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User Guide: SelexION Technology for 5500 and 6500

1. e Create an acquisition method optimizing the compound parameters source parameters and the LC flow rate first and then optimizing the DMS parameters This section describes the second method of optimizing the DMS parameters The first method is a subset of the second method described in this section Optimize DMS Parameters in Manual Tuning This section describes how to e Create an acquisition method in the Manual Tuning mode and optimize DMS parameters without a modifier e Purge the modifier e Create an acquisition method and optimize DMS parameters in the Manual Tuning mode with a modifier selected Analyst 1 6 3 Software User Guide 26 of 77 RUO IDV 05 0275 C Optimize DMS Parameters Note To acquire data using a modifier create the acquisition method and then optimize the DMS parameters with the modifier selected in the method The DMS parameters Separation Voltage SV Compensation Voltage COV and DMS Offset DMO are affected by the choice of a modifier Therefore adding or changing the modifier or the modifier concentration after optimizing the SV COV and DMO parameters will require a re optimization of these parameters Prerequisites e TheSelexlON orSelexION technology is installed on the mass spectrometer and the controller module is turned on Note Before turning the controller module on or off to temporarily add the SelexION technology to or remove it from the system first deactivate t
2. ssscssscscssccscsesecscceieeieeeseeaseesieeeseaseassassseasseseeeeseeees 26 Create an Acquisition Method and Optimize DMS Parameters without a Mod ifiets ii3 02 a rieniec had a a a a whuhthehahaldadindawaidaied aiacuiinedhkanieanh 27 Create an Acquisition Method with a Modifier Selected and Optimize DMS ParaMmeters s ste itah ach eatneasinasishea then S ahah ahalhs aiehairs E iat aia iain tate 32 Real Time Modifier Parameters Comtrol ccssssssscssssssscsesssssssscsssssssscsesssssscsesssssscsesesacssscsesesausssccasasanecsesasasessesaeasess 35 Puitge the Modifiers i2 a tak aiahatatiadasaieinda dh eeataea de wae ea dale Maka deeaiaunueednn eens 35 Optimize DMS Parameters using Compound Optimization ccscsseseeesseseeeeeeeeeeeeseeseseeseeeeseees 39 Optimize DMS Parameters Only with T Infusion Optimization Type c ccssssesesssssssscssssssssessssssssessesstesssssassssens 39 Optimize Compound and DMS Parameters with T Infusion Optimization Typ ccssscscssssssesssssescssssssseseseassesens 42 Optimize COV Through Flow Injection FIA sssssssssesecesscceesceeeeeeeeeasssesassasasseassaesasieaseeeesees 45 instrument Optimization sirain rn anisa aiie tiisdei aade Ate ctedanecth adadini adnia aiad 47 Chapter 4 Create and Submit BatchesS sssssssuunsenrnunreunnnnunnnuunnnnunnununnunnnnunnnnnnnnnnnnennnnnnnnnunnenunnn unnan nnna 48 Create an Acquisition Method with Fixed DMS Parameters in Acquire Mode sssssessessss
3. or SelexlON Technology on page 19 2 Using the small slotted screwdriver loosen the adjustment screws until the electrodes move freely in the ion mobility cell and then remove the electrodes from the ion mobility cell User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 21 of 77 Using the SelexION Technology Figure 2 8 SelexION lon Mobility Cell Spacer tool Used to align the electrodes a E Note If the adjustment screws are completely removed from the ion mobility cell make sure that the bowed washers are replaced in the original orientation 3 Clean the surfaces of the electrode using a lint free wipe dampened with the methanol water solution Tip If cleaning with water and methanol does not improve performance clean the electrodes with a non abrasive detergent such as Alconox If this does not improve performance lightly scrub the flat surfaces with 600 sandpaper 4 Allow the electrodes to dry 5 Move the spacer tool through the gap in the front of the electrodes and then using the small slotted screwdriver align the electrodes in the ion mobility cell so that the spacer tool is centered in the ion mobility cell Make sure that the spacer tools fits between the electrodes and then adjust the screws on each side of the ion mobility cell to center the electrodes 6 Tighten the adjustment screws to secure the electrodes 7 Position the SelexION ion mobility cell on the SelexlON orifice plate and
4. 1 6 3 Software RUO IDV 05 0275 C 17 of 77 Using the SelexION Technology Figure 2 6 lon Mobility Cell Installation Description lon mobility cell Vacuum interface with the ring installed Installation of the ion mobility cell Correct position vertical Incorrect position angled 10 Tighten the thumbscrews evenly applying constant pressure Note Do not loosen the nuts on the pins close to the thumbscrews 11 Align the pins of the SelexION curtain plate with the holes in the ion mobility cell and then press the SelexION curtain plate onto the ion mobility cell Analyst 1 6 3 Software User Guide 18 of 77 RUO IDV 05 0275 C Using the SelexION Technology 12 Make sure that the two source latches on the ion source are pointing upwards in the 12 o clock open position 13 Position the ion source on the adapter ring Make sure that the guide pins on the ion source fit into the receptacles in the adapter ring push the ion source toward the interface until it is fully seated and then rotate the source latches downward to the 6 30 locked position to lock the ion source in place Refer to Figure 2 3 on page 15 14 Turn on the power to the controller module The power switch is located on the back of the controller module WARNING Toxic Chemical Hazard Take care when filling or re filling modifier bottles Refer to chemical product Safety Data Sheets and take appropriate safety precautions Do not refill th
5. Filesi ticnsnan hac ohta mara cain dn death dh nan deiiaincamnmaiiawnmammmmedediddis 58 Create Quantitation Methods and Generate Results Tables c ccessesseesseteseeeeeeeeeeeceeaeseeteneeateteneaeasaneteneaeaeeneees 59 Quantify Isobaric COMPOUNAS c csscscssssssssssssscsecscssscscssssssescsesscsescsusscassssceecassseseueasassuscsecasacesseessasessosseasarecsesasaressons 59 Report Data 2tcsnde ade Lad aden aga saga Sas ana ane a a sone ain eae nana saan 59 Analyze Qualitative Dala rnani nan ses chev cits en R RAA EA ARAR 59 Review a Data File Acquired with the Ramped COV Parametel cccccccscsssssssssssssssscssesscsceeseeseeseeseeeceersreeeeeeeeeterensees 59 Show a Contour Plot for Data Acquired with the Ramped COV Parameter Ramp GOV for Cycle Option Only icc sheenhauhsbookakscgkankads aunannniwawunenennsawabannnals 61 View Ramped DMS Parameters in File Information While Viewing Data Files c c cccssssssessssssesssssssssesessseseesees 63 Chapter 6 Use DMS Parameters in IDA ssecceseceeeteeeeeeeeeeeeeeeneeee ences seneeeeesaaesseseeeeeeneesesaeeeeeeesensaeeeneees 64 Create an IDA Acquisition Method to Ramp COV During Batch Acquisition c ccsssssceceseeeeeseeeeseeeseeees 64 Create an IDA Acquisition Method to Ramp COV During the Batch Acquisition Mode iisccissiviivet ah tilehiat ahiediudinai E iar iia ia tin iti SE EAE danny 65 View the IDA Data Acquired with Ramped COV Parameter in the IDA ExplOrel ccccsccs
6. If the duration is not changed a tuning method with a mass spectrometer scan duration that is shorter than the Shimadzu time program duration cannot be stopped with the Analyst software when the mass spectrometer has finished scanning The run can only be stopped with the Run key on the Shimadzu CBM Prerequisites Before starting T Infusion optimization create an acquisition method that will be used as the starter acquisition method for T Infusion optimization This method should include the following An isocratic LC method optional if an external isocratic LC pump is being used A syringe pump method optional if an external syringe pump is being used An MRM or Q1 MI scan type Optimized Source Gas parameters Optimized DMS temperature parameter with default SV COV and DMO values Modifier type and flow may or may not be specified If an AAO driver or an integrated Shimadzu driver is used as LC pump set the LC duration long enough for acquisition The Analyst software cannot modify the LC time Maximum number of compounds is 20 Optimize DMS Parameters Only with T Infusion Optimization Type Use this procedure to automatically optimize the SV COV and DMO parameters using T Infusion User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 39 of 77 Optimize DMS Parameters 1 Make sure a hardware profile is active If the starter method contains a syringe pump method or an LC pump method the hardware profile must
7. Mass Spec icon on the status bar 9 For the selected modifier and the MDC value tune the SV COV and DMO parameters as described in Create an Acquisition Method and Optimize DMS Parameters without a Modifier on page 27 until the signal and separation are satisfactory Note For each change in modifier type or concentration allow the system to equilibrate for at least 30 min before optimizing the DMS parameters To test a different modifier concentration High or Low of the same modifier selected in step 6 select a different MDC value Low or High and then re optimize the SV COV and DMO parameters as described in Create an Acquisition Method and Optimize DMS Parameters without a Modifier on page 27 Analyst 1 6 3 Software User Guide 34 of 77 RUO IDV 05 0275 C Optimize DMS Parameters To use a different modifier do the following a Purge the modifier line Refer to Purge the Modifier on page 35 b Select a different modifier in the acquisition method and then specify the MDC value for the new modifier c Re optimize the SV COV and DMO parameters as described in Create an Acquisition Method and Optimize DMS Parameters without a Modifier on page 27 10 If needed optimize the DR parameter as described in Create an Acquisition Method and Optimize DMS Parameters without a Modifier on page 27 11 Save the acquisition method Real Time Modifier Parameters Control If data is acquired in Manual Tuning using the acquisition
8. compounds might optimize even higher than 30 volts In the presence of a modifier we recommend using at least 60 volts to 20 volts COV range because the negative COV shifts can be very large for some compounds 11 Select the check box in the Optimize column for COV The Total of Injections and Total Sample Volume fields update automatically The Mass Spec Duration field shows the duration from the starter method selected in 2 12 Click Finish to begin the optimization process The Analyst software runs the specified values of source and compound dependent parameters including COV and selects the value with the highest response to get the best signal for the compounds of interest As the software proceeds through the optimization it creates a FIA optimization report The FIA optimization report will report the optimal COV for the SV specified in the starter method for each compound 13 The software generates a final optimized FIA acquisition method called _DMS dam You can open this method and save it using a simpler name Analyst 1 6 3 Software User Guide 46 of 77 RUO IDV 05 0275 C Optimize DMS Parameters To optimize COV at a different SV value modify the starter method and then run FIA optimization again Instrument Optimization Instrument optimization with the SelexION or SelexION technology installed should only be used for troubleshooting or correcting minor resolution or calibration issues For full inst
9. density and molecular weight of the selected modifier and the Curtain Gas flow rate to calculate the modifier pump flow rate and then apply that flow rate automatically to the pump flow rate The density of a custom modifier The Analyst software uses this density along with the Modifier MW and the Curtain Gas flow rate to determine the modifier pump flow rate Medium 225 C High 300 C Default None 2 propanol Acetonitrile Methanol Acetone Custom Off 0 Default Low 1 5 or higher High 3 0 Specify the density in g mL for the modifier Analyst 1 6 3 Software 71 of 77 DMS Parameters Parameter Name Modifier MW MDW Separation Voltage SV Compensation Voltage COV Analyst 1 6 3 Software 72 of 77 The molecular weight in g mol of a custom Specify the molecular weight modifier The Analyst software uses the value g mol of the modifier of this parameter along with the Modifier Density and the Curtain Gas flow rate to determine the modifier pump flow rate The peak to peak amplitude of the separation Specify the Separation Voltage voltage waveform to be applied e Default 0 0 e Range 0 to the maximum SV value based on the DT and TEM parameters in each method A DC offset potential between the two Specify the Compensation electrodes of the mobility device For example Voltage to be applied if COV is 5 volts then one of the two electrodes e De
10. 3 Software RUO IDV 05 0275 C 63 of 77 Use DMS Parameters in IDA 6 This section describes how to e Create an Information Dependent Acquisition IDA method to ramp Compensation Voltage COV during batch acquisition mode e View the IDA data acquired with ramped COV in the IDA Explorer Prerequisites The SelexION or SelexION technology is installed on the instrument and the controller module is turned on Use the IDA acquisition method to create and submit batches to acquire data Refer to the IDA Tutorial System User Guide for the mass spectrometer or the Analyst software Advanced User Guide Create an IDA Acquisition Method to Ramp COV During Batch Acquisition Instead of using liquid chromatography LC for analysis of samples use the SelexION or SelexION technology with infusion to separate the compounds of interest and filter out the chemical noise or interference With the SelexION or SelexION technology the ramping COV feature of the Analyst software can be used to mimic the LC gradient In addition to the Manual Tuning mode the COV parameter can also be ramped during batch acquisition by selecting the Ramp COV check box in an acquisition method in the Acquisition Method editor The COV parameter is treated as a cycle dependant parameter The ramping COV functionality works for a single period DMS acquisition method The IDA Dynamic Fill Time DFT and Scheduled MRM algorithm methods withou
11. SCIEX Analyst 1 6 3 Software SelexION Technology tor 5500 and 6500 Series Systems and SelexlION Technology for 6500 Series Systems User Guide RUO IDV 05 0275 C July 2015 This document is provided to customers who have purchased SCIEX equipment to use in the operation of such SCIEX equipment This document is copyright protected and any reproduction of this document or any part of this document is strictly prohibited except as SCIEX may authorize in writing Software that may be described in this document is furnished under a license agreement It is against the law to copy modify or distribute the software on any medium except as specifically allowed in the license agreement Furthermore the license agreement may prohibit the software from being disassembled reverse engineered or decompiled for any purpose Warranties are as stated therein Portions of this document may make reference to other manufacturers and or their products which may contain parts whose names are registered as trademarks and or function as trademarks of their respective owners Any such use is intended only to designate those manufacturers products as supplied by SCIEX for incorporation into its equipment and does not imply any right and or license to use or permit others to use such manufacturers and or their product names as trademarks SCIEX warranties are limited to those express warranties provided at the time of sale or license of its prod
12. Separation Voltage SV from the right click menu Anew column called SV volts is added to the mass ranges table The optimized SV value is also added e Right click in the mass ranges table and then click Compensation Voltage COV A new column called COV volts is added to the mass ranges table The optimized COV value is also added e Right click in the mass ranges table and then click DMS Offset DMO A new column called DMO volts is added to the mass ranges table The optimized DMO value is also added 6 Repeat step 5 for all of the MRM transitions in the acquisition method 7 Click Edit Parameters The Period 1 Experiment 1 parameter Table dialog opens 8 Type the optimized values of the compound parameters on the Compound tab Type the optimized values of the ion source and gas parameters on the Source Gas tab Make sure that the source temperature specified Analyst 1 6 3 Software User Guide 52 of 77 RUO IDV 05 0275 C Create and Submit Batches here is the same value as the one used for optimizing the DMS parameters Refer to the Manual Optimization Tutorial 9 Select the DMS tab and select the required values for the DMS Temperature DT Modifier MD and DMS Resolution Enhancement DR parameters Make sure that the DMS temperature specified here is the same value as the one used for optimizing the DMS parameters 10 Click OK 11 If required provide values for the parameters of the peripheral devices included in the a
13. TUNNO ssiiec deed Alda adie Sale agata ih hegiaGainhamadacmGaiedean aad A 8 DMS Off Operation Modes erennere sblvcvepevoveres avs oszeveuevesseavseseswavevene sever dt soars R E ETRE ETEA 8 Chapter 2 Using the SelexION Technolog 1ccescccceseeeceeeeeeseeseneeeeesseeseneneeeseeessenaeeeeeneeseseaeeeeeeesensaeeeneees 10 Install the SelexION or SelexlON Technology ccccccccscsssssssssssscssscscscecscecscssscesesesecececeseceseceseseseseeseeseeeeeeeeeeeeeeeeeeeenensees 13 Remove the SelexlON or SelexlON Technology cccccccscsssssssssscssscscscscececesecesececeseseseseceseseceseeeseseeeseseseseeeeeeeeeseenenerensnes 19 Clean and Align the Electrodes of the SelexlON lon Mobility Cell cccccscssscsscssssssscsssssssscsssssssssesesesssscsesesarsnseessasens 21 Clean and Align the Electrodes of the SelexlION lon Mobility Cell with Jet Injector Technology ivi aaauiehi aiid dada ndiuniiannad aaah daddanndadandanhadaadaanadaadacdandddades 23 Refill the Modifier Bottle ccssssscsssssssscsssssssssscsssssssscscscsssssesscsssssusssassussusssausssusscasacsusecaeauassueasasaueusscasaueceesasateneeeeees 25 Clean the Controller Module Surfaces c sscssssssssssssssssssssssscsssssssscsessesessscssssssuscsecscsusseusssacaueseecasasaseueasasansssecasaressetasatass 25 Chapter 3 Optimize DMS Parameters cccccsecccescceesseeeeeeeeeeeceeseneeeeeeseeseeeeeeesseeeseseeeeeeneesesnaeeeeeeesenseeeneees 26 Optimize DMS Parameters in Manual TUNING
14. acceptable SV range is large Use the same COV range for ramping and then click Start to evaluate the signal again Data is shown in the panes below the Tune Method Editor Note the maximum signal intensity and COV value at which the maximum signal was achieved 10 Repeat the process of stepping SV and ramping COV and then note the SV value that gives the best signal intensity After the signal intensity starts to decrease stop the process Further fine tune the SV value by repeating the above process with smaller SV steps in the 100 volt to 200 volt range as used above and by ramping COV After the optimal SV and COV pair is determined set the SV and COV parameters to these values in the method Ramp DMO for the Optimized SV and COV Combination 1 Oy eS Click Edit Ramp The Ramp Parameter Settings dialog opens Select DMS Offset in the Parameter field Type 100 in the Start field Type 100 in the Stop field Use the default value in the Step field or type a number and click OK Click Start User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 31 of 77 Optimize DMS Parameters Data is shown in the panes below the Tune Method Editor The allowed range for DMO is 100 volts to 100 volts Create an Acquisition Method with a Modifier Selected and Optimize DMS Parameters Note Modifiers cannot be used with the NanoSpray ion source Users are able to create acquisition methods that include modifier information an
15. also contain a syringe pump or an LC pump respectively Refer to Creating Hardware Profiles and Projects in the Getting Started Guide 2 T infuse the sample into the LC stream Refer to T nfuse Sample into LC Stream on page 76 3 On the Navigation bar under Tune and Calibrate double click Compound Optimization Figure 3 10 Instrument Settings Dialog in a 6500 Series Instrument Instrument Settings Please set the rotumert condition Idee gt Iphasion gt AA Delat Acq Method Rack Code Rack Postion Piste Code Fige Pornon Ingection Yoke O Tir n Deiat Acq Method 4 On the Instruments Settings page in the Inlet group click T Infusion Figure 3 11 Instrument Settings Dialog in a 6500 Series Instrument Instrument Settings Relat Acq Method Rach Code Rack Position Piste Code Pigte Porton Ingection Volume Tirso Delak Acq Method OMS Orly Analyst 1 6 3 Software User Guide 40 of 77 RUO IDV 05 0275 C Optimize DMS Parameters 5 Inthe Default Acq Method field select the acquisition method that will be used as the starter method from the list 6 Make sure that DMS Only check box is selected The Mass Spectrometer option MS Analysis or MS MS Analysis is set based on the scan type in starter acquisition method 7 Click Next Figure 3 12 DMS Options Dialog Set the DMS parameter range The COV wil be ramped at each SV level Use Defautts The DMS Options dialog ope
16. controller module and associated electronics along with a customer installed interface device Figure 2 1 QTRAP 6500 System with the SelexlON Technology Controller module with side tray FSE upgrade 2 lonDrive Turbo V ion source The figure shows the lonDrive Turbo V ion source on a 6500 series sytem The Turbo V is used with the 5500 series of instruments The lonDrive Turbo V is used with the 6500 and 6500 series systems Analyst 1 6 3 Software User Guide 10 of 77 RUO IDV 05 0275 C Using the SelexlION Technology Note The NanoSpray ion source can be installed on a 5500 or 6500 series system equipped with SelexlON technology or a 6500 system equipped with the SelexION technology However modifier use is not available Users can create acquisition methods that include modifier information and flows but when executed the modifier pump will be disabled The SelexION technology for 5500 and 6500 series instruments includes the following components SelexiON controller module e lon mobility cell e Adapter ring Two adapter rings are available the NanoSpray ring used with the NanoSpray ion source and the standard ring used with all other supported ion sources e SelexlON orifice plate e SelexlON curtain plate The SelexiON technology for 6500 series instruments includes the following components e SelexION controller module e lon mobility cell with jet injector technology
17. modifier to calculate the flow rate of the modifier and then applies that flow rate automatically 8 If Custom was selected for the Modifier MD parameter in step 6 then provide the density and molecular weight of the custom modifier as shown in Figure 3 4 so that the software can calculate the flow rate for the modifier for the specified setting Low or High and then apply it User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 33 of 77 Optimize DMS Parameters Figure 3 4 DMS Parameter Settings Source Gas Compound DMS Resolution Detector DMS Temperature Reached DMS Temperature DT Low Modifier MD Custom Modifier Composition MDC Low Modifier Density g mL MDD 0 0000 lt Modifier MW MDW Separation Voltage SV 0 0 Compensation Voltage COV Too DMS Offset DMO ET DMS Resolution Enhancement ott DR Modifier Density g mL MDD Specify the density of the custom modifier The software uses this density along with the Modifier Molecular Weight MDW and the Curtain Gas flow rate value to determine the flow rate of the custom modifier Modifier MW MDW Specify the molecular weight of the custom modifier in g mol The software uses the value of this parameter along with the Modifier Density MDD and the Curtain Gas flow rate value to determine the flow rate of the custom modifier Tip To view the modifier pump flow rate in the Mass Spec Detailed Status dialog double click the
18. typically common chromatography solvents for example isopropanol 2 propanol acetonitrile or methanol affects the mobilities of ions in the device lons entering the mobility cell form clusters with the modifier molecules which alters their mobility characteristics The clusters can form under low electric field conditions but fall apart again under high electric fields which is referred to as the dynamic cluster decluster model The net effect of the cluster formation is that the differences between high and low field mobilities are amplified yielding better separation power and increased peak capacity Moreover since cluster formation itself depends on the specific interaction between an analyte ion and a user selected modifier the use of modifiers offers an additional separation dimension to traditional chromatographic and mass spectrometric approaches Further information on the effects of modifiers can be found in the following journal article B B Schneider T R Covey S L Coy E V Krylov and E G Nazarov Anal Chem 2010 82 1867 1880 Because modifier use involves gas phase ion chemistry certain general behaviors can be expected In positive ion mode if the modifier has a greater proton affinity than the analyte ion the charge may be stripped from the analyte resulting in lower signal but not necessarily lower signal to noise Alternatively if the modifier has greater gas phase acidity than the analyte the negative ion current
19. 275 C 23 of 77 Using the SelexlION Technology Figure 2 9 Adjustment Screw on the SelexlION lon Mobility Cell with Jet Injector Technology Note If the adjustment screws are completely removed from the ion mobility cell make sure that the bowed washers are replaced in the original orientation 3 Clean the surfaces of the electrode using a lint free wipe dampened with the methanol water solution Tip If cleaning with water and methanol does not improve performance clean the electrodes with a non abrasive detergent such as Alconox If this does not improve performance lightly scrub the flat surfaces with 600 sandpaper 4 Allow the electrodes to dry 5 Position the spacer tool between the electrodes and then insert the electrodes into the ion mobility cell from the back Make sure that the bottoms of the electrodes are flush with the cell and then rotate the electrodes until the screw holes in the electrodes are aligned with the screw holes in the cell Analyst 1 6 3 Software User Guide 24 of 77 RUO IDV 05 0275 C Using the SelexION Technology Figure 2 10 Spacer Tool 6 Tighten the adjustment screws to secure the electrodes 7 Position the SelexION ion mobility cell on the SelexION orifice plate and then tighten the thumbscrews Refer to Install the SelexION or SelexION Technology on page 13 Refill the Modifier Bottle WARNING Toxic Chemical Hazard Take care when filling or re filling modifier bot
20. 5 C OMS Offset 0 a Resob sion Exhancemnert open 7 0w Total Scan Time aD hed rehides pauses e Period Summary X n Dey Timer 0 sec M OMS Of Cycles Data is shown in the panes below the Tune Method Editor If the signal obtained for the peak of interest is not satisfactory then change the DT value to either Medium or High and then evaluate the signal again until the best signal is obtained Note For each DT value change let the system equilibrate for at least 30 minutes before optimizing the DMS parameters Modifier MD Make sure that the value of this parameter is None Separation Voltage SV and Compensation Voltage COV The SV and COV are tested together iteratively to find the SV and COV combination that gives the best signal and separation Step SV through 0 to the maximum allowed SV range while ramping COV through the full COV range Refer to Ramp the Separation Voltage and Compensation Voltage on page 31 Note The full COV range is 100 volts to 100 volts However most compounds optimize between 20 volts to 30 volts in the absence of a modifier Some compounds might optimize even higher than 30 volts In the presence of a modifier we recommend using at least 60 volts to 20 volts COV range because the negative COV shifts can be very large for some compounds The maximum SV value is linked to DT and TEM parameters DMS Offset DMO Ramp DMO for the optimized SV and COV combination Refer to R
21. O IDV 05 0275 C Optimize DMS Parameters 2 On the Instruments Settings page in the Inlet section click T Infusion 3 Inthe Default Acq Method field select the acquisition method that will be used as the starter method from the list 4 Click Compound and DMS The Mass Spectrometer options are enabled 5 Click MS Analysis or MS MS Analysis depending on the scan type selected in the default acquisition method 6 Click Next The lons to use in MS MS Analysis dialog opens 7 On the lons to use in MS MS Analysis dialog type the values for all the fields Refer to the Automatic Optimization Tutorial 8 Click Criteria next to the Auto Select option 9 In the Product lon Auto Selection Criteria dialog type the values for all the fields Refer to the Automatic Optimization Tutorial 10 Click OK to save the changes to the selection criteria 11 Click Next 12 In the Target Components dialog type the names of the compounds and their Q1 and Q3 masses Refer to the Automatic Optimization Tutorial 13 Click Next User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 43 of 77 Optimize DMS Parameters Figure 3 13 DMS Options Dialog Set the DMS parameter range The COV wil be ramped at each SV level 300 0 wo 100 The DMS Options dialog opens The default Start Stop and Step values for the SV COV and DMO parameters are shown in the dialog 14 In the DMS Options dialog specify the values to use to
22. Refer to Connect the Tubing and Cables topic in the ion source Operator Guide Analyst 1 6 3 Software User Guide 76 of 77 RUO IDV 05 0275 C Revision History Peo First released version of document May 2013 Updated for 6500 and SelexION technology Rebranded Added warning July 2015 not to remove covers No serviceable parts inside User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 77 of 77
23. Technology DMS is a method of separating ions based on the difference between ion mobility in high and low electric fields in gases at or near atmospheric pressure DMS is a variant of ion mobility spectrometry IMS In DMS technology Separation Voltages SV are applied across the ion transport channel perpendicular to the direction of the transport gas flow as shown in Figure 1 1 Due to the difference between high and low electric field ion mobility coefficients ions migrate toward the walls and leave the flight path Their trajectory is corrected by a counterbalancing DC voltage called Compensation Voltage COV User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 5 of 77 Introduction to DMS Technology Figure 1 1 DMS Technology Description lon species in gas stream Separation Voltage SV Compensation Voltage COV Positive ions To mass spectrometer Negative ions Instead of recording the flight time of an ion through the ion transport channel the DMS technology records the COV required to correct the trajectory of a particular ion for a range of SV amplitudes The COV can be scanned to serially pass ions according to their differential mobility or set to a fixed value to pass only the ion species with a particular differential mobility Certain combinations of SV and COV fields allow the target ion to pass through the SelexION or SelexlON device analytical region without colliding with the electrodes Therefo
24. alizing mode an acquisition method and a batch file are created in the background During the Equilibrating mode the system is equilibrating Analyst 1 6 3 Software User Guide 36 of 77 RUO IDV 05 0275 C Optimize DMS Parameters Figure 3 7 Purge Modifier Dialog p Purge Modifier bo a 0 100 Status Durations Initializing Equilibrating Expected 00 04 00 The status in the Purge Modifier dialog then changes from Initializing Equilibrating to Purging which indicates that the modifier is being cleared from the modifier pump During the modifier purge the mass spectrometer performs a scan and collects data in the API Instrument Data folder After the purge is complete the purge acquisition method batch file and data are automatically deleted During purging the Purge button changes to Abort The expected purge time four minutes and the time elapsed in the purge cycle are shown The Analyst software automatically sets the DMS and source parameters to new values for four minutes expected purge time To view these values refer to Values of DMS and Source Parameters Used During Modifier Purge on page 74 Tip Users can view the status of the modifier purge process in the Mass Spec Detailed Status dialog Double click the Mass Spec icon on the status bar to view this dialog Figure 3 8 Purge Modifier Dialog P Purge Modifier f O ms 100 Status Durations Complete Expected 00 04 00 Purging the modifie
25. ameters Figure 3 1 Default DMS Parameter Settings Source Gas Compound OMS Resolution Detector DMS Temperature Reached DMS Temperature DT Low Modifier MD None Separation Voltage SV Compensation Voltage COV DMS Offset DMO DMS Resolution Enhancement off OR 3 0 0 0 0 3 0 2 Y All of the DMS parameters have default values The Separation Voltage SV and the Compensation Voltage COV are set to zero 6 Optimize the DMS parameters to get the best separation and sensitivity The following parameters must be optimized in the specified order Analyst 1 6 3 Software 28 of 77 User Guide RUO IDV 05 0275 C Optimize DMS Parameters a DMS Temperature DT Click Start to test this parameter with the default value Low For the test use the default values for other DMS parameters SV 0 COV 0 Modifier None or switch to the DMS Off mode by selecting the DMS Off check box on the MSS tab Figure 3 2 Tune Method Editor with Default DMS Parameter Settings in a 6500 Series Instrument Aare Sat ERa MS mehos z Sourceties Compound OMS Rerchtion Oetecsor MS Advanced MS OMS Temperature Reached y F Scheduled MAM Iimpat Lint Seantype MRM MAM OMS Tempersture DT flow QI Mass a OF Mase Ma Timo imsec LJ Mositier MD None Separation Votage SV Compensation Votsge COV T Polssty Postive Negative User Guide RUO IDV 05 027
26. amp DMO for the Optimized SV and COV Combination on page 31 Analyst 1 6 3 Software 29 of 77 Optimize DMS Parameters e DMS Resolution Enhancement DR e 6500 and 6500 series systems For a single compound the Open no throttle gas is being added DR value should be used Other DR values Off Low Medium or High are used when the separation of compounds must be improved For example when two compounds have close COV and need to be baseline separated test the Off Low Medium or High DR values to get the best separation Select the required value Off Low Medium or High for the DR parameter and then click Start to ramp COV at a particular SV value to evaluate the signal and separation of the compounds Test the different DR values until you are satisfied with the separation of the compounds e 5500 series systems For a single compound the Off no throttle gas is being added DR value should be used Other DR values Low Medium or High are used when the separation of compounds needs to be improved Note For 6500 and 6500 series systems when the value of DR is set to Off Low Medium or High gas flow is enabled between the SelexION or SelexiON device exit and the orifice inlet into the mass spectrometer which improves the resolution of the device For 5500 series systems DR value of Low Medium or High enables the gas flow between the SelexlON device exit and the Orifice inlet into the mass spectrometer Table 3 1
27. ault duration for Shimadzu methods is 90 minutes When tuning with a mass spectrometer scan duration shorter than the Shimadzu time program duration as in the default tune method you will not be able to stop the tune run using the software after the mass spectrometer has finished scanning Press Run on the controller to stop the run or change the default Shimadzu run duration to match the MS duration in the Shimadzu method editor User Guide RUO IDV 05 0275 C DMS Parameters DMS Parameter Descriptions The temperature applied on the ceramic heater Default Low 150 C Parameter Name DMS Temperature DT Modifier MD Modifier Composition MDC Modifier Density g mL MDD User Guide RUO IDV 05 0275 C that is mounted in the back of the curtain plate heat exchanger For each DT value change allow the system to equilibrate for at least 10 minutes to 15 minutes before optimizing any DMS parameters When the new temperature is reached DMS Temperature reached is shown above the DT field A chemical that is added into the Curtain Gas flow to help improve the separation of ions If the MD value is set to None the MDC MDD and MDW parameters are not available If the MD value is set to a value other than None the MDC parameter becomes available If MD is set to Custom the MDC MDD and MDW parameters become available The parameter that controls the modifier concentration The Analyst software uses the
28. be used to create reports Analyze Qualitative Data Review a Data File Acquired with the Ramped COV Parameter 1 Open the project folder containing the acquired data 2 On the Navigation bar under Explore double click Open Data File The Select Sample dialog opens 3 From the Data Files list select the wiff file containing the acquired data User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 59 of 77 Analyze and Process Data 4 If required in the Samples list click a sample and then click OK Figure 5 1 XIC The XIC for the selected data file opens The x axis displays the COV in volts and the y axis displays the intensity in cps The XIC for each compound is displayed in a different color 5 Select a COV range in the XIC right click and then select Show Spectrum Figure 5 2 Spectrum The spectrum for the selected COV range is shown under the XIC with intensity on the y axis and Q1 Q3 masses in Da on the X axis It shows the intensity of all the compounds that appear in the ion mobility cell or the ion Analyst 1 6 3 Software User Guide 60 of 77 RUO IDV 05 0275 C Analyze and Process Data mobility cell with jet injector technology in the selected COV range The selected COV range is shown in the title of the open spectrum Show a Contour Plot for Data Acquired with the Ramped COV Parameter Ramp COV for Cycle Option Only The Analyst software can show a contour plot for the data that is acquired usi
29. can be recovered by removing and re seating the ion source or by turning both the mass spectrometer and controller module off and then on and then reactivating the hardware profile 4 Turn the two source latches upward to the 12 o clock position to release the ion source 5 Pull the ion source gently away from the vacuum interface 6 Remove the curtain plate by pulling it straight off the vacuum interface It is held in place by three retaining ball catches mounted on the orifice plate 7 Position the adapter ring on the vacuum interface housing aligning the connector on the ring with the source connector on the vacuum interface and fitting the two thumbscrews on the adapter ring into the receptacles in the vacuum interface Make sure that the source connector is fully seated and that there are no gaps between the adapter ring and the vacuum interface Note The adapter ring is equipped with a locator pin on the bottom that presses down onto a spring loaded plate in the dual drain housing Position the locator pin on the dual drain housing tilt the adapter ring away from the mass spectrometer then tilt the top of adapter ring towards the mass spectrometer If the adapter ring equipped with a latch item 8 is being installed then proceed directly to step 8 Analyst 1 6 3 Software User Guide 14 of 77 RUO IDV 05 0275 C Using the SelexION Technology Figure 2 3 Adapter Ring and Dual Drain Description Standard adapter ring Rece
30. ch between single graph and multiple graph displays e To view the active graph only click Show only active graph e To return to multi graph view click Show all the graphs Analyst 1 6 3 Software User Guide 68 of 77 RUO IDV 05 0275 C Use DMS Parameters in IDA e To view all the graphs in Explorer click Export all the graphs to Explorer Figure 6 5 Buttons in IDA Explorer WW Le REA sii 5 Bay Mass Window Da 5 000 TIC of MRM 7 pairs Exp 1 from Sample 1 IDA 2705 17 78 2 5e5 35 30 25 20 15 10 COW Volts A a TD D T A Bi eet G D A a a sl ee E Show all the graphs Show only active graph Export all the graphs to Explorer User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 69 of 77 Troubleshooti An error message reports that a discharge has been detected in the ion mobility cell or the ion mobility cell with jet injection technology during sample acquisition or equilibration When the SelexION controller module is turned on or off the Mass Spectrometer icon in the Analyst software turns and remains red When running FIA Compound Optimization using the Shimadzu LC System the optimization process appears to have stalled Analyst 1 6 3 Software 70 of 77 ng 7 Corrective Action Lower the SV by 100 volts and then re optimize the DMS parameters When a discharge is detected in the ion mobility cell or the ion mobility cell with jet injector technology during samp
31. ctive hardware profile and then save the acquisition method Ina Scheduled MRM algorithm acquisition method the pause time between mass ranges is tied to the DMS Resolution Enhancement DR value but users can use their preferred value However the use of pause time between mass ranges lower than the default value 20 ms set by the software results in signal loss Create an Acquisition Method to Ramp COV during Batch Acquisition For analysis of samples by infusion for example metabolism using surface sampling techniques the SelexION or SelexION technology can be used for separation of compounds instead of liquid chromatography LC and the ramping Compensation Voltage COV feature can be used to mimic the LC gradient In addition to the Manual Tuning mode the COV parameter can also be ramped during batch acquisition by selecting the Ramp COV check box in the acquisition method in the Acquisition Method editor The COV parameter is treated as a cycle dependant parameter The ramping COV functionality works for a single period DMS acquisition method Use this procedure when the values or acceptable default values for all of the DMS parameters except the COV parameter have been optimized 1 Activate a hardware profile Refer to Create Hardware Profiles and Projects in the Analyst software Getting Started Guide or the System User Guide for the system 2 On the Navigation bar under Acquire double click Build Acquisition Met
32. d flows but when executed the modifier pump will be disabled If the compounds of interest did not get adequately separated in the DMS mode a modifier can be introduced to help separate these compounds A modifier is a chemical that is added into the Curtain Gas flow to help improve the separation of compounds Select a modifier and optimize the DMS parameters in Manual Tuning mode and then create an acquisition method to save the optimized parameter settings Before selecting a modifier for the first time or when changing the modifier purge the modifier line Refer to Purge the Modifier on page 35 Prerequisites e There is sufficient modifier in the modifier bottle for acquisition For more information about calculating modifier consumption refer to Calculate the Appropriate Modifier Consumption for a Batch e To refill the modifier bottle refer to Refill the Modifier Bottle on page 25 1 T infuse the sample into the LC stream T Infuse Sample into LC Stream on page 76 2 On the Navigation bar under Tune and Calibrate double click Manual Tuning 3 Select a scan type and then type the mass ranges transitions scan speed and other required information Optimize the compound and source parameters Then optimize the LC flow rate according to your chromatographic method setup Refer to the Manual Optimization Tutorial Tip As a starting point an existing acquisition method that has been optimized for the compound to be anal
33. dow Figure 1 2 DMS Off Check Box in the Tune Method Editor MS Advanced MS Impost List Scantype 01 Multiple lons Q1 MI on mass a Time msec sa Polarity Positive Negative Total Scan Time includes pauses sec Period Summary Duration 0 000 min Delay Time 0 sec Nl cra TI lm th A yA ts ll A nn hrm A REEI Oe a a a a ks we Ae ka In the DMS Off operation mode the following changes occur Analyst 1 6 3 Software User Guide 8 of 77 RUO IDV 05 0275 C Introduction to DMS Technology e Most of the DMS parameters are no longer available Refer to State of DMS Parameters in the DMS Off Mode on page 74 Only the DMS Temperature DT parameter is visible in the DMS Off mode and it can be optimized in this mode to obtain the best sensitivity e The DMS parameters SV COV and DMO are removed from the parameter list in the Ramp Parameter Settings dialog e The default pause time between mass ranges becomes 5 ms User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 9 of 77 Using the SelexlON Technology 2 WARNING Electrical Shock Hazard Do not remove the cover or attempt to service the controller module It contains no serviceable parts The SelexlON differential mobility separation technology device for 5500 and 6500 series instruments or the SelexION differential mobility separation technology for 6500 series instruments includes a Field Service Employee FSE installed
34. e Adapter ring Two adapter rings are available the NanoSpray ring used with the NanoSpray ion source and the standard ring used with all other supported ion sources SelexlON orifice plate e SelexlON curtain plate User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 11 of 77 Using the SelexlION Technology Figure 2 2 SelexION Technology for 6500 Series Systems 1 Vacuum interface housing FSE upgrade 2 Dual drain assembly FSE upgrade lon mobility cell Customer installable 5 Adapter ring Customer installable SelexION orifice plate FSE upgrade o 6o SelexION curtain plate Customer installable Analyst 1 6 3 Software User Guide 12 of 77 RUO IDV 05 0275 C Using the SelexION Technology Install the SelexION or SelexION Technology WARNING Hot Surface Hazard Let the ion source and vacuum interface cool for at least 30 minutes before starting any maintenance procedures Some surfaces of the vacuum interface and the ion source become hot during operation With the lonDrive Turbo V ion source let the ion source cool for at least 90 minutes CAUTION Potential System Damage Handle vacuum interface components with care They are very fragile and expensive CAUTION Potential System Damage Make sure that vacuum interface components are kept clean and free of chemical or dust contamination To prevent contamination always wear powder free gloves when handling these components Follow these steps to
35. e dialog opens 13 Type the optimized values for the compound parameters on the Compound tab Type the optimized values for the ion source and gas parameters on the Source Gas tab Make sure that the source temperature specified here is same as the one used for optimizing the DMS parameters Refer to the Manual Optimization Tutorial 14 Select the DMS tab and then select the required values for the DMS Temperature DT Modifier MD and DMS Resolution Enhancement DR parameters Make sure that the DMS temperature specified here is same as the one used for optimizing the DMS parameters User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 49 of 77 Create and Submit Batches Figure 4 1 Period 1 Experiment 1 Parameter Table dialog Period 1 Experiment 1 Parameter Table Source Gas Compound DMS Temperature DT Modifier MD DMS Resolution Enhancement Open X DR Apply the following parameters to all other experiments of the same polanty l Source Gas l Compound Cancel Help 15 Click OK 16 If required provide values for the parameters of the peripheral devices included in the active hardware profile 17 Save the acquisition method The pause time between mass ranges is tied to the DMS Resolution Enhancement DR value but users can use their preferred value However the use of pause time between mass ranges lower than the default value 20 ms set by the software may result in signal loss Note To optimi
36. e is shown below the contour plot window It shows the intensity y axis of all m z values x axis in the selected COV range The selected COV range is shown in the title of the open spectrum Analyst 1 6 3 Software 62 of 77 RUO IDV 05 0275 C Analyze and Process Data View Ramped DMS Parameters in File Information While Viewing Data Files The experimental conditions used to collect data are stored in the data file along with the results Users can see the ramped DMS parameters that were used to acquire samples in File Information of the data files Ds On the Navigation bar under Explore double click Open Data File The Select Sample dialog opens 2 In the Data Files pane select the wiff file to view 3 In the Samples pane select the sample to view and then click OK The XIC for the selected sample opens 4 To view the file information click the Show File Info icon on the toolbar The File information pane opens below the TIC 5 Click Period 1 in the left pane of the File Information pane The start stop and step values used for the ramped COV parameter are displayed along with other information in the right pane of the File Information pane Select the required period and experiment in the left pane to see the various experimental settings used in the acquisition method that were used to collect the data All of the DMS parameters used during the sample acquisition are recorded there too User Guide Analyst 1 6
37. e is shown in the Purge Modifier dialog Figure 3 9 Purge Modifier Dialog P Purge Modifier o a 0 100 Status Durations Queue Busy Expected 00 00 00 If the Purge button is clicked then a message is shown indicating that the acquisition is currently in progress For the purge to continue complete or cancel the acquisition process and then make sure that no samples are waiting in the queue Modifier Purge Status The system is ready to start the Purge process Initializing Equilibrating An acquisition method and batch files are created during Initializing mode The system is equilibrated during Equilibrating mode Modifier purge is in progress Analyst 1 6 3 Software User Guide 38 of 77 RUO IDV 05 0275 C Optimize DMS Parameters Optimize DMS Parameters using Compound Optimization The T infusion optimization type in the Compound Optimization mode allows users to automatically optimize the following e DMS Parameters SV COV and DMO e Compound and DMS Parameters SV COV and DMO Use the FIA optimization type to optimize only the COV parameter for a specified SV for the SelexION or SelexlON technology It can also be used to optimize the source and compound dependent parameters Note The default duration for Shimadzu LC methods is 90 minutes If a Shimadzu LC system is being used for FIA compound optimization use the Method Editor to change this time in the Time Program for the Shimadzu LC system
38. e modifier bottle while it is in the side tray Disconnect the fluid line from the bottle refill the bottle in a safe location then reinstall the bottle and fluid line in the side tray 15 If SelexION or SelexION experiments using modifiers will be run then purge the modifier pump Refer to Purge the Modifier on page 35 Remove the SelexION or SelexiION Technology Follow these steps to e Remove the SelexlON curtain plate e Remove the adapter ring e Remove the SelexION ion mobility cell or the SelexION ion mobility cell with jet injector technology e Install the standard curtain plate This procedure restores the 5500 6500 or 6500 series system to standard performance Required Materials e Powder free gloves nitrile or neoprene recommended WARNING Hot Surface Hazard Let the ion source and vacuum interface cool for at least 30 minutes before starting any maintenance procedures Some surfaces of the vacuum interface and the ion source become hot during operation With the lonDrive Turbo V ion source let the ion source cool for at least 90 minutes CAUTION Potential System Damage Handle vacuum interface components with care They are very fragile and expensive User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 19 of 77 Using the SelexION Technology CAUTION Potential System Damage Make sure that vacuum interface components are kept clean and free of chemical or dust contamination To prev
39. ent contamination always wear powder free gloves when handling these components 1 Complete any ongoing scans or click Acquire gt Abort Sample 2 Shut off the sample flow to the mass spectrometer 3 Deactivate the active hardware profile Note Failure to deactivate the active hardware profile before turning the controller module on or off to temporarily add or remove the SelexION or SelexION technology to or from the system may cause the mass spectrometer to enter an unstable state resulting in loss of control from within the Analyst software If the hardware profile is not deactivated and the mass spectrometer enters this unstable state control can be recovered by removing and re seating the ion source or by turning both the mass spectrometer and controller module off and then on and then reactivating the hardware profile 4 Turn off the power to the controller module The power switch is located on the back of the controller module 5 Remove the adapter ring by loosening the thumbscrews and then pulling the adapter ring off the vacuum interface 6 Remove the ion mobility cell or the ion mobility cell with jet injector technology by loosening the thumbscrews and then pulling the cell off the orifice plate Refer to Figure 2 5 on page 17 7 Install the standard curtain plate Note Removal of the SelexiON orifice plate and the dual drain assembly is not required 8 Make sure that the two source latches on the i
40. er Manual Tuning or Acquire mode then on the Navigation bar click Acquire or Tune and Calibrate 4 Click the Purge Modifier icon on the toolbar User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 35 of 77 Optimize DMS Parameters Figure 3 5 Purge Modifier Dialog P Purge Modifier Eo E 0 100 Status Durations Ready Expected 00 00 00 The Purge Modifier dialog opens The status shows as Ready which indicates the system is ready to start the purge process 5 Click the Purge button The purge process starts If the modifier purge was initiated from the Manual Tuning mode the system is automatically entered into a non Tuning mode and the Reserve Instrument for Tuning icon becomes deselected on the toolbar Refer to About the Purge Process on page 36 6 Click X to close the Purge Modifier dialog When the purge finishes equilibrate the system for approximately 30 minutes To equilibrate the system open the acquisition method to be run and start it Then stop the acquisition Wait 30 minutes About the Purge Process If the modifier purge was initiated in Manual Tuning mode the system is automatically entered into a non tuning mode and the Reserve Instrument for Tuning icon becomes deselected on the toolbar Figure 3 6 Purge Modifier Dialog P Purge Modifier e 0 100 Status Durations Ready Expected 00 00 00 en a The purge process enters the Initializing Equilibrating mode While in the initi
41. fault 0 0 has 5 volts higher potential applied than the e Range 100 to 100 other one User Guide RUO IDV 05 0275 C Parameter Name DMS Offset DMO DMS Resolution Enhancement DR User Guide RUO IDV 05 0275 C DMS Parameters The voltage applied to the two electrodes of the ion mobility cellor the ion mobility cell with jet injector technology relative to the orifice potential For example if the DMS offset potential is 5 volts and the orifice potential is at 100 volts then the two electrodes in front of the orifice inlet have 105 volts potential The DMS Offset is a way to tune the transmission out of the cell into the mass spectrometer Use of the DR parameter increases the residence time of ions in the ion mobility cellor the ion mobility cell with jet injector technology leading to reduced sensitivity due to larger diffusional signal loss When the DR value is changed the pause time between mass ranges and the total scan time will be updated to account for ion transport through the cell When performing RF DC scans quadrupole scans the pause time between mass ranges and the total scan time will be updated Controls the flow of the nitrogen gas that can be enabled between the SelexION or the SelexION device exit and the orifice inlet into the mass spectrometer DR is also referred to as throttle gas 6500 and 6500 series systems When the value of DR is set to Off Low Medium or High gas
42. flow is enabled which improves the resolution of the SelexION or SelexiON technology 5500 series systems When the value of DR is set to Low Medium or High gas flow is enabled which improves the resolution of the SelexION technology Specify the DMS Offset value e Default 3 0 volts in positive polarity 3 0 volts in negative polarity Range 100 to 100 6500 and 6500 series systems e Open 0 default Off 10 Low 22 Medium 34 High 43 5500 series systems e Off 0 default Low 10 Medium 25 High 40 Analyst 1 6 3 Software 73 of 77 DMS Parameters State of DMS Parameters in the DMS Off Mode DMS Parameters DMS Off Mode DMS Temperature DT Visible on UI user Low default interface oe wo Compensation Voltage COV DMS Offset DMO Hidden 3 0 volts in positive polarity 3 0 volts in negative polarity DMS Resolution Enhancement DR Hidden 6500 and 6500 series systems Open 5500 series systems Off Values of DMS and Source Parameters Used During Modifier Purge Parameter Name Value Set During Modifier Purge Modifier Pump Flow Rate DMS Resolution Enhancement DR 0 Separation Voltage SV a ces Compensation Voltage COV a o O MS of 0 E a lon Source Gas 1 GS1 C O 0 2 3 5 lon Source Gas 1 GS2 5 in 0 5 0 0 Analyst 1 6 3 Software User Guide 74 of 77 RUO IDV 05 0275 C DMS Parameters Parameter Name Value Set During Modif
43. g on the HPLC stack you are using type the following Table 3 4 Instrument Settings Page Inlet FIA Default Acq Method Starter acquisition method Rack Code Autosampler specific Rack Position Autosampler specific User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 45 of 77 Optimize DMS Parameters Table 3 4 Instrument Settings Page continued Injection Volume Amount of sample to be injected in pL 3 Click Next 4 On the FIA Target Compounds page do not select the Int Std check box because any transition that is marked as an Internal Standard will not be optimized 5 In the Resolution section select Unit in both the Q1 Resolution and Q3 Resolution fields 6 Click Next 7 On the FIA Source Parameters page if needed for each parameter to be optimized type at least two values to optimize and then select the check box in the Optimize column Refer to the Automatic Optimization Tutorial 8 Click Next 9 On the FIA Compound Parameters page if needed for each compound type the values to use to optimize for Declustering Potential Collision Energy and Collision Cell Exit Potential Refer to the Automatic Optimization Tutorial 10 On the same page for each compound type the values to optimize for the COV parameter in the Values for Optimization column separated by semicolons For example 2 1 2 2 2 3 Note Most compounds optimize at between 20 volts to 30 volts in the absence of a modifier Some
44. he System User Guide for the system 2 On the Navigation bar under Acquire double click Build Acquisition Method The Acquisition Method window opens 3 Click Mass Spec in the Acquisition method pane The Ramp COV check box on the MS tab page is cleared to allow the use of a fixed COV value and not ramp the COV parameter 4 Select a scan type and then type as applicable the mass range MRM transitions dwell time scan speed and other required information Refer to the Manual Optimization Tutorial Analyst 1 6 3 Software User Guide 48 of 77 RUO IDV 05 0275 C Create and Submit Batches 5 Right click in the mass ranges table and then select Separation Voltage SV A new column called SV volts is added to the mass ranges table 6 Type the optimized SV value in the first row of the SV volts column 7 Right click in the mass ranges table and then click Compensation Voltage COV A new column called COV volts is added to the mass ranges table 8 Type the optimized COV value in the first row of the COV volts column 9 Right click in the mass ranges table and then click DMS Offset DMO A new column called DMO volts is added to the mass ranges table 10 Type the optimized DMO value in the first row of the DMO volts column 11 Type the masses and other information including SV COV and DMO values for all the other compounds in the mass ranges table 12 Click Edit Parameters The Period 1 Experiment 1 parameter Tabl
45. he active hardware profile within the Analyst software Failure to do so might cause the mass spectrometer to enter an unstable state resulting in loss of control from within the Analyst software If the hardware profile is not deactivated and the mass spectrometer enters this unstable state control can be recovered by removing and re seating the ion source or by turning both the mass spectrometer and controller module off and on and then reactivating the hardware profile Create an Acquisition Method and Optimize DMS Parameters without a Modifier Use this procedure to create an acquisition method and optimize the DMS parameters for the compound in the Manual Tuning mode A modifier is not required for this procedure 1 Activate a hardware profile containing a syringe pump Refer to Creating Hardware Profiles and Projects in the Getting Started Guide or the System User Guide 2 T infuse or split infuse the sample into the LC stream Refer to T nfuse Sample into LC Stream on page 76 3 On the Navigation bar click Tune and Calibrate double click Manual Tuning 4 Select a scan type and then type the mass ranges transitions scan speed and other required information Optimize the compound and ion source parameters Then optimize the LC flow rate for the chromatographic method setup Refer to the Manual Optimization Tutorial 5 Click the DMS tab User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 27 of 77 Optimize DMS Par
46. hod 4 Select the Ramp COV check box on the MSS tab and then type the following COV values in the allowed COV range of 100 volts to 100 volts Table 6 1 Ramp Parameters a e a Start Type the voltage at which the ramping starts Stop Type the voltage at which the ramping stops Note Most compounds optimize between 20 volts to 30 volts in the absence of a modifier Some compounds might optimize even higher than 30 volts In the presence of a modifier we recommend using a COV range of at least 60 volts to 20 volts because the negative COV shifts can be dramatic for some compounds User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 65 of 77 Use DMS Parameters in IDA Figure 6 2 MS Parameters 5 Click Edit Parameters The Period 1 Experiment 1 Parameter Table dialog opens 6 Type the optimized values of the ion source and gas parameters on the Source Gas tab Make sure that the source temperature TEM specified here is the same as the one used for optimizing the DMS parameters Refer to the Manual Optimization Tutorial 7 Type the optimized values of the compound parameters on the Compound tab Refer to the Manual Optimization Tutorial 8 Select the DMS tab and do the following a Select the required values for the DMS Temperature DT Modifier MD and DMS Resolution Enhancement DR parameters Make sure that the DMS temperature specified here is the same as the one used for optimizing the DMS para
47. hod The Acquisition Method window opens 3 Click Mass Spec in the Acquisition method pane 4 Select a scan type and then as applicable type the mass range MRM transitions dwell time scan speed and other needed information for all the compounds Refer to the Manual Optimization Tutorial 5 Select the Ramp COV check box on the MS tab page and then type the following COV values in the allowed COV range of 100 volts to 100 volts User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 53 of 77 Create and Submit Batches Table 4 1 Ramp Parameters Type the voltage at which the ramping starts Type the voltage at which the ramping stops Set the size of the steps on each cycle Note Most compounds optimize between 20 to 30 volts range in the absence of a modifier Some compounds may optimize even higher than 30 volts In the presence of a modifier we recommend using at least 60 to 20 volts COV range because the negative COV shifts can be very large for some compounds Figure 4 3 MS Tab MS Advanced MS Expecnent 1 v D Endid Import List E __ Seantype MAM MRM v Polary Durston su e Delay Tene 0 zec Postre Negsrve CE vots Total Scan Time rcha pauses Ede Pavometers CDMS on Ramp COV Start Stop Step 40000 20000 0250 6 Click Edit Parameters The Period 1 Experiment 1 parameter Table dialog opens 7 Type the optimized values of the compound parameters on the C
48. ier Purge lonSpray Voltage IS lon Transfer Voltage ISVF for PhotoSpray ion source Collision Gas CAD System Default Values of DMS and Source Parameters After Modifier Purge is Completed or Aborted es ee oR GS1 GS2 CUR AD C SCIEX Triple Quad 5500 6500 or 6500 series systems 6 QTRAP 5500 6500 or 6500 systems 9 medium User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 75 of 77 T Infuse Sample into LC Stream B WARNING Electrical Shock Hazard Do not bypass the grounding union connection The grounding union provides grounding between the mass spectrometer and the sample introduction device AA WARNING Radiation Hazard Biohazard or Toxic Chemical Hazard Make sure that the sample tubing nut is tightened properly before operating this A equipment to prevent leakage Note T infusion split infusion can also be performed using an external tee to connect the three lines The LC and syringe streams connect to the tee which in turn is connected to the two way grounding union 1 Replace the two way grounding union with a three way grounding union Fitting union 0 15 mm Bore PN 018786 Fitting Tee Ring PN 018787 on the ion source 2 Connect the red PEEK tubing from the syringe pump to the grounding union on the ion source 3 Connect the grounding union on the ion source to an LC pump 4 Connect the sample tubing nut to the grounding union through a 30 cm piece of red PEEK tubing
49. ing Data Files The experimental conditions used to collect data are stored in the data file along with the results The DMS parameters that were used to acquire samples are shown in the File Information pane of the data file E On the Navigation bar under Explore double click Open Data File The Select Sample dialog opens In the Data Files pane select a wiff file to view In the Samples pane select the sample to view and then click OK The data acquired from the sample opens To view the file information click the Show File Info icon The File information pane opens below the graph Expand the required period in the left pane of the File Information pane and then click the required period experiment link The start stop and step values of the COV parameter used during sample acquisition are recorded under the period section The COV start and stop values for each compound are recorded under the period experiment Analyst 1 6 3 Software User Guide 58 of 77 RUO IDV 05 0275 C Analyze and Process Data section All the DMS parameters except COV and modifier parameters used during the sample acquisition are recorded in the Parameter table section for the selected period and experiment Refer to the Analyze and Process Data section in the Analyst software Getting Started Guide or the System User Guide for the mass spectrometer Create Quantitation Methods and Generate Results Tables Use the information available in the Q
50. install the ion mobility cell adapter ring and SelexION curtain plate Note The illustrations in this section show the SelexION ion mobility cell The procedure for installing the SelexiON ion mobility cell with jet injector technology is identical Prerequisite Procedures Make sure that both the ion mobility cell and the vacuum interface are clean Use methanol to clean the surfaces If the NanoSpray interface components are installed remove them and install the standard interface components For detailed instructions refer to the NanoSpray lon Source Operator Guide Note The mass spectrometer must be shut down and vented before the interface components are changed Required Materials e Powder free gloves nitrile or neoprene recommended 1 Complete any ongoing scans or click Acquire gt Abort Sample 2 Shut off the sample flow to the mass spectrometer 3 Deactivate the active hardware profile User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 13 of 77 Using the SelexlION Technology Note Failure to deactivate the active hardware profile before turning the controller module on or off to temporarily add or remove the SelexION or SelexION technology to or from the system may cause the mass spectrometer to enter an unstable state resulting in loss of control from within the Analyst software If the hardware profile is not deactivated and the mass spectrometer enters this unstable state control
51. le acquisition the software aborts the sample acquisition and logs the error in the event log Double click the aborted sample in the queue to see an error message If a discharge is detected in the cell then to avoid repeating the discharge when using the same method use lower Separation Voltage SV or DMS Temperature DT value in the acquisition method The DMS parameters will need to be re optimized for the new SV or DT value If there are discharges with SV and DT combinations that have worked in the past then clean and align the cell electrodes Refer to Clean and Align the Electrodes of the SelexlION lon Mobility Cell on page 21 or Clean and Align the Electrodes of the SelexION Ion Mobility Cell with Jet Injector Technology on page 23 When the fault is cleared the instrument goes into the Standby mode Before turning the controller module on or off to temporarily add or remove the SelexION or SelexION technology to or from the system first disable the active hardware profile within the software Failure to do so may cause the mass spectrometer to enter an unstable state resulting in loss of control from within the software If the hardware profile is not deactivated and the mass spectrometer enters this unstable state control may be recovered by removing and re seating the ion source or by turning both the mass spectrometer and controller module off and then on and then reactivating the hardware profile The def
52. meters b Type the optimized SV value for all the compounds in the Separation Voltage SV field c Type the optimized DMO value for all the compounds in the DMS Offset DMO field Analyst 1 6 3 Software User Guide 66 of 77 RUO IDV 05 0275 C Use DMS Parameters in IDA Figure 6 3 Period 1 Experiment 1 Parameter Table Period 1 Experiment 1 Parameter Table X SourceiGas Compound OMS DMS Temperature OT low Modifier MD 2Propanct Modifier Composition WOC Separation Voltage SV OMS Offset DMO DMS Resolution Enhancement Open OR A Apply the following parameters to all other experiments of the same polarity M Source Gas I Compound OK Cancel Help 9 Click OK 10 If required provide values for the parameters of the peripheral devices included in the active hardware profile 11 Save the acquisition method It can be used to ramp COV during batch acquisition and acquire data Note If the dependant scan is an LIT scan then it is advisable to increase the settling time by 20 ms in the survey scan to avoid the residual ions from showing up in survey scan in some cases View the IDA Data Acquired with Ramped COV Parameter in the IDA Explorer If data is acquired with an IDA method then the data does not open in the IDA viewer until the acquisition has finished but it is shown in the Explore window during acquisition To easily view IDA data set the IDA Explorer as the preset viewer Use
53. method created in the previous topic and the user changes the MDC value from Low to High or High to Low during acquisition then the software immediately calculates the required modifier pump flow rate and adjusts the modifier pump accordingly Similarly if during acquisition the user changes the molecular weight or molecular density of the custom modifier specified in the acquisition method then the software immediately calculates the required modifier pump flow rate and then adjusts the modifier pump accordingly Purge the Modifier Before using a new modifier purge the modifier currently being used from the modifier pump Purging the modifier will take about four minutes during which the mass spectrometer will be unavailable for use A modifier can be purged or cleared from the modifier pump from the Manual Tuning or Acquire mode when the controller module is turned on 1 Make sure that the SelexlION or SelexiON controller module is turned on and then activate a hardware profile Refer to Creating Hardware Profiles and Projects in the System User Guide 2 Connect the bottle containing the other modifier to the modifier pump 3 Do one of the following e Ifthe software is in Acquire mode with samples in the acquisition queue then refer to Purge Modifiers from Acquire Mode with Samples in the Acquisition Queue on page 38 e Ifthe software is already in Manual Tuning or Acquire mode then go to step 4 e Ifthe software is not in eith
54. modifier pump flow rate for the pre defined modifiers in the Analyst software is calculated by the software using the modifier density and the modifier molecular weight The density and molecular weight of the pre defined modifiers in the Analyst software are listed in Table 4 2 Table 4 2 Density and Molecular Weight of Pre defined Modifiers Modifier Molecular Weight g mol Density g cm 2 propanol 60 10 0 7860 Acetonitrile 41 05 0 7822 Methanol 32 04 0 7918 Acetone 58 08 0 7925 The Analyst software uses the following formula to calculate the modifier pump flow rate in L min 0 1636 x CUR 1 7726 x MDC x 0 04089 x MDW x 1000 Modifier Pump Flow Rate 100 MDC x MDD where e MDW is the Modifier Weight in g mol e MDCis the Modifier Composition e MDD is the Modifier Density in g mL e CUR is the Curtain Gas flow value Example Modifier Consumption Calculation As an example approximate modifier consumption calculations for all the pre defined modifiers in the Analyst software at a Curtain Gas flow of 20 psi and at different modifier concentrations for a 24 hour batch is shown in Table 4 3 Table 4 3 Approximate Modifier Consumption in mL at a Curtain Gas Flow Rate of 20 psi for a 24 Hour Batch Modifier Concentration Low 1 5 mL 24hrs High 3 0 mL 24hrs 2 Propanol 240 2 487 8 Acetonitrile 164 9 334 8 Analyst 1 6 3 Software User Guide 56 of 77 RUO IDV 05 0275 C Create a
55. nd Submit Batches Table 4 3 Approximate Modifier Consumption in mL at a Curtain Gas Flow Rate of 20 psi for a 24 Hour Batch continued Modifier Concentration Low 1 5 mL 24hrs High 3 0 mL 24hrs Calculate the Appropriate Modifier Consumption for a Batch 1 Determine the duration of the batch 2 Determine the modifier pump flow rate from the Mass Spec Detailed Status dialog by clicking the Mass Spec icon on the Status bar in the bottom right corner of the Analyst software window while running the method from the Analyst software Note We recommend using a 2 L bottle for the modifier when running long batches at high CUR value and high modifier concentration 3 Multiply the modifier pump flow rate uL min with the batch duration minutes to obtain the approximate volume of modifier required for a batch User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 57 of 77 Analyze and Process Data 5 This section describes how to do the following View DMS parameters in File Information while viewing data files Create a quantitation method and a generate Results Table Quantify isobaric compounds Report data Review a data file acquired with the ramped COV parameter Display a contour plot for data acquired with the ramped COV parameter View ramped DMS parameters in file information while viewing data files Analyze Quantitative Data View DMS Parameters Used for Acquisition in File Information While View
56. ng an acquisition method with a ramped COV parameter and a full scan type Contour plots provide visualization of the separation of the compounds For more information about contour plots refer to Contour Plots in the Analyze and Process Data section in the Analyst software Getting Started Guide and Qualitative Data Analysis in the Analyst software Advanced User Guide 1 On the Navigation bar under Explore double click Open Data File 2 In the Select Sample dialog in the Data Files list select a data file wiff file 3 In the Samples pane select a sample 4 Click OK Figure 5 3 TIC The TIC for the selected sample opens The x axis shows the COV in volts and the y axis shows the intensity in cps 5 Highlight the range to view in the contour plot If a selection is not made then the whole range is shown 6 Right click in the TIC and then click Show Contour Plot User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 61 of 77 Analyze and Process Data Figure 5 4 Contour Plot The contour plot for the selected sample is shown under the TIC window The X axis shows the COV in volts and the y axis shows the m z in Da 7 To view the spectrum select a region in the contour plot right click and then click Show Spectrum Figure 5 5 Spectrum E e dnt tem Compe Eee Bang Pv OS OFA BAS m D T ot EMC amy Wen Tete lam Damad Smeeted Imoebet Sasemet em tet oe The spectrum for the selected COV rang
57. ns The default Start Stop and Step values for the SV COV and DMO parameters are shown in the dialog 8 Inthe DMS Options dialog specify the values to use to optimize the SV COV and DMO parameters Use the default values or a smaller range which can reduce the time required for the optimization process The default step size is used unless a different step size is specified for the SV COV and DMO parameters The allowed range for SV COV and DMO are listed in Table 3 2 User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 41 of 77 Optimize DMS Parameters Table 3 2 Ranges Parameter name Separation Voltage SV The maximum allowed SV based on the DT and TEM values specified in the starter acquisition method will be displayed in this field DNS OHO COV is ramped at each level of SV After COV ramping DMO is ramped Note Most compounds optimize at between 20 volts to 30 volts in the absence of a modifier Some compounds might optimize even higher than 30 volts In the presence of a modifier we recommend using at least 60 volts to 20 volts COV range because the negative COV shifts can be dramatic for some compounds 9 Click Finish to begin the optimization process The optimization process starts The screen actively displays two windows a text file window and an acquisition window If necessary minimize one of them to see the other The x axis shows the parameter that is being optimized for example COV in
58. ompound tab Refer to the Manual Optimization Tutorial 8 Type the optimized values of the ion source and gas parameters on the Source Gas tab Make sure that the source temperature TEM specified here is the same value as the one used for optimizing the DMS parameters Refer to the Manual Optimization Tutorial 9 Select the DMS tab and update the fields using the information in the following table Analyst 1 6 3 Software User Guide 54 of 77 RUO IDV 05 0275 C Figure 4 4 DMS Tab Period 1 Experiment 1 Parameter Table amp SourceiGas Compound OMS OMS Temperature OT low l Modifier MD 2 Propanol Modifier Composition MOC Separation Voltage SV OMS Offset OMO OMS Resolution Enhancement OR Apply the following parameters to all other experiments of the same polarity M Source Gas Tl Compound Cancel Help Parameter DMS Temperature DT Create and Submit Batches Select the required value Make sure that the DMS temperature specified here is the same as the one used for optimizing the DMS parameters 10 Click OK 11 If required provide values for the parameters of the peripheral devices included in the active hardware profile 12 Save the acquisition method It can be used for ramping COV during batch acquisition of samples and acquiring data User Guide RUO IDV 05 0275 C Analyst 1 6 3 Software 55 of 77 Create and Submit Batches Modifier Consumption Calculation The
59. on source are pointing upwards in the 12 o clock open position 9 Position the ion source on the adapter ring Make sure that the guide pins on the ion source fit into the receptacles in the adapter ring push the ion source toward the interface until it is fully seated and then rotate the source latches downward to the 6 30 locked position to lock the ion source in place Refer to Figure 2 3 on page 15 Analyst 1 6 3 Software User Guide 20 of 77 RUO IDV 05 0275 C Using the SelexION Technology Clean and Align the Electrodes of the SelexION lon Mobility Cell Clean and align the electrodes when contamination is observed on the surfaces or when repeated high voltage discharge errors occur Required Materials Powder free glove Small slotted screwdriver 1 1 methanol water solution Lint free wipe Spacer tool WARNING Hot Surface Hazard Let the ion source and vacuum interface cool for at least 30 minutes before starting any maintenance procedures Some surfaces of the vacuum interface and the ion source become hot during operation With the lonDrive Turbo V ion source let the ion source cool for at least 90 minutes CAUTION Potential System Damage Make sure that vacuum interface components are kept clean and free of chemical or dust contamination To prevent contamination always wear powder free gloves when handling these components 1 Remove the ion mobility cell Perform step 1 to step 8 in Remove the SelexlION
60. optimize the SV COV and DMO parameters Use the default values or a smaller range that can reduce the time required for the optimization process The default step size is used unless a different step size is specified for SV COV and DMO The allowed ranges for SV COV and DMO are listed in Table 3 3 Table 3 3 Allowed Ranges for SV COV and DMO Parameter name Separation Voltage SV The maximum allowed SV based on the DT and TEM values specified in the starter acquisition method will be displayed in this field DSO OHO COV is ramped at each level of SV After COV ramping DMO is ramped Analyst 1 6 3 Software User Guide 44 of 77 RUO IDV 05 0275 C Optimize DMS Parameters Note Most compounds optimize at between 20 volts to 30 volts in the absence of a modifier Some compounds might optimize even higher than 30 volts In the presence of a modifier we recommend using at least 60 volts to 20 volts COV range because the negative COV shifts can be very large for some compounds 15 Click Finish to begin the optimization process The optimization process starts The screen actively displays two windows a text file window and an acquisition window You may need to minimize one of them to see the other The x axis shows the parameter that is being optimized for example COV in volts The y axis shows the intensity in counts per second cps The text file window is updated as results are generated At the end of the optimi
61. ptacles for ion source guide pins Thumbscrew pa Interface connector O e oee User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 15 of 77 Using the SelexlON Technology Adapter ring Correctly installed no gap L 2 Incorrectly installed gap highlighted 8 Tighten the thumbscrews evenly alternating between the two thumbscrews applying constant pressure Tip After tightening the thumbscrews fully pull on the extension ring to make sure that it is secured properly If a gap appears tighten the ring further Tip To verify that the ring is installed correctly install the ion source and then open the Analyst software In Manual Tune mode set GS1 and GS2 to 80 If a loud hissing is audible at the front of the instrument there is a gap The ring is not installed correctly Tip To tighten the thumbscrews on the NanoSpray ring use a screwdriver Analyst 1 6 3 Software User Guide 16 of 77 RUO IDV 05 0275 C Using the SelexION Technology Figure 2 5 SelexION lon Mobility Cell Description 9 Position the SelexION ion mobility cell on the SelexION orifice plate keeping the ion mobility cell vertical perpendicular to the plane of the orifice plate and making sure that the connectors are aligned with the sockets on the orifice plate Note Keep the surfaces of the orifice plate and the ion mobility cell clean and do not scratch the ceramic seal on the ion mobility cell User Guide Analyst
62. r from the modifier pump takes about four minutes After the Purge process is complete the status in the Purge Modifier dialog changes to Complete The Abort button changes back to Purge The system automatically re enters Manual Tuning mode if the modifier purge was initiated from Manual Tuning mode The values of some DMS and source parameters are reset To view the reset values refer to Values of DMS and Source Parameters After Modifier Purge is Completed or Aborted on page 75 Abort the Purge Process e Inthe Purge Modifier dialog click Abort User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 37 of 77 Optimize DMS Parameters The purge cycle is terminated and the values of some DMS and source parameters are reset To view the reset values refer to Values of DMS and Source Parameters After Modifier Purge is Completed or Aborted on page 75 The Status changes to Aborted and the Abort button changes to Purge If the modifier purge was initiated from Manual Tuning mode after abort the system is set back into Manual Tuning mode After the modifier purge is aborted allow the system to equilibrate for approximately 30 minutes with the required source conditions and the new modifier running before acquiring new samples Purge Modifiers from Acquire Mode with Samples in the Acquisition Queue If the system is in the Acquire mode with samples in the acquisition queue and the user selects the Purge Modifier icon then a Queue Busy messag
63. re by scanning or fixing SV and COV the device can operate in the following modes Analyst 1 6 3 Software User Guide 6 of 77 RUO IDV 05 0275 C Introduction to DMS Technology e Aparticular SV and COV combination can be selected resulting in continuous filtration of particular ion species e When SV is fixed and COV scanned a linear DMS spectra can be recorded Benefits of DMS Technology The SelexlON differential mobility separation technology device for 5500 and 6500 series instruments or the SelexlON differential mobility separation technology for 6500 series instruments adds an additional dimension of separation to the LC MS MS system e It enhances the quality of mass analysis and quantitative accuracy by reducing chemical noise and by pre separating ions of similar mass e It provides fast ion transit times and offers a transparent mode of operation similar to when the SelexiION or SelexION technology is not installed on the system that allows all ions to be transmitted without discrimination when SV and COV are set to zero e It supports simultaneous transmission of ions of both polarities and subjects each to separation based on their differential mobility constants Role of Modifiers in DMS Technology Modifiers can be added to the gas transporting the ions through the SelexION or SelexION device to increase the peak capacity and separation power of this device The presence of these modifiers which are
64. rument optimization we recommend that the ion mobility cell or the ion mobility cell with jet injector technology be removed from the ion source before instrument optimization is performed User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 47 of 77 Create and Submit Batches 4 This section describes how to perform the following tasks e Create an acquisition method with fixed DMS parameters in Acquire mode e Learn about the capability of the SelexION or SelexlON technology to separate isobaric compounds e Differentiate isobaric compounds in MRM and Scheduled MRM algorithm acquisition methods e Createa Scheduled MRM algorithm acquisition method with DMS parameters e Create an acquisition method to ramp COV in the batch acquisition mode e Learn about modifier consumption calculations Prerequisites e TheSelexlON orSelexION technology is installed on the mass spectrometer and the controller module is turned on Use the methods created in this section to submit batches to acquire data Refer to the Getting Started Guide or the System User Guide for the mass spectrometer Create an Acquisition Method with Fixed DMS Parameters in Acquire Mode Use this procedure if the DMS parameters have already been optimized and an acquisition method must be created using these optimized parameters 1 Activate a hardware profile Refer to Create Hardware Profiles and Projects in the Analyst Getting Started Guide or t
65. sesesesesesssesesesereseeseerereeeeeees 67 Chapter 7 Troubleshooting cis scccctteseseseccsceerscoteres sacel ious cxeduareseage canada dudes en sedesdendddvadecwended edesuerssauevendes iia 70 Appendix A DMS Parametelrs cssccccceccsseeeeeeeeeeseeeeeeneeesenessesaeeeeseeeeesaeeeeeeeeeseaaeeeeeeeesecaeseseeeesesaeseseeeeees 71 DMS Parameter DESCriptionss a a n a a a Aa S A AT aa AEA Eaa NA Ea divieiuetiedes ausebestuedbantostes 71 State of DMS Parameters in the DMS Off Mode c secssecsesessesesescsesecseeecsesacseeacseeacseeacseeacaeeaceneasaneaseneaseneaseneaseneasenees 74 Values of DMS and Source Parameters Used During Modifier PUurge cssssscsssssscscsssscsessssssscssessssssesssssessesearsesees 74 Values of DMS and Source Parameters After Modifier Purge is Completed or ORC ee gt deca ee au ah A eee 75 Appendix B T Infuse Sample into LC Streamn cccccceecceeeceeseeeeeeeeeceeeeeeseeeeseeeeeeeeseeeseeeeeeeesaeeseaeenenenses 76 Revision HIStONY 222220 neiii eaa naaa aa aaaea aaea ao Vesa scenes sat cevedaeeweibecsdsteecsets vdsendeectieddendescteegdaieeas 77 Analyst 1 6 3 Software User Guide 4 of 77 RUO IDV 05 0275 C Introduction to DMS Technology 1 Note For safety information refer to the System User Guide for the mass spectrometer This section describes Differential Mobility Spectrometry DMS technology and its benefits and the role of modifiers The DMS Off operation mode is also discussed here About DMS
66. shows the different DR values and the corresponding Pause between mass ranges times Table 3 1 DR Values and the Corresponding Pause Between Mass Ranges Time DR Values Pause Between Mass Ranges Values 6500 and 6500 Series 5500 Series Systems Systems Open default for 6500 and 6500 20 ms default series systems Note The DR readbacks show the actual pressure in the Mass Spec Detailed Status dialog Double click the Mass Spec icon on the status bar to open this dialog Off default for 5500 series 20 ms 20 ms systems 7 Save the acquisition method after all of the DMS parameters have been successfully optimized Analyst 1 6 3 Software User Guide 30 of 77 RUO IDV 05 0275 C Optimize DMS Parameters Ramp the Separation Voltage and Compensation Voltage OM ee SOS Start with an SV value of 0 Click Edit Ramp The Ramp Parameter Settings dialog opens Select Compensation Voltage in the Parameter field Type 20 in the Start field Type 30 in the Stop field Use the default value in the Step field or type a required step size and then click OK The Ramp Parameter check box is selected Click Start Data is shown in the panes below the Tune Method Editor Note the maximum signal intensity The COV value at which this maximum sensitivity is achieved should be zero Change the SV value to a number between 0 and the maximum allowed SV range for example 2000 Use SV in increments of 500 or more because the
67. srssrssresresresresresrenresresrenrenrenns 48 Separate Isobaric Compounds Using the SelexlON Technolog ssssssscecccsseeeeeeeseeeeseeiesseeaeeessees 50 Differentiate Isobaric Compounds in MRM and Scheduled MRM Algorithm ACQUISITION M thOdS cccccccssssesesssessssssscsescsesessssssssssssssssssssesesesesesesesesesesesesesestseseseseseseseseseeeseeeeeeeseseeeeererenereneeersnsees 51 Use DMS Parameters in a Scheduled MRM Algorithm Acquisition Me thod cccccccccccssccscscscsescsseesesseeecseseeeeceeseeeeerersnes 52 Create an Acquisition Method to Ramp COV during Batch Acquisition ccsssssseseseeeseeeseesenseeeeensees 53 Modifier Consumption Calculations sses anne ied fied Bole HE ie ANS ee Oa ee 56 Example Modifier Consumption Calculation c cccssssssssssssssssssssssssssscsecsssscsessssssssesecassescsessssussscsasacasecsecasanessesasasess 56 Calculate the Appropriate Modifier Consumption for a Batch c csscsssscsscsssssssssssssssscsessssssssesssassssessasatscsessassesees 57 Chapter 5 Analyze and Process Data cccccsseecceseceeeseeeeeeeeeeeeeseneeeeeesaeseeseeeessaeeseseeeeeeneesesnaeeeeseesenseeenenes 58 User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 3 of 77 Contents Analyze Quantitative Data ccccsssssssssssssssssssssssssssssssssssssesesssesesesessesesesesesssseesessseseseeeseseeeseeeeeseseeeeeneeeeeeesenerenereeenenes 58 View DMS Parameters Used for Acquisition in File Information While Viewing Data
68. t ramped COV parameter will run for the required method duration but the IDA and DFT methods with ramped COV will run for the required number of cycles based on the ramping COV start stop and step values The method run will terminate when the last step of COV is acquired and not when the method duration is reached The COV value is dynamically calculated and set for each cycle The COV SV DT and DMO values of the MRM transitions in the survey scan or any other supported IDA survey scans are automatically propagated to the dependant scans in an IDA method The same applies toa Scheduled MRM algorithm IDA method and to the DFT pre scan for an MRM triggered IDA method with DFT scans The modifier used in the survey scan of an MRM IDA method also gets automatically propagated to the dependant scans Analyst 1 6 3 Software User Guide 64 of 77 RUO IDV 05 0275 C Use DMS Parameters in IDA Use this procedure after all of the DMS parameters have been optimized except COV Create an IDA Acquisition Method to Ramp COV During the Batch Acquisition Mode 1 Activate a hardware profile Refer to the Create Hardware Profiles and Projects in the Analyst software Getting Started Guide or the System User Guide for the mass spectrometer 2 Create an IDA method with an MRM scan as survey scan Refer to the IDA Tutorial 3 In the Acquisition method editor in the open IDA method click MRM in the Acquisition method pane Figure 6 1 MRM Met
69. the IDA Explorer tab in the Appearance Options dialog to use the IDA Explorer to view IDA data Users can also select the columns for the Mass List List view pane The IDA Explorer is preset to show IDA samples For more information refer to View IDA Data in the IDA Tutorial 1 Open the project folder containing the acquired IDA data User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 67 of 77 Use DMS Parameters in IDA 2 On the Navigation bar under Explore double click Open Data File The Select Sample dialog appears 3 From the Data Files list select the wiff file containing the acquired IDA data to view 4 In the Samples list click the required sample and then click OK Figure 6 4 IDA Explorer Macs Telarc 0800 Os We aie oe Mavs window Dar 5500 il Miass Uat List View a Conai m Tenatmard Scan Cf Z eeeseegsece fk gt amp amp amp amp 8 amp 8 amp 8 amp 8 8 S i e 4 l z 20 20 i Fi Iza gt j i Tase View Lat View The IDA Explorer opens The left portion of the pane shows a list of masses sent to the dependent scan as a tree view or as a list view Switch between views by clicking Tree View or List View at the bottom of the Mass List pane The right portion of the pane shows the acquired IDA data graphically Instead of time the ramped COV range is shown on the x axis in the TIC and XIC graphs 5 Use the two buttons above the graph to swit
70. then tighten the thumbscrews Refer to Install the SelexION or SelexIlON Technology on page 13 Analyst 1 6 3 Software User Guide 22 of 77 RUO IDV 05 0275 C Using the SelexION Technology Clean and Align the Electrodes of the SelexlION lon Mobility Cell with Jet Injector Technology Clean and align the electrodes when contamination is observed on the surfaces or when repeated high voltage discharge errors occur Required Materials Powder free glove Small slotted screwdriver 1 1 methanol water solution Lint free wipe Spacer tool WARNING Hot Surface Hazard Let the ion source and vacuum interface cool for at least 30 minutes before starting any maintenance procedures Some surfaces of the vacuum interface and the ion source become hot during operation With the lonDrive Turbo V ion source let the ion source cool for at least 90 minutes CAUTION Potential System Damage Make sure that vacuum interface components are kept clean and free of chemical or dust contamination To prevent contamination always wear powder free gloves when handling these components 1 Remove the ion mobility cell Perform step 1 to step 8 in Remove the SelexlION or SelexlON Technology on page 19 2 Using the small slotted screwdriver loosen the adjustment screws until the electrodes move freely in the ion mobility cell and then remove the electrodes from the ion mobility cell User Guide Analyst 1 6 3 Software RUO IDV 05 0
71. tified based on their Compound ID User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 51 of 77 Create and Submit Batches Use DMS Parameters in a Scheduled MRM Algorithm Acquisition Method The software supports the use of DMS parameters with the Scheduled MRM algorithm to obtain the best signal and separation of the compounds of interest You can use this procedure when you already have the optimized values for all the DMS parameters and you need to create a Scheduled MRM algorithm acquisition method Note Instead of creating a Scheduled MRM algorithm acquisition method use an existing acquisition method that contains optimized compound ion source DMS parameters and LC flow rate as a starting point Add the required information about MRM scheduling to this acquisition method Refer to the Scheduled MRM Algorithm Tutorial 1 Activate a hardware profile Refer to Create Hardware Profiles and Projects in the Analyst software Getting Started Guide or the System User Guide for the system 2 On the Navigation bar under Acquire double click Build Acquisition Method The Acquisition Method window opens 3 Click Mass Spec in the Acquisition method pane 4 Create a Scheduled MRM algorithm acquisition method Refer to Scheduled MRM Algorithm Tutorial 5 Add the optimized SV COV and DMO values to the mass ranges table for the MRM transition using the following steps e Right click in the mass ranges table and select
72. tles Refer to chemical product Safety Data Sheets and take appropriate safety precautions Do not refill the modifier bottle while it is in the side tray Disconnect the fluid line from the bottle refill the bottle in a safe location then reinstall the bottle and fluid line in the side tray 1 Disconnect the fluid line from the modifier bottle in the side tray 2 Refill the modifier bottle in a safe location taking the appropriate safety precautions if needed 3 Reinstall the modifier bottle in the side tray and then reconnect the fluid line Clean the Controller Module Surfaces Clean the external surfaces of the controller module after a fluid spill or when they become dirty e Using warm soapy water and a soft cloth wipe the external surfaces User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 25 of 77 Optimize DMS Parameters 3 The DMS parameters must be optimized to obtain the best signal and separation of compounds of interest For more information about DMS parameters refer to DMS Parameter Descriptions on page 71 Optimize the DMS parameters with or without a modifier in the Manual Tuning mode The DMS parameters can be optimized in the Tune and Calibrate mode in one of the following ways e As a starting point use an existing acquisition method that was created for the compound to be analyzed and that contains optimized compound parameters source parameters and LC flow rate and then optimize the DMS parameters
73. uantitative Analysis section in the Analyst software Getting Started Guide to create a quantitation method and generate a Results Table Refer also to the System User Guide for the system or the Analyst software Advanced User Guide Quantify Isobaric Compounds While creating a quantitation method for isobaric compounds it is much easier to identify them if their compound name was entered in the Compound ID field in the acquisition method This is because the name of each isobaric compound or any compound present in the acquisition method is automatically entered next to its Q1 Q3 mass in the Analyte table when building a quantitation method If the compound name was not provided in the acquisition method for the isobaric compounds then while creating the quantitation method identify the isobaric compounds correctly and manually type their names next to their Q1 Q3 masses Refer to Differentiate Isobaric Compounds in MRM and Scheduled MRM Algorithm Acquisition Methods on page 51 For quantifying isobaric compounds and generating Results Table for them use the information available in the Quantitative Analysis section in the Getting Started Guide Report Data Create reports from a Results Table using the Reporter Software Refer to the Reporter User Manual available at Start gt All Programs gt SCIEX gt Reporter 3 2 gt Reporter 3 2 User Manual If the MultiQuant software is used to quantitate data the Reporter Software can
74. ucts and are SCIEX s sole and exclusive representations warranties and obligations SCIEX makes no other warranty of any kind whatsoever expressed or implied including without limitation warranties of merchantability or fitness for a particular purpose whether arising from a statute or otherwise in law or from a course of dealing or usage of trade all of which are expressly disclaimed and assumes no responsibility or contingent liability including indirect or consequential damages for any use by the purchaser or for any adverse circumstances arising therefrom For research use only Not for use in diagnostic procedures AB Sciex is doing business as SCIEX The trademarks mentioned herein are the property of AB Sciex Pte Ltd or their respective owners AB SCIEX is being used under license 2015 AB SCIEX AB Sciex Pte Ltd Blk 33 04 06 Marsiling Ind Estate Road 3 Woodlands Central Indus Estate SINGAPORE 739256 Analyst 1 6 3 Software User Guide 2 of 77 RUO IDV 05 0275 C Contents Chapter 1 Introduction to DMS Technolog ccccccssccceseceeeseeeeeeeeeeseeeeesneeeeeneesesnaeeeeeeeseanaeeeneeeeessaeseneneees 5 About DMS Technology oran ann e cides etvchs vet luctuschs E ETE 5 Benefits of DMS Technology i ssssacadsin dade a aa a a a decades 7 Role of Modifiers in DMS Technology c ssssssssssssscsessssssssessssssescsecsssssssesssscscscsecassusssusseacsusceesssasscsusssasaceeesasasessesaeasass 7 Instrument
75. utive isobaric compounds with the same Q1 and Q3 masses is saved the software shows a warning The warning indicates that if this method is used for quantitation then the chromatograms in the Results Table for the isobaric compounds will be identical and will correspond to only one of the isobaric compounds Figure 4 2 Warning Message Transitions 1 and 2 have duplicate Q1 and Q3 masses If you use this method for quantitation then the chromatograms in the Results Table for transitions 1 and 2 will be identical and wall correspond to one of the compounds Add at least 0 001 Da to either the QI mass or the Q3 mass to differentiate the compounds Click OK to save the method Click Cancel to change the Q1 or Q3 mass a _ coe To resolve this conflict in the acquisition method differentiate the isobaric compounds by adding at least 0 001 Da to either the Q1 or Q3 mass of one or more of the isobaric compounds For example the Q1 masses of some consecutive isobaric compounds could be changed in the following manner 700 000 700 001 700 002 and so on Another method to differentiate the isobaric compounds is to type the name of the isobaric compounds in the Compound ID field in the acquisition method This helps the user to correctly identify the isobaric compounds while creating the quantitation method for these compounds If the MultiQuant software is used for data analyses and quantitation then identical masses are separately quan
76. volts The y axis shows the intensity in counts per second cps The text file window is updated as results are generated At the end of the optimization process the combination of parameters that provides the highest signal intensity is saved If the intensity is below the minimum value 100 cps an error message will be displayed in the text file window After the optimization process is successfully completed the optimized parameters are added into a copy of the starter method and the new method is saved with the name startmethodname _DMS dam in the lt drive gt Analyst Data Projects Your_Project folder Acquisition Methods folder The text file is saved in lt drive gt Analyst Data Projects Your_Project folder Log folder All the wiff files generated during the optimization process are saved in the lt drive gt Analyst Data Projects Your_Project folder Data folder Optimize Compound and DMS Parameters with T Infusion Optimization Type The Analyst software provides an option to optimize both compound and DMS parameters together in the Compound Optimization mode When this option is used first the compound parameters are optimized in T infusion using a similar workflow as the infusion optimization and then the DMS parameters are optimized at the end similar to the DMS Only option 1 On the Navigation bar under Tune and Calibrate double click Compound Optimization Analyst 1 6 3 Software User Guide 42 of 77 RU
77. will be reduced Knowing the characteristics of the analyte and modifier can inform the appropriate choice of modifier Using 2 propanol as a modifier is a good starting point for investigating the effect of modifiers on a given DMS separation because it has been observed to improve the separation power for a wide range of compounds User Guide Analyst 1 6 3 Software RUO IDV 05 0275 C 7 of 77 Introduction to DMS Technology Instrument Tuning Before installing the SelexION or SelexION technology on the mass spectrometer make sure that the mass spectrometer is tuned and calibrated DMS Off Operation Mode When the SelexION or SelexION technology is installed on the mass spectrometer users might need to acquire spectral data without using the SelexION or SelexION technology Instead of removing the technology from the system users can use the DMS Off operation mode to acquire data The Analyst software provides a DMS Off operation mode which allows the user to work in an environment similar to when the technology is not installed on the mass spectrometer However in the DMS Off mode signal intensities will be significantly decreased as compared to the signal intensities of data acquired with the technology physically removed from the mass spectrometer To work in the DMS Off operation mode select the DMS Off check box available on the MS tab in the Acquisition method window or on the MS tab in the Tune Method Editor win
78. yzed can be used The existing method can use no modifier or it can use a different modifier than the one currently in use The method used as a starting point provides optimized source and compound parameters and an LC flow rate The DMS parameters must be modified for the required modifier 4 Click the DMS tab 5 Optimize the DT parameter as described in Create an Acquisition Method and Optimize DMS Parameters without a Modifier on page 27 6 In the Modifier MD parameter select a modifier from the list Select one of the pre defined modifiers To use a modifier other than the pre defined ones select Custom Analyst 1 6 3 Software User Guide 32 of 77 RUO IDV 05 0275 C Optimize DMS Parameters Figure 3 3 DMS Parameter Settings Source Gas Compound OMS Resolution Detector DMS Temperature Reached DMS Temperature DT Low X Modifier MD 2 Propanoi Modifier Composition MDC kow Separation Voltage SV o0 Compensation Votage COV 0 0 DMS Offset DMO 3 0 DMS Resolution Enhancement on v OR j The Modifier Composition MDC parameter is shown with its default value which is set to Low 7 Inthe MDC parameter if required select High to test the modifier concentration that would provide the optimal separation Low is 1 5 or higher and High is 3 0 concentration of modifier The software uses the Curtain Gas flow rate value and the density and molecular weight of the selected
79. zation process the combination of parameters that provides the highest signal intensity is saved If the intensity is below the minimum value 100 cps an error message will be displayed in the text file window After the optimization process is successfully completed the optimized parameters are added into a copy of the starter method and the new method is saved with the name startmethodname _DMS dam in the lt drive gt Analyst Data Projects Your_Project folder Acquisition Methods folder The text file is saved in lt drive gt Analyst Data Projects Your_Project folder Log folder All the wiff files generated during the optimization process are saved in the lt drive gt Analyst Data Projects Your_Project folder Data folder Optimize COV Through Flow Injection FIA COV is the only DMS parameter that can be optimized using the FIA method The FIA method is also used to fine tune the source and compound dependent parameters Before starting FIA optimization create an acquisition method with optimized source compound and DMS parameters using the T infusion method described in Optimize Compound and DMS Parameters with T Infusion Optimization Type on page 42 Make sure that an autosampler is included in methods used for FIA optimization This method will be used as the starter method for FIA 1 On the Navigation bar under Tune and Calibrate double click Compound Optimization 2 On the Instrument Settings page dependin
80. ze different values for DMS parameters open the acquisition method in the Manual Tuning mode and then optimize the parameters again with different values Separate Isobaric Compounds Using the SelexlON Technology Isobaric compounds have the same nominal mass and thus cannot be distinguished by the mass spectrometer The SelexlION or SelexION technology automatically eliminates crosstalk and it can separate isobaric compounds Analyst 1 6 3 Software User Guide 50 of 77 RUO IDV 05 0275 C Create and Submit Batches When creating an MRM acquisition method for multiple isobaric compounds we recommend alternating isobaric masses with mass ranges of other compounds if possible and avoiding having isobaric masses in consecutive MRM transitions Perform the following tasks if there are two isobaric compounds and two non isobaric compounds in an MRM method 1 Type the mass ranges of one isobaric compound 2 Type the mass ranges of one non isobaric compound 3 Type the mass of the second isobaric compound 4 Type the mass of the second non isobaric compound If consecutive isobars are unavoidable in a given method the software will take precautions to avoid crosstalk at the expense of a slightly longer cycle time Differentiate Isobaric Compounds in MRM and Scheduled MRM Algorithm Acquisition Methods When an MRM Q1 MI Q3 MI acquisition method or a Scheduled MRM algorithm acquisition method containing two or more consec

User Guide: SelexION Technology for 5500 and 6500

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