the ring electrodes have different diameters An lon Funnel efficiently colle
99. ounter flow of neutral heated drying gas typically nitrogen evaporates the solvent decreasing the droplet diameter and forcing the surface charges closer together see Figure 3 2 EVAPORATION m mm Avi EIGH COULOMB LIMIT EXPLOSION REACHED DROP FT Figure 3 2 Coulomb explosions produce charged droplets within the spray chamber e analyte When the force of the Coulomb repulsion equals that of the surface tension of the droplet the Rayleigh limit see Figure 3 3 the droplet explodes producing charged daughter droplets that are subject to further evaporation This process repeats itself and droplets with a high surface charge density are formed When charge density reaches approximately 10 V cm ion evaporation will occur maxis User Manual Version 1 1 3 5 Understanding API and APCI Electrospray Bruker Daltonik GmbH F Rayleigh Stability Limit d 10 vient Be Rayleigh Jets GH Ou C ZS Rayleigh Explosions 4 Ba i Pa fi a lon Evaporation fy lonization 10 M Droplet Radius 10 M Figure 3 3 Process of ESI The choice of solvents and buffers is a key to successful ionization with electrospray Solvents like methanol that have lower heat capacity surface tension and dielectric constant promote nebulization and desolvation 3 6 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 2 1 4 lon evaporation The process of ion formation has b
100. over damage resulting from customer mishandling Do not open the shipping container unless a BRUKER representative is present Opening of the container without authorized persons will void the warranty of the instrument Our service engineers will set up the instrument in the customer s laboratory The surface on which the instrument is to be located must be able to safely support the full 345 kg 760 lbs weight In addition tables or benches will be required to set up the LC unit the computer monitor and printer It is recommended that the table height should be between 23 and 28 inches 58 to 71 cm Once deliverer the machine must remain on the delivery palette in readiness for a Bruker representative to move the instrument to its desired location Please note Only a Bruker representative is permitted to undertake the initial installation and commissioning of the maXis 1 8 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 IDENTIFYING SYSTEM COMPONENTS This chapter is an overview of the maXis hardware and gives a short theory explanation CONTENTS Subject Page Number ZN OVVIE W ee eren 2 3 22 SalnPle INPUT CEVICES asia ect ers Gnd crea tec nate ana See aon coat cate dead dea E 2 6 2 2 1 FU SY SU i ca hacen tle E S e Aare cient aa E la TOR 2 6 2 2 2 eh Al Let lr TEE 2 2 2 3 Divert valve at ee Eet Le DEE 2 9 ZA Route through the TOF Mass Spectrometer nnnnennnnsnnnnnsnnnenrnrnsnrnns
101. p and a cap in front of the glass capillary causes an electrical field This causes the transition from molecules to ions which begin moving toward the entrance of the glass capillary This arrangement results in flow rates of about 30 nl min Slight hydrogen backpressure on the sample needle also helps to force the sample out of the needle Figure 2 40 Schematic of an Off line Nano Electrospray Source Glass capillary innere 0 5 0 6 mm Spray needle tip Spray chamber 2 44 maXis User Manual Version 1 1 Bruker Daltonik GmbH 2 7 1 8 On line NanoElectrospray On line NanoElectrospray is a spray technique specially developed for coupling with capillary LC flow rates 100 nl min 400 nl min The Bruker On line NanoElectrospray ion source Figure 2 42 is an ESI source specially designed to handle extremely small sample flows Typically this source is used together with a Nano LC system for measurements at flow rates between 50 and 500 ni min Rather than a nebulizer assembly a needle is used for sample transportation from the Capillary LC into the spray chamber In the needle holder itself the LC capillary is connected to the metal spray needle The potential difference between spray needle tip and a cap covering the glass capillary creates an electrical field This causes the transition from molecules to ions which begin moving toward the entrance of the glass capillary Due to the small sample and solvent volum
102. pillarycap 4 kV UV lamp Spray cham ber Figure 2 34 Schematic of an APPI interface maxXis User Manual Version 1 1 2 41 Identifying System Components Bruker Daltonik GmbH 2 7 1 5 Capillary Electrophoresis CE Capillary Electrophoresis CE is a migration of electrically charged compounds in solution under the influence of an applied electrical field CE has the following special features CE MS compared to LC MS provides different selectivity higher separation efficiency and short analysis time Although CE MS offers a greater mass sensitivity than LC MS its concentration limit of detection is about 1000 times higher because of the lower mass loading capacity and dilution by the sheath liquid CE reduces sample preparation and analysis time for compounds in complex matrices and MS n allows unambiguous identification CE MS is suited to the analysis of compounds at ppm concentrations in small complex matrix samples 2 42 Figure 2 36 Capillary Electrophoresis CE System maxXis User Manual Version 1 1 Bruker Daltonik GmbH 2 7 1 6 Multimode The multimode source combines the ESl source with the function of APCI The electrospray is separated by a metal shield one part of the spray passes through the multimode source without any additional ionization the other part of the spray passes the APCI needle and is ionized The great advantage is that both masses of the spray ESI and APCI
103. rates ions inside the source to a kinetic energy of several keV After leaving the source orthogonal acceleration stage the ions pass a field free drift region in which they are separated as a result of their m z ratio This separation is due to ions with a fixed kinetic energy and different m z values being accelerated to different velocities in the ion source The time of flight in combination with values for the acceleration voltage and length of the drift region allows for the determination of the m z value of the ions 2 3 6 4 Dual Stage Reflector Due to the different velocities and positions of the ions prior to orthogonal acceleration slight differences in final kinetic energy are observed The primary task of a reflector is to normalize these energy differences and thus to improve resolution lons of the same mass but of unequal kinetic energies will penetrate the reflector field to different depths which compensates for their varying starting energies The reflector in the maXis has two different stages In the first reflection stage the incoming ions are decelerated from high velocities to relatively low flying speed The second reflection stage softly slows the ions down to the reversal point and deflects them back to the flight tube On re entering the first reflection stage the ions get accelerated back to flight tube speed Accurate compensation for the varying starting energies is achieved as a result of the low flight speed in
104. rce is extremely thin Avoid touching it and causing a puncture wound especially when working with dangerous and toxic substances maxis User Manual Version 1 1 5 3 Maintenance Bruker Daltonik GmbH 5 3 High Temperatures Many parts of the maXis operate at temperatures that can cause serious burns These parts include e Mechanical pumps e APPI UV lamp e Drying gas heater e Capillary and capillary cap e Drying gas e Spray shield e APCI heater vaporizer Also exercise care with any other parts that come into contact with the drying gas the entire spray chamber capillary capillary cap and lamp can also present a burn hazard Most of these parts are normally covered or shielded Therefore the covers also become hot Avoid touching these parts WARNING Many of these parts remain hot for a substantial period of time after the maXis has been shut down or switched off Pay attention when working on a recently shut down instrument to avoid burn injuries 5 4 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 4 Hazardous Voltages WARNING Never remove any of the instrument covers while the mass spectrometer is switched on and connected to a power source WARNING Never open the spray chamber while the instrument is in Operate or in Standby mode WARNING Any interruption of the protective conductor inside or outside the instrument or disconnection of the protective earth terminal could resul
105. resulting potential is higher than V the resulting fundamental frequency is also increased On the other hand ions may couple with the quadrupolar RF field by parametric resonance lons will exchange energy with the RF field if the fundamental frequency meets half the quadrupole operation frequency Considering a full fundamental oscillation cycle and assuming the ion starts on the left side the ion follows the pseudopotential moving to the axis During this first quarter of the fundamental oscillation the ion also gets energy from the RF field After the ion crossed the axis i e in the second quarter of the fundamental cycle the RF phase changes its polarity causing the ion to lose less kinetic energy then it obtained during the first quarter In the third quarter of the fundamental oscillation ion moves back to the axis the RF phase has changed its polarity again Hence the ion converts its energy from the pseudopotential plus some extra energy from the RF into kinetic energy In the fourth quarter ion moves from the axis to the left side the RF phase is reversed again causing the ion to lose less energy then it gained earlier This is very similar to a swing From each reversal point of the oscillation to the lowest point one lowers the center of mass getting some extra energy from the gravitation field while one lifts the center of mass on the way from the lowest point to the highest point The up and down movement of the cen
106. rnrrenrrrsrrrrnn 2 11 2 3 1 eelere eet EE 2 11 2 3 1 Apolo Source EE 2 12 E e al NeDUIZO areas cates obiaaiesd dear eacaeictand sodesinstcumeaondsuie besememesddedaeeaealal Sogaaens 2 13 E a EN ENC CIOS Le E 2 14 2 3 1 3 Spray shield and capillary Cap 2 14 2o kE RVING Ge EE 2 15 2 9 1 5 Ee te IR En EE 2 15 2 3 2 LOM Transfer Le EE 2 16 2 3 2 1 Double Stage lon Funnel 2 16 222 MUOG EE 2 17 293 3 Quadrupole neo a a a 2 18 2 3 4 Collision Cooling Re EE 2 19 Z3 A amp P ee Ee LR TEE 2 19 2 3 9 ele ln tee NEE 2 20 2 3 6 TOP ASSAY oe sasc tote totes detest oe E T 2 21 2 3 6 1 Orthogonal Acceleration Pulser cc ccecccceeeeeeseeeeeeeeeeeeesseeeeesaeeeeeeeeees 2 22 EN AV ei 2 22 2 3 6 3 Determination of the m z ano 2 23 2 3 6 4 Dual Stage E 2 23 PO DELOC EEN 2 24 24 Ee E E elei et EE 2 25 2 4 1 LED DIS el E 2 26 maxXis User Manual Version 1 1 2 1 Identifying System Components Bruker Daltonik GmbH 2 5 2 6 2 2 2 2 4 2 Peripheral Interface External start for data acquisition ccccseeeeeseeeees 2 2 PC COMMU ATOM EE 2 30 REMOS SENICE merrianad prt stale tas ea cheaconctal suet ns a vans eels aeaebeoatd alee 2 31 2 6 1 Initiating Remote Gervice EE 2 32 Opna S OULCCS series host a tient sian teh sade T 2 36 Zot Al GE lee e 2 37 Zt AZ APLLSOU CO oaa 2 38 ES a E d E Rule LE EE 2 40 ZA SAPP We le 2 41 2 1 5 Capillary Electrophoresis CEA 2 42 ZA CHEN eege ee EE EE ee 2 43 2 7 1 7 Off li
107. ry similar to methane or ammonia Cl in GC MS In APCI the Cl reagent gas is the HPLC mobile phase such as water methanol or isopropanol The vaporized mobile phase reagent gas reacts with electrons from the corona discharge to form various adduct ions These adducts based on proton affinity will transfer a proton in the case of the positive ion mode to the analyte Depending on the analyte and solvent system other reactions are possible e Protonation such as HOT and bases e Charge exchange e De protonation acids e Electron capture halogens aromatics APCI requires that the analyte must be in the gas phase to occur for ionization To bring the mobile phase and analyte into the gas phase APCI is typically operated at vaporizer temperatures of 400 C 500 C In APCI the vaporizer temperature must be carefully controlled Most compounds work best at higher temperatures while a few compounds work best at lower temperatures It may be necessary to evaluate a couple of temperatures to determine the optimal AC vaporizer temperature 3 3 1 When to Use AC There are some reasons and also some requirements to change to APCI to get better results e Sample exhibits a poor electrospray response e Sample contains no acidic or basic sites such as hydrocarbons alcohols aldehydes ketones esters e Sample is thermally stable and can be vaporized e Flow rates solvents or additives are not compatible with electrospray
108. s 5 24 maXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 2 Reassembling the Lens block Feed the green and yellow wires through the apertures in the body of the cartridge and connect them to the Lens Block This can be awkward but using tweezers makes it easier _2xT6 screws a a Connect the yellow and b Hold the Lens Block in c Ensure the red green green wires and note the place while securing the and yellow wires are location of the pin for the two Torx T6 screws reconnected to the red wire cartridge Align the pin for the red wire with the appropriate hole in the transfer cartridge compress the spring and secure the lens block with the two Torx T6 screws 3 Reassembling Funnel 2 EZIZ i CEL a Feed the Funnel 2 wires b Plug wires into the c Position four Torx T8 through the apertures in correct sockets screws in Funnel 2 the transfer cartridge screw holes lower Funnel 2 into the recess and tighten down the screws maXis User Manual Version 1 1 5 25 Maintenance Bruker Daltonik GmbH 4 Reassembling Funnel 1 Funnel one has only one possible assembly position because of the screw positions Fasten with four Torx T10 screws and relocate the wires into the correct sockets in the transfer cartridge The connectors should be pushed sub flush to ensure a good connection d Use four Torx T10 e Plug wires into the f Ensure that the female screws to secure correct sockets connector
109. s User Manual Version 1 1 2 27 Identifying System Components Bruker Daltonik GmbH micro OF Peripheral Interface D Sub 5pins Pin signal Start ee stop GND GND AGND Analog out or ground Analni Analog out or signal Analn lt mmm mmm eege fung mmm mmm mmm mm mm Figure 2 19 External Start Stop acquisition function 1 Note Connection between AGND and Analn1 Figure 2 19 should be made only when there is no differential output available on the HPLC Closed contact gt Starts acquisition Opened contact gt Stops acquisition Please refer to the corresponding Software Settings on the Mode page Figure 2 20 2 28 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components Mode ER Source Pa MS MS By Sample Info elle Chramatagram cd Calibration TOF jie Auto Tune External Control IY Save Spectra Je Active Configure Include Profile Spectra Spectra Acquisition __ Focus Ce Always Threshold 1000000 C Off Segment Parameter Mark as Calibration Segment Figure 2 20 Features of the Mode page x External Start __ Signal Polarity Stat Off C Positive Negative f Remote Control Stop Ce Positive Negative Ready Delay Time DI sep Ce Positive Negative UV Signal 1 Ce Positive Negative UY Signal 2 Ce Positive Negat
110. s are pushed Funnel 1 to the transfer sub flush to ensure a cartridge secure contact 5 26 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance Refitting the Grab Handle The Grab Handle and the neoprene O ring are essential to ensure positive connection between the Multipole Cartridge and the connector pads in the transfer stage L a Neoprene Ring c Use three Torx T10 screws to attach the d Fit the neoprene O Ring into the annular Grab Handle to the three spacer bolts groove 5 6 8 3 Re fitting the Multipole Cartridge to the maXis 5 Installation of the Multipole Cartridge The multipole cartridge uses an alignment pin to ensure that the contact pads in the lon Transfer Stage casing connect with the spring connectors on the multipole assembly see below Alignment pin Alignment hole b The alignment hole can be found on the left hand side of the Transfer Stage cavity a The alignment pin is mounted on the edge of the Multipole Transfer cartridge Push the Multipole Cartridge into the Transfer Stage cavity ensuring that the pin located in its socket maxXis User Manual Version 1 1 5 27 Maintenance Bruker Daltonik GmbH 6 Install Desolvation Unit and Source Chamber There is a neoprene O ring fitted to the rear side of the desolvation unit This O ring is critical in maintaining a vacuum inside the maXis Before installing the desolvation unit ensure that the O ring is properly seate
111. s may be altered in micrOTOFcontrol Smart mode Expert mode and Service mode users should only operate Smart or Expert mode depending on their experience Service mode is reserved for use by Bruker Service Agents This appendix illustrates the range and type of values that can be adjusted in Smart and Expert modes DP ee OR tan 88 PO DBR EE Ostet Oe Sr View dropdown menu View Service sl T Mode Pp Source E wi A L I Zeie bie oi Cheommstogam i Cabane of instrument Tara 2 Zeen TEE RES ee inoia Go ve s SME iiie En F irmi F Aa backas T me mja ie ee Stee la sche Fake z ie E byi Expert r Se e brite Profle pacha Darmon wie g pit Service E iiag Values and Ranges Tabs Figure 6 5 Locations of the View menu and the Tabs Select Smart or Expert view from the pull down view selection menu and click on the appropriate Tab Values and Ranges Tabs to display the associated pages The following section provides guidance on individual values and ranges that can be changed on each page 6 10 maXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 1 Smart View Values and Ranges Smart view is intended as default view to be used by inexperienced operators Nevertheless a large number of the parameters can be adjusted in the Smart view pages 6 4 1 1 Smart View Mode Tab J Mode ER Source Zi MS MS By Sample Info ail Chramat
112. ser Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 1 13 Smart View Calibration TOF Tab E Made ie t Source ES MS MS fey Sample Info jl Chromatogram h Calibration TOF Auto Tune Reference List Mode Enhanced Quadratic Calibrate Accept Pence Result StdDey 0 40 ppm Show gt gt oam i Last Calibration Date 2008 11 25 12 32 51 User BD ALCDE There are no values to set in the Calibration TOF page 6 4 1 14 Smart View Auto Tune Tab Mode Te h Source p MS MS EA Sample Info Chramatagram Z Calibration TOF sie Auto Tune Take Result List Jh TOF Detector Mast abundant Mass B220 mz Gi Clear Start Cancel Accept There are no values to set in the Auto Tune page maxXis User Manual Version 1 1 Appendix Bruker Daltonik GmbH 6 4 1 15 Expert View Values and Ranges Expert view is intended for use by experienced operators It allows the same parameters to be changed as in Smart view plus some additions 6 4 2 Expert View Mode Tab e Ge KS 3 en S 8 8 Mode ES Source Ze MS MS ey Sample Info 4 Chromatogram cl Calibration TOF fie Instrument Tune Spectra Acquisition l Focus Processing External Control Iw Active Absolute Threshold 10 Configure Include Profile Spectra Peak Summation width z pe f Always C Threshold 1000000 Of Segment Parameter
113. ser Manual Version 1 1 2 9 Identifying System Components Bruker Daltonik GmbH Sample loop Divert valve e A i T s Figure 2 7 Front view of the maXis showing Divert Valve fitted with sample loop 2 10 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 3 Route through the TOF Mass Spectrometer Dual Stage Reflector Collision Quadrupole Cooling Cell TOF Spectrometer Transfer Source COIRF KI E D i Aen GE BE atl lo FOCLLS FOCA 1 L Fioce LA Aitor Figure 2 8 Source spray chamber and capillary lon Transfer Stage funnel 1 funnel 2 multipole Quadrupole Collision Cooling Cell and TOF spectrometer orthogonal accelerator dual stage reflector detector 2 3 1 maXis User Manual Version 1 1 Identifying System Components Bruker Daltonik GmbH Apollo Source ESI The Bruker Apollo source Figure 2 9 is the standard ion source used with the maXis for the measurements of singly charged samples such as benzodiazepines and multiple charged samples such as proteins and peptides The solved sample is introduced through the nebulizer assembly into the spray chamber where it is subjected to the ESI process by means of an electrical field between the inner chamber wall and the spray shield and with the aid of a nebulizer gas N2
114. t in an electrical shock Intentional interruption is strictly prohibited When the maXis is connected to the mains hazardous voltages are applied to assemblies such as e Mechanical pumps e Wiring and cables between these parts e Transformers and power supplies in e High voltage electrodes capillary the maXis cabinet and end plate in the spray chamber e RF generators e Dynode cables e Drying gas heater e Multiplier cables e APCI heater e Lens voltage cables e APCI corona needle e Needle NanoSpray e APPI UV lamp e Needle holder NanoSpray e HV voltage cable NanoSpray maxis User Manual Version 1 1 5 5 Maintenance Bruker Daltonik GmbH 5 5 Maintenance Schedule General maintenance tasks are listed in the table below Performing these tasks on schedule avoids problems prolongs system life and reduces overall operating costs Keep a record of all system performance characteristics and maintenance operations performed This will help in detecting deviations from normal operation Table 5 1 Maintenance Schedule Flush sample path Clean spray chamber spray shield capillary cap contacts and the tip of the corona needle Check the ventilation air filters on both sides of the instrument Replace lubricant reservoir on Turbo Pump 1 Pfeiffer Inspect hoses power cords and cables Empty drain bottle Replace nebulizer needle Clean or replace entire capillary Clean or replace funnel
115. ter of mass is the parametric excitation whilst the oscillation of the swing is the fundamental oscillation Due to the resonant excitation the transmission of lighter ions falls rapidly if there is parametric resonance maxis User Manual Version 1 1 4 9 Understanding maxis Basic Principles Bruker Daltonik GmbH 1 RF cycle LG fundamental excitation cycle next RF cycle plane of symmetry fundamental excitation d Figure 4 7 Plane of symmetry 410 maXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding maxis Basic Principles This behavior is also reflected in the stability diagram for the quadrupole The triangle is an excerpt from the diagram of the stability regions of the Matthieu differential equation The q axis represents the RF whereas the a axis represents the DC The q axis itself represents the RF only quadrupole which can be used as an ion guide Only ions within the nearly triangular shaped area are transmitted by the quadrupole For them there are stable trajectories Adding a DC always narrows the transmission mass range of the quadrupole unstable DC defocusing DC potential over unstable comes focusing resonant excitation pseudopotential d Stable trajectories 1 m AC Figure 4 8 Stability diagram On the left hand side of the triangle the heavy ions are lost because the DC pushes them towards the rods On the r
116. the second reflection stage maxis User Manual Version 1 1 2 23 Identifying System Components Bruker Daltonik GmbH To obtain high quality mass spectra with a reasonable signal to noise ratio the geometry of a reflector has to fulfill specific electrical and size requirements mainly with respect to the dimensions of the flight tube and type and size of the reflector employed 2 3 6 5 Detector A detector converts an ion signal into an electrical signal In the maXis the electrical signals from the TOF detector are transmitted to a digitizer card which is mounted in the PC 2 24 maxXis User Manual Version 1 1 Bruker Daltonik GmbH 2 4 External Connections Peripherial Interface Identifying System Components a sgeal Trigger Signal R Out 6 B disco Reset Digitizer Se i ia chen nite deu Greecb a fiche Collision Source 6 Figure 2 16 External Connections on the maXis The following connections are accessible on the lower right hand side of the housing Figure 2 16 e Peripheral interface HPLC system e Serial interface for the PC e Digitizer input For the patch cable of the signal adapter box e Signal and trigger lines for the digitizer on the PC e Main circuit breaker e Switched socket inlet for the unit e Switched socket outlet for the roughing pump 1200 VA e Collision gas inlet e No inlet 5 5 6 bar for the ion source nebulizing and drying gas and for venting
117. the vacuum system Caution maxXis User Manual Version 1 1 To avoid damage to the digitizer card do not disconnect the signal lines before switching off the main power to both the mass spectrometer and the computer 2 25 Identifying System Components 2 4 1 LED Display Shutdown green Vacuum LED Standby green Vacuum LED yellow Status LED Operate green Vacuum LED green Status LED Aquisition green Vacuum LED blinking green Status LED 2 26 Bruker Daltonik GmbH The instrument is equipped with two groups of LEDs Figure 2 17 and Figure 2 18 located on the lower right hand side at the front of the housing Vacuum Status Figure 2 18 LED display The table below explains what the LEDs mean and how they display instrument status Venting blinking yellow Vacuum LED Vented yellow vacuum LED Pumping Down green Vacuum LED Error red Status LED maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components 2 4 2 Peripheral Interface External start for data acquisition Table 2 1 Pin assignment of the peripheral interface Analog Input 1 differential inputs for Analog In 1 max input voltage 10V Analog Input 1 Analog Input 2 differential inputs for Analog In 2 max input voltage 10V w Analog Input 2 Ready digital output open drain must be connected with external pull up resistor to 5V pin 12 C e C RE maXi
118. there are obvious deposits elsewhere on the shield Use a Cotton Tipped Applicator and mixture of isopropyl alcohol and water to clean the inner rim of the main hole in the spray shield Clean the capillary cap with the sand paper Only the end surface of the cap needs to be cleaned in this way unless there are obvious deposits elsewhere on the shield The inner rim of the hole in the cap may occasionally need cleaning Put the capillary cap into a solvent bath and clean it with an ultrasonic cleaner Reinstall the capillary cap Reinstall the spray shield Close the spray chamber maxXis User Manual Version 1 1 Bruker Daltonik GmbH Maintenance 5 6 11 Replacing the Nitrogen Gas Filter When required Replacing the Nitrogen gas filter is necessary when it is saturated and chemical background appears when other sources of chemical background such as solvents and spray chamber contamination can be excluded If ions are present and no sample or solvent is flowing this is also an indicator that the Nitrogen Gas Filter requires replacement Tools requires e Wrench 1 2 x 9 16 inch open end Parts required e Nitrogen Gas Filter 219454 Preparation e Procedure e Shut down the maXis section 5 6 1 e Turn off the gas flow at its source e Remove the old Nitrogen gas filter by unscrewing the unions e Connect the Pipe from the nitrogen source to the inlet of the new Nitrogen Gas Filter e Turn on the flow of nitrogen gas at
119. through a viewing window in the spray chamber The needle assembly is electrically grounded maXis User Manual Version 1 1 2 13 Identifying System Components Bruker Daltonik GmbH 2 3 1 2 Electrospray Electrospray describes the dispersion of a liquid into many small charged droplets as a result of an electrostatic field In the early seventies initial experiments were conducted with oligomers dissolved in a volatile solvent which were guided through a N sprayer into a cell filled with N2 Dispersion was initialized by the application of a potential of some 1000 volts between the sprayer and shield Figure 2 10 Evaporation of the solvent during this process result in the droplets reduced in size and causes a build up of charge density on their surface finally resulting in coulombic forces which break up the droplets further This process is repeated until final desolvation generates sample ions as shown in Figure 2 10 Needle tip grounded Spray shield Figure 2 10 Principle of the ESI process 2 3 1 3 Spray shield and capillary cap A high voltage is applied to the spray shield to attract the ions The small charged droplets generated by the nebulizer are accelerated by the electrical field between the nebulizer ground potential and in the case of positive charged droplets the negatively charged spray shield A further potential difference of about 500V between Transfer of ions from the solvent into the gas phase
120. tion 2 3 1 ESI nano Sprayer section 2 8 1 3 APPI source section 2 8 1 4 Capillary Electrophoresis section 2 8 1 5 Multimode section 2 8 1 6 Nanospray sources Offline section 2 8 1 7 separate manual PN 73821 Online section 2 8 1 8 separate manual PN 74831 2 36 maxXis User Manual Version 1 1 Bruker Daltonik GmbH 2 7 1 1 APCI Source Atmospheric Pressure Chemical lonization APCI is a combined Liquid Chromatography and Mass Spectrometry LC MS technique closely related to Electrospray lonization The Bruker APCl source Figure 2 26 and Figure 2 27 is best used for the analysis of polar and nonpolar analytes The nebulization process for this ion source is similar to that for the Apollo source However APCI nebulization takes place in a heated vaporizer tube with typically temperatures ranging from 250 C to 400 C The heat evaporates the spray droplets resulting in gas phase solvent and sample molecules On leaving the vaporizer tube gas phase solvent molecules are ionized by a current regulated discharge from a corona needle at a voltage of 1 4 kV By transferring their charge the solvent ions convert sample molecules to sample tons maxXis User Manual Version 1 1 Identifying System Components Figure 2 26 APCI source with 1 APCI nebulizer 2 APCI heater cable and 3 corona needle Sample inlet Nebulizer grounded Nebulizer gas inlet Ny pressure contr
121. uid Chromatographs and Mass Spectrometers Anal Chem 1985 57 675 679 Wong S F C K Meng and J B Fenn Multiple Charging in Electrospray lonization of Poly ethylene glycols J Phys Chem 1988 92 546 550 Yamashita M and J B Fenn Negative lon Production with the Electrospray lon Source J Phys Chem 1984 88 4451 4459 Yamashita M and J B Fenn Electrospray lon Source Another Variation on the Free Jet Theme J Phys Chem 1984 Apffel A S Fischer P Goodley F Kuhlmann Eliminating Signal Suppressions of TFA Containing Solvents for Electrospray MS by the Addition of Selected Organic Solvents Proceedings 42nd ASMS Conference on Mass Spectrometry and Allied Topics 1994 3 18 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 4 2 Reference articles for APCI 1 Thomson B A Atmospheric pressure ionization and liquid chromatography mass spectrometry together at last J Am Soc Mass Spectrom 1998 9 187 193 Lacorte S Molina C and Barcelo D Temperature and extraction voltage effect on fragmentation of organophosphorus pesticides in liquid chromatography atmospheric pressure chemical ionization mass spectrometry J Chromatogr A 1998 795 13 26 Barnes K A Fussell R J Startin J R Pegg M K Thorpe S A and Reynolds S L High performance liquid chromatography atmospheric pressure chemical ionization mass spectrometry with ioniz
122. ument to a power source that is not equipped with a protective earth contact creates a shock hazard for the operator and can damage the instrument Likewise interrupting the protective conductor inside or outside the instrument or disconnecting the protective earth terminal creates a shock hazard for the operator and can damage the instrument WARNING The instrument must be disconnected from its power source before any cover is removed or it is opened Bruker Daltonik GmbH WARNING All connections of the instrument must be used in correct way The instrument should only be used with the wires and cables delivered with the system or otherwise provided by the manufacturer Instrument Identification Each instrument is identified by a serial number This numbers is located on the rear of the instrument When corresponding with Bruker Daltonik GmbH about your instrument be sure to include the model name and the full serial number Write the serial number of the instrument here for reference Serial maxXis User Manual Version 1 1 Manual part number 257874 Bruker Daltonik GmbH Technical Support If you encounter problems with your system please contact a Bruker representative in your area Or Bruker Daltonik GmbH Fahrenheitstr 4 28359 Bremen Germany Tel 49 421 2205 450 Fax 49 421 2205 370 E mail esi support bdal de E mail software support esi sw support bdal de Inter
123. uum system including the rough pump and complete electronics Included with the maXis there is the data system PC and a syringe pump for both low flow and high flow direct infusion work The PC incorporates a fast digitizer for data acquisition The Compass software includes micrOTOFcontrol for instrument control and data acquisition DataAnalysis for data post processing and HyStar which provides full automation of LC MS workflow The maXis is a time of flight instrument used in combination with LC MS MS applications Sample delivery to the source is generally either by a syringe pump or HPLC system Figure 2 2 and Figure 2 4 If the mass spectrometer runs in combination with an offline nanospray source section 2 8 1 7 no external sample delivery device is required as the solved sample is manually placed into a specific position in the source The HPLC may contain a column to perform a pre separation of sample compounds before they enter the mass spectrometer This combination of HPLC and MS allows for the detection of masses in a complex matrix LC MS can be used for analytes that do not have chromophores and is considered a highly selective and sensitive technique Figure 2 2 shows the mass spectrometer with its atmospheric pressure interface API and the Liquid Chromatographic System The PC the rough pump and the syringe pump are not shown here HPLC High Performance Liquid Chromatography
124. w Instrument Tune gt TOF Tab 6 34 65 Pateni ee aa cs as ce sare see ee ase 6 35 Ile LE EE 7 1 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Table of Changes Version Date Changes 1 0 2008 07 15 maxXis User Manual 1 1 2008 12 05 Adapted to upgrade in micrOTOF control maxXis User Manual Version 1 1 Remarks First Edition Bruker Daltonik GmbH General 1 GENERAL This manual provides an overview of the Bruker maXis system components and how they work together This section deals with general topics mentioned throughout the manual CONTENTS Subject Page Number E WEE a OR VENMONS EE 1 1 t2 Site Preparation SPECICATION EE 1 2 ko EE 1 3 1 3 1 Safely SVMB S EE 1 3 13 2 Operating Precautions EE 1 4 1 3 3 SAE EE 1 5 1 3 4 Environmental Conditions ccccccsecccsesceceeseeceeeeeceeeseusessegeessuseessueeeseneessaes 1 6 1 4 Facility and Electrical Heourements 1 7 1 5 Unpacking Installation and First Gen 1 8 1 1 Text Conventions Throughout this manual special fonts are used to differentiate instructions commands and button names from normal descriptive text Menu Options and Module names are printed in bold Buttons you click with the mouse are highlighted in quotation marks Group boxes are highlighted in apostrophes Filenames are displayed in italic sans serif fonts micrOTOFcontrol commands are written in courier font Special keyboard keys are printed in bold courier font and w
125. water are most common but other mixtures can be used with success Acetonitrile water isopropyl alcohol water and n propyl alcohol water are good starting mixtures for negative ionization APl electrospray sensitivity is best with either acetonitrile or methanol and water Typically the pH of the mobile phase is adjusted in order to cause the highest yield of ionization in the solution phase Partial list of solvents and their suitability for ESI Commonly used Special cases Water lt 80 Benzenet MethanolCarbon disulfidet EthanolCarbon tetrachloride n Propyl alcoholCyclohexane Isopropyl alcoholHexanet t Butyl alcoholLigroin AcetonitrileMethylene chloride AcetoneToluene 2 Tetrahydrofuran Acetic acid Formic acid Chloroform Formamide 1 Requires modifier Normal phase chromatography 3 10 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Understanding API and APCI Electrospray 3 2 2 6 Buffers Buffers are used for many reasons including e Adjusting solution pH to support ion formation in solution generally positive analyte ions are formed more readily in acidic solutions and negative analyte ions are formed more readily in basic solutions e Ensure formation of specific desired adduct ions or prevent the formation of undesirable adducts e Assist or optimize chromatography If you are using chromatographic separation some consideration must be given to why a buffer is added Buffers that assist or
126. y 150D Ene Aca Fe J SILE Alternate Collision Energy 322 00 10 00 50 0 1 Fragmentation Tune Collision Energy 1522 00 15 00 70 0 ZE Strategy Fragments D Collision Cooler Number 3 D Hange from 0 0 ey to 200 0 e Import d New Delete Delete All Up Down Set Values Parameter Polarity Group Description GUI Unit Typic Max I M P Tune Collision Energy Number Range from Range to 6 28 maXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 4 2 8 Expert View MS MS TabsISCID 2 Mode fo Source Fat MS MS E Sample Infa jk Chromatogram cl Calibration TOF aie Instrument Tune E Auto MS MS pe Preference Scan Mode SILE TC MS MS MS ISCID MS Settings Calis neler ISCID rio Energy DI ei MS MS ISCID Settings ISCID Ened FO el Set Values Parameter Polarity Group Description GUI Unit Typic Min Max P MS Settings ISCID Energy eV MS MS Settings ISCID Settings ISCID Energy eV maxXis User Manual Version 1 1 6 29 Appendix Bruker Daltonik GmbH 6 4 2 9 Expert View MS MS Tab gt Collision Cooler E Mode fo Source Zi MS MS ae Sample Info all Chromatogram cd Calibration TOF she Instrument Tune ei SH Bens Collision Sweeping Preference i en Acquisition Active SILE Mode lon Cooler RFA Collision Energy Ss Fragmentation eee Start End Start End 400 0 Yop z000 Yop 100 2
127. y waste Conclusion e constant flow irrespective of valve position e loop must be filled during runtime of the LC analysis e filling time of loop should be optimized with flow rate of syringe e calibration is undertaken by post processing software this is not a feature of micrOTOF control 6 8 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Appendix 6 3 3 Example 3 Sample flow through the divert valve without loop port 3 from HPLC e port 4 to nebulizer Ka be E rd port 5 calibrant from syringe pump es sy v port 6 to waste Figure 6 4 Sample flow through the divert valve without loop Divert valve in source position e green HPLC to yellow nebulizer e blue calibrant via loop to gray waste Divert valve in waste position e green HPLC is connected to grey waste gt HPLC flow is not connected to source this is useful for flushing HPLC or column e blue calibrant is connected to yellow nebulizer Conclusion e no constant flow flow rate is dependent on valve position HPLC flow lt gt syringe flow e calibration can be done in micrOTOF control software or in post processing software e valve can be used for switching HPLC flow directly to waste e syringe pump can be used for infusions maxis User Manual Version 1 1 6 9 Appendix Bruker Daltonik GmbH 6 4 Values and Ranges in micrOTOF control Although there are three modes in which settings for maXi
128. ystem may contain a column to perform a pre separation of sample compounds before they enter the mass spectrometer 2 6 maxXis User Manual Version 1 1 Bruker Daltonik GmbH Identifying System Components solvent cabmet re a el Bega degasser En am binary pump em pe waere geg control module a ee E EE il autosampler gess column compartment UW detector Figure 2 3 Agilent HPLC 1100 series System 2 2 2 Syringe pump A small syringe pump see Figure 2 4 is included with the maXis system to facilitate the introduction of samples directly into either the electrospray or APCI ion sources The syringe pump is supplied with a 250 ul syringe Smaller and larger syringes can also be used maxXis User Manual Version 1 1 2 7 Identifying System Components Bruker Daltonik GmbH d a Figure 2 4 Syringe pump coupled to the Apollo source When used with electrospray ionization two modes of operation are available Either the syringe pump can deliver the sample in solution directly to the nebulizer under low flow conditions typically 1 ul min 10 ul min or it can supply a small flow that is tee d into the flow from an LC system This combined operation is particularly convenient for the optimization of instrument parameters and the development of MS MS methods The syringe pump LC delivery approach is recommended for APCl This is because the APCI ion source is designed for a minimu

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