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SCIEX X500 QTOF, System User'S Manual

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Sample Type Filter

Table 6-16 Sample Type Filter Descriptions

Description

Filter Type

Shows only Unknown samples, which are normal samples of unknown concentration. When
Standard samples are used, their concentration is back-calculated from the calibration curve
and reported in the Results Table as the Calculated Concentration.

Unknowns

Shows only samples of known concentration. These samples are used for the creation of the
calibration curve.

Standards

Shows only Quality Control samples. These samples of known concentration are used to
check the accuracy of the calibration curve but do not influence its actual construction.

Quality Controls

Shows only Blank samples. These are generally samples that contain the internal standard
compounds, if used, but no analytes, and that have been through the normal sample
preparation procedure. These samples are not used in the construction of the calibration
curve. To include them, select the Standard sample type and then set the Actual Concentration
at 0.

Blanks

Shows only Double Blank samples. These are samples with neither internal standards nor
analytes.

Double Blanks

Shows only Solvent samples. These are double blanks that have not been through the normal
sample work-up procedure.

Solvents

Acceptance Criteria

Use the acceptance criteria to define a qualifying row. A qualifying row matches the selected criteria for the
following filters:

• Pass: Show the rows that match the criteria that was defined in the processing method.

• Fail: Shows the rows that do not match the criteria that was defined in the processing method.

• Any: Shows all of the rows.

Table 6-17 Acceptance Criteria

Description

Label

Shows the user-defined criteria for integration quality using the value of the quality column
in the Results Table, asymmetry factor column, total width column, and the retention time
error columns (either %error column or absolute delta column).

Integration
acceptance

Shows the accuracy of the standard and quality control samples tolerance.

Accuracy

SCIEX X500 QTOF System

System User Guide

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RUO-IDV-05-2334-E

Operating Instructions—Software

Summary of Contents for X500 QTOF

Page 1: ...SCIEX X500 QTOF System System User Guide August 2017 RUO IDV 05 2334 E...

Page 2: ...nd 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...

Page 3: ...Decommissioning and Disposal 15 Equipment Use and Modification 16 Qualified Personnel 16 Contact Us 17 Technical Support 17 Documentation Symbols and Conventions 17 Chapter 2 Principles of Operation...

Page 4: ...rs 53 Deactivate a User 53 Remove a User 54 Enable Full Screen Mode 54 Select Laboratory Information Management System LIMS Settings 54 Select Queue Options 54 Select Regional Settings 55 Manage the C...

Page 5: ...e Columns 87 Add a Component Component Concentration Column 87 Delete a Component Concentration Column 87 Queue Icons 88 MS Method Workspace 88 Create an MS Method 88 MS Method Experiments 90 About MS...

Page 6: ...tegration Algorithm Parameters 186 MQ4 Integration Algorithm Parameters 186 AutoPeak Integration Algorithm Parameters 188 Edit Report Templates 189 Reporter Templates 191 MS Tune 192 Perform a Quick S...

Page 7: ...e and Handling 212 Move the Mass Spectrometer 213 Generate a Support Package 219 Chapter 8 Mass Spectrometer Troubleshooting 220 Appendix A Recommended Calibration Ions 223 APCI Calibration Ions 223 E...

Page 8: ...ult in serious injury This safety information is intended to supplement federal state provincial and local environmental health and safety EHS regulations The information provided covers system relate...

Page 9: ...ectives 2014 35 EU as implemented in these standards EN 61010 1 EN 61010 2 061 Waste Electrical and Electronic Equipment WEEE Waste Electrical and Electronic Equipment 2012 96 EEC as implemented in EN...

Page 10: ...le management practices to control electrical cables This will reduce the chance of a tripping hazard For information about system electrical specifications refer to the Site Planning Guide AC Mains S...

Page 11: ...ion source This supplementary grounding will reinforce the safety configuration specified by SCIEX Chemical Precautions WARNING Radiation Hazard Biohazard or Toxic Chemical Hazard Determine whether d...

Page 12: ...f the local regulations for the storage handling and disposal of biohazardous toxic or radioactive materials Recommended Use secondary containment trays beneath the roughing pump the solvent bottles a...

Page 13: ...hat the air quality is maintained in compliance with local health and safety regulations The source exhaust system and roughing pump must be vented to a dedicated laboratory fume hood or an external e...

Page 14: ...source exhaust output Dispose of sharps following established laboratory safety procedures Environmental Precautions Use qualified personnel for the installation of electrical mains heating ventilatio...

Page 15: ...ich is suitable for use in all establishments other than domestic and those directly connected to a low voltage power supply network which supplies buildings used for domestic purposes Derived from CI...

Page 16: ...njury Hazard Use SCIEX recommended parts only Use of parts not recommended by SCIEX or use of parts for any purpose other than their intended purpose can put the user at risk of harm or negatively imp...

Page 17: ...rning Center SCIEXUniversity For the latest guidance on cybersecurity for SCIEX products visit sciex com productsecurity Technical Support SCIEX and its representatives maintain a staff of fully train...

Page 18: ...zes significant information in a procedure or description Tip Tip provides useful information that helps apply the techniques and procedures in the text for a specific need and provides shortcuts but...

Page 19: ...QTOF mass spectrometer with a roughing pump A Turbo V TM ion source that uses either the twin ESI probe or the twin atmospheric pressure chemical ionization APCI probe Refer to the Turbo V TM Ion Sou...

Page 20: ...Hardware Overview Figure 2 1 Front and Right Side View X500R System User Guide SCIEX X500 QTOF System RUO IDV 05 2334 E 20 234 Principles of Operation...

Page 21: ...lternate left location for diverter valve For more information contact an FSE 2 Ion source Refer to the ion source Operator Guide 3 Calibrant bottles Refer to Replace the CDS Bottle on page 41 4 Panel...

Page 22: ...Figure 2 3 Back and Left Side View X500R System User Guide SCIEX X500 QTOF System RUO IDV 05 2334 E 22 234 Principles of Operation...

Page 23: ...me ion sources connect to this port 3 AUX IO connection Not used 4 Ethernet connection Used for communication with the acquisition computer 5 Zero air gas supply 6 Exhaust waste Refer to Empty the Sou...

Page 24: ...ata Scanning Blue Lit when the system encounters a system fault Fault Red After the system is turned on the power LED illuminates and the fault LED flashes for a few seconds Then the vacuum LED begins...

Page 25: ...counted and the number of pulses is directly proportional to the quantity of ions entering the detector The mass spectrometer converts the voltage pulses to a signal and then correlates the signal to...

Page 26: ...of two types of data views total ion chromatogram TIC and extracted ion chromatogram XIC TIC The plot of the total ion current as a function of time Figure 2 5 Example TIC XIC An ion chromatogram crea...

Page 27: ...rticular scan was obtained which can be derived from the scan number A chromatogram provides a general view of the data usually time dependent when using an LC column but it does provide information a...

Page 28: ...entrations of each sample are then available in a Results Table Integration In LC MS MS data integration refers to obtaining the area under a curve for the peak associated with a specific compound Thr...

Page 29: ...not a comprehensive list and other guidances should be used in determining the best practice in developing a calibration curve for the laboratory Note In some analytical runs single point calibration...

Page 30: ...y 1 y If y 10 8 then w 10 16 Otherwise w 1 y 2 1 y 2 If x 0 then an error is generated If x 10 5 then w ln 10 5 Otherwise w ln x ln x If y 0 then an error is generated If y 10 8 then w ln 10 8 Otherw...

Page 31: ...x ln y Linear The linear calibration equation is y mx b The slope and intercept are calculated as where Linear Through Zero The linear through zero calibration equation is y mx The slope is calculated...

Page 32: ...If there is some linearity and some curvature in the line of points then use power regression instead of linear or quadratic regression to produce a line somewhere between these fits Quadratic The qua...

Page 33: ...alitative analysis is the identification of a target or unknown compound In mass spectrometry determining which compound is present is accomplished using mass accuracy retention time isotope pattern l...

Page 34: ...on its molecular formula Figure 2 7 shows the isotope pattern for imazalil Figure 2 7 Isotope Pattern Library Searching Comparing acquired MS MS spectra from unknown samples to a database of compounds...

Page 35: ...as the purity except that only masses that occur in the unknown spectrum are included in the sums The reverse fit is a measure of the degree to which the unknown spectrum is contained in the library...

Page 36: ...learance requirements Contact us for a copy of the Site Planning Guide if required For contact information go to sciex com contact us The source exhaust gas compressed air and nitrogen gases are conne...

Page 37: ...then relieve the pressure in the gas lines before disconnecting it Tip If the mass spectrometer will not be used for a length of time then leave it in Standby mode with the ion source in place If the...

Page 38: ...hing pump mains supply cable from the mains supply outlet 9 If the mass spectrometer will be vented and out of service for more than eight hours then turn off the nitrogen gas supply Unless the gas su...

Page 39: ...ernal loop When the valve switches to Position B the sample is injected Plumb the valve for injector mode Figure 3 2 Diverter Valve Injector Mode Position A Figure 3 3 Diverter Valve Injector Mode Pos...

Page 40: ...Plumb the Diverter Valve in Diverter Mode When the valve is in Position A the flow goes to waste When the valve switches to Position B the flow goes to the mass spectrometer Plumb the valve for divert...

Page 41: ...ent calibration Replace the CDS Bottle WARNING Toxic Chemical Hazard Refer to the chemical product Safety Data Sheets and follow all of the recommended safety procedures when handling storing and disp...

Page 42: ...Control dialog opens Figure 3 6 Device Control CDS 2 Click Start Stop the CDS 1 On the status panel click the Direct CDS Control icon 2 Click Stop Flush the CDS WARNING Toxic Chemical Hazard Refer to...

Page 43: ...IEX OS follow these steps to put the CDS into Wash mode a On the status panel click the Direct CDS Control icon The Device Control dialog opens Figure 3 7 Device Control CDS b Select Wash Mode This al...

Page 44: ...tube into the new bottle of calibrant solution To conserve sample purge for only 10 seconds or until 2 mL to 3 mL of solution accumulates in the waste container Tip We recommend that the tubing be flu...

Page 45: ...st select the required model 7 Click Settings to edit settings or restore default values 8 Click Test Device to verify that the device is configured correctly and available for use 9 Click Save 10 Rep...

Page 46: ...ot valid and requires updates 8 Click Save 9 Click Activate Devices All of the devices that are selected in the Devices list are activated Delete Devices Note If the device that is being deleted is pa...

Page 47: ...3 Click Deactivate SCIEX X500 QTOF System System User Guide 47 234 RUO IDV 05 2334 E Configure Devices...

Page 48: ...rmissions Users can be assigned to more than one role Table 5 1 Role and Permissions Reviewer Analyst Method Developer Administrator Permission No Yes Yes Yes Access the Queue workspace No Yes Yes Yes...

Page 49: ...eate reports and save unlocked Results Tables Modify column settings Add custom columns Unlock Results Tables Yes No Yes Yes Transfer to LIS No Yes Yes Yes Access the following basic quantitation sett...

Page 50: ...erring data to a LIMS and reporting The other sources of output data such as copying and pasting from Results Tables are not controlled Do not use uncontrolled output methods for regulated purposes Ta...

Page 51: ...ject Secure Export Settings No Yes Yes Yes Add samples to the Results Table No Yes Yes Yes Remove samples from the Results Table No No Yes Yes Modify the Sample Name No Yes Yes Yes Modify Sample Type...

Page 52: ...es Modify the processing method for the Results Table component Yes Yes Yes Yes Create use or export Metric Plots in Results Tables No No Yes Yes Add Rename or Modify custom columns No No Yes Yes Remo...

Page 53: ...or Group dialog opens 3 Add the user as required and then click OK 4 Click OK The new user is included in the list of users in the left panel of the workspace 5 Click the new user in the left panel 6...

Page 54: ...tion Management System LIMS Settings Use this feature to connect to an LIS server Users can import batch information from as well as export results to an LIS 1 Open the Configuration workspace 2 Click...

Page 55: ...proceeds to the next sample if a sample is missing 6 Select the If calibration fails proceed to the next sample check box The queue proceeds to the next sample if the calibration is failing 7 Select t...

Page 56: ...m the Add to Compound Library list Type the name of the library in the Add to Compound Library list field 9 Click Next Note If the user cancels the import before all of the compounds have been copied...

Page 57: ...ave already been imported remain in the database The software does not revert the database to the pre import state 10 Resolve any conflicts if required 11 Click Finish Import a Cliquid Package 1 Expan...

Page 58: ...File 1 Expand the Compounds list in the Manage pane 2 Click All Compounds 3 Click the Import icon 4 Click Excel file xls on the Library Importer dialog 5 Navigate to the appropriate file on the Open d...

Page 59: ...y compounds that have already been imported remain in the database The software does not revert the database to the pre import state 15 Resolve any conflicts if required 16 Click Finish Import a Libra...

Page 60: ...ounds to a library Select the appropriate library from the Add to Compound Library list Type the name of the library in the Add to Compound Library list field 9 Click Next Note If the user cancels the...

Page 61: ...on dialog opens 7 Type the license key exactly as shown in the appropriate field If a license key is not available then contact sciex com request support 8 Click Generate Computer ID This creates a un...

Page 62: ...library containing a group of compounds or installing individual compounds the software searches the database for compounds with the same name or formula as a compound in the package If compounds are...

Page 63: ...rwrite All on the Library Importer dialog to overwrite all of the compound information stored in the database with the corresponding compound information from the import package Click Resolve beside t...

Page 64: ...he search criteria is typed the visible columns are searched and refreshed to show only the information that matches the criteria specified 5 Double click the appropriate compound 6 Double click the a...

Page 65: ...one of the following to add spectrum to the compound For IDA data click Add Spectrum in the Acquired Spectrum pane For EPS MRM and looped data double click the TIC and then click Add Spectrum in the...

Page 66: ...Access to workspaces is determined by the role assigned to the user as well as the software license Within each workspace the user can manually start acquisition or view and explore data that is being...

Page 67: ...ently open workspace remains active and the workspace icon is shown in the ribbon To close the active workspace click To return to the home page click 6 Functions Acquisition Processing and Management...

Page 68: ...ive workspace 2 Shows the status of the workspaces A dark blue background indicates that the workspace is closed A light blue bar at the left indicates that the workspace is active A light blue backgr...

Page 69: ...maining for the batch to be acquired View the system status or status of the individual devices that have been activated in Devices list in the Configuration workspace Access direct device control Vie...

Page 70: ...Figure 6 4 SCIEX OS Status Panel System User Guide SCIEX X500 QTOF System RUO IDV 05 2334 E 70 234 Operating Instructions Software...

Page 71: ...icon to access controls for the device The optional syringe can be started or stop on the Device Control dialog 5 Shows the status of the device The icon is a view only indicator of the status of the...

Page 72: ...OK Show the Status Panel Click the colored bar at the top of the minimized status panel Hide the Status Panel Click the colored bar at the top of the status panel The status panel minimizes to the rig...

Page 73: ...n Stop 5 Click to save data Save 6 Click to explore data in real time 7 User Workflows Analysts Table 6 1 Analyst Workflow Software Access Task Refer to About the Home Page on page 66 and About the St...

Page 74: ...ethods Administrators Software Access Task Refer to Select Laboratory Information Management System LIMS Settings on page 54 Configure the LIMS Refer to Configure Access to the Software on page 48 Add...

Page 75: ...s Click Manage Insert Row Insert a row Click Manage Delete Row Delete a row Click Manage Select Columns Refer to Show or Hide Columns on page 87 Select columns Click Manage Add component concentration...

Page 76: ...ave As The Save As Batch dialog opens 11 Type a file name in the File Name field and then click Save 12 To use the plate layout as a reference for selecting or confirming a sample location click Plate...

Page 77: ...pens 4 Do the following a Type the file location or file name b Optional Click the Append to the current batch check box c Click Import 5 To use the plate layout as a reference for selecting or confir...

Page 78: ...cally provides well and vial positions for unassigned samples 7 Type the batch information in the grid 8 Optional Click Save 9 Make sure that the column oven temperature is reached before submitting t...

Page 79: ...e of the valid choices for the autosampler specified in the LC method Describes the rack type for the autosampler Rack Code Numerical value The position of the rack on the tray Rack Position Must be o...

Page 80: ...in the MS method for MRM scans or in the processing method for other scans The name is validated during method creation MRM HR scans The name of a compound defined in the MRM method Other scans The na...

Page 81: ...t sample positions as needed in the graphical representation to populate the grid in the Batch workspace If sample positions are typed directly in the grid in the Batch workspace then the graphical re...

Page 82: ...Calibrate The Batch Automatic Calibration Editor dialog opens 3 Click Edit The Ion Reference Table Editor dialog opens 4 Click New Tip Use the Tab key to move between cells and press Enter to add a r...

Page 83: ...eck box to the left of the Auto Calibrate button is selected 8 Create and submit a batch Calibrate the System Using an LC Method 1 Open the Batch workspace 2 Click Auto Calibrate The Batch Automatic C...

Page 84: ...system is equilibrated prior to submitting a batch Refer to Equilibrate the System on page 84 Note Run the sample again in the event of an abnormal termination during sample acquisition If the abnorm...

Page 85: ...the acquired selected batches or samples a Click the batch header b Click Manage Move row to top Move the selected batch or sample to the top of the queue a Click the sample b Click Manage Move row up...

Page 86: ...nt the queue Submit a Single Sample to the Queue 1 Select the row index number of the sample 2 Make sure that the system is equilibrated prior to submitting the batch 3 Click Submit If errors are show...

Page 87: ...mponent Concentration Column Use this procedure to add a component concentration column to the batch Note Component concentration columns added with this procedure are editable for all samples Compone...

Page 88: ...sample or batch is being acquired In Progress The sample or batch has not been acquired yet or is not in the process of being acquired Waiting There was a barcode reading error or a mismatch of the b...

Page 89: ...ameter Users can set the starting and ending voltages and the size of the steps in between Ramping can be used to optimize parameter for ions For TOF MS methods users can ramp DP parameter For TOF MSM...

Page 90: ...the procedure is completed the parameters are used to populate the MRM HR method Table 6 6 Basic Method Experiment Definition Type Mass analysis using the TOF region The m z values of the ions are ret...

Page 91: ...quire high quality MS MS data from compounds with known masses and retention times This acquisition can also be used to extract fragment masses with narrow widths 0 02 Da from TOF MSMS spectra The nar...

Page 92: ...nt and then click Delete TOF MS of MRM HR Note Only applied to the looped experiments In an MRM HR experiment remove the TOF MS from the method Click the list next to Experiment and then click Delete...

Page 93: ...harge states for optimal performance Dynamic Collision Energy TOF MS TOF MSMS IDA SWATH MRM HR Shown when the Apply intact protein mode feature is selected Select this feature when analyzing intact pr...

Page 94: ...to focus the ions as they pass through the collision cell the preset for the CAD parameter is in fixed mode For MS MS scan types the CAD gas helps to fragment the precursor ions When the precursor io...

Page 95: ...voltage the higher the energy imparted to the ions If the DP parameter is too high then unwanted fragmentation might occur Declustering potential TOF MS TOF MSMS IDA SWATH MRM HR The DP spread paramet...

Page 96: ...n time Q1 Type the start mass for the Q1 scan range Start mass Q1 Type the stop mass for the Q1 scan range Stop mass Q1 The time required to scan the Q1 mass range Scan time SWATH Click to open the Au...

Page 97: ...S Q1 IDA Select a resolution to use to separate closely spaced components Q1 resolution is the resolving ability of the quadrupole When more sensitivity is required in an MSMS experiment the resolutio...

Page 98: ...ratio is high The dynamic background subtract filter can be used with the other standard filters in the IDA criteria section Dynamic background subtraction Specify the minimum intensity ion counts pe...

Page 99: ...out the acquisition Dynamic accumulation Select to specify the m z range for the candidate ions The candidate mass range is always the subset of the TOF MS mass range Candidate mass range Select to sp...

Page 100: ...sity cps Specify the intensity threshold for the ion on the inclusion list If the candidate ion surpasses the threshold in cps then it is preferentially selected for MS MS Inclusion List Select the ch...

Page 101: ...automatically calculates the associated molecular weight MW The MW tolerance Da is the window centered around the calculated MW If a candidate ion has a mass defect that meets the mass defect the mass...

Page 102: ...which to perform MS MS For example monoisotopic ion or most intense ion Isotopic Calculator Automatically calculate the isotope pattern based on a user specified formula or charge state and H charge a...

Page 103: ...second TOF MS experiment Note High CE is greater than the Low CE value for positive polarity Low CE is greater than the High CE value for negative polarity Tolerance mass Specify the tolerance applie...

Page 104: ...Verify the Presence of an Analyte 1 Open the Explorer workspace 2 Click File Open Multiple Samples Figure 6 7 File Menu Options 3 In the Select Samples dialog select the samples from the Available lis...

Page 105: ...lick Show Data and Peaks Table Figure 6 9 Show Menu Options 9 Review the peak area intensity masses and charge states of the compounds Extract Ions Used to calculate one or more overlaid extracted ion...

Page 106: ...d the file click the sample and then click the arrow 4 Click OK 5 Click Show Extract Ion Chromatogram XIC Figure 6 11 Show Menu Options The Specify XIC Ranges dialog opens 6 Type the Center Width and...

Page 107: ...Specify XIC Ranges dialog and then use the features shown Figure 6 12 Specify XIC Ranges Dialog Right click Menu 8 Click OK If the active graph contains overlaid series from different samples then th...

Page 108: ...and the file click the sample and then click the arrow 4 Click OK 5 Click Show Total Ion Chromatogram TIC If the active graph contains overlaid series from different samples then the Process All Overl...

Page 109: ...f required click Font to adjust the font properties and then click OK The caption is added at the x y position where the user right clicked to open the menu After the caption has been added the user c...

Page 110: ...mage 7 Deletes the selected image from the graph Delete Image 8 Open a Base Peak Chromatogram Generates a plot of the intensity of the largest peak in each spectrum as a function of time 1 Open the Ex...

Page 111: ...es is active when the base peak chromatogram is being generated then the time range defaults to the time range for the selection Otherwise the last time range is used The limited time range saves the...

Page 112: ...unless the user holds the Shift key to change the option Show the Data and Peaks Table The Data and Peaks Table contains two different tables The Data table shows the raw x y values comprising a data...

Page 113: ...ble list and then click the arrow to move the files to the Selected list Tip To select one sample expand the file click the sample and then click the arrow 4 Click OK 5 Click Show Data and Peaks Table...

Page 114: ...then click Export Peak List as Text Saves the entire peak list to the specified file This does not include peaks that are below the current threshold set in the y axis of the associated graph The vari...

Page 115: ...he sample and then click the arrow 4 Click OK 5 Click Show Sample Information Show the Graph Selection Information This window shows information about the selected region in a chromatogram or spectrum...

Page 116: ...the arrow to move the files to the Selected list Tip To select one sample expand the file click the sample and then click the arrow 4 Click OK 5 Click Window Graph Selection Window The Graph Selectio...

Page 117: ...e graph Figure 6 24 Graph Selection Info 7 Select an option from the list Default Info XY Info Standard Deviations or Signal Noise 8 Use the features in Table 6 12 as required SCIEX X500 QTOF System S...

Page 118: ...k in data points at half of its height If no peak was found in the selected region then this field is not shown Points Across Peak at 50 The width of the peak at its base If no peak was found in the s...

Page 119: ...iation is shown for the noise region Average and Std Deviation For the peak selection or selections this is the peak height minus the average y value from the noise region that is the peak height abov...

Page 120: ...e graph is obscuring the information Semi transparent when not active 3 10 Optional Click the Fill Peaks icon In the active graph switches between a mode in which peaks are filled using alternating da...

Page 121: ...Click Edit and then use the features in Figure 6 27 Figure 6 27 Edit Menu Options Description Label Item Copies the current data to the clipboard When a spectrum or chromatogram is active a picture o...

Page 122: ...ranges Refer to Set Options on page 143 Options 6 Use this option to return to the default Explore options Refer to Reset Options on page 143 Reset Options 7 Work with Data in Graphs 1 Open the Explo...

Page 123: ...Figure 6 28 Blue Arrow on the Y axis 5 Use the features shown in Figure 6 29 SCIEX X500 QTOF System System User Guide 123 234 RUO IDV 05 2334 E Operating Instructions Software...

Page 124: ...Figure 6 29 Graph Menu Options System User Guide SCIEX X500 QTOF System RUO IDV 05 2334 E 124 234 Operating Instructions Software...

Page 125: ...ata file b Select a portion of the graph c Click Graph Expand Selected Y Values by d In the Expand Selection dialog type the expansion factor e Click OK Expand Selected Y Values By 2 Removes all of th...

Page 126: ...less intense color than normal Use this feature to focus on the active trace The inactive traces are less distracting To return to the original style select the feature again In a graph that has more...

Page 127: ...s the Set Trace Colors Using Pattern Matching dialog When multiple graph traces are overlaid the software uses default colors for the overlays Use this option to set specific colors for traces for whi...

Page 128: ...Depending on where the cursor is released the first pane changes positions relative to the second As the user drags the pane one side of the second pane is highlighted in red to indicate where the fir...

Page 129: ...ot kept That is negative y values are discarded Hold the Shift key to keep the points with negative intensity Subtract Data Overlays the active data in the source graph on the target graph After the o...

Page 130: ...l Item Opens a window showing information for the selected region in the active graph For example the x range of the selection the intensity range of the selected points and so on If this window is al...

Page 131: ...ssian Smooth Applies a Gaussian smoothing algorithm This is a filter of a specified width where the weighting factors follow a Gaussian or normal function 1 Open the Explorer workspace 2 Click File Op...

Page 132: ...ph then select Process all overlays otherwise active data only to apply the operation to all of the traces If the Only show this dialog again if the shift key is down check box is selected then the se...

Page 133: ...old Data If the active graph contains overlaid series from different samples then the Process All Overlays dialog opens Figure 6 35 Process All Overlays Dialog 6 If the Process All Overlays dialog ope...

Page 134: ...ata 1 Open the Explorer workspace 2 Click File Open Multiple Samples Figure 6 36 File Menu Options 3 In the Select Samples dialog select the samples from the Available list and then click the arrow to...

Page 135: ...nge the option Baseline Subtract Chromatogram Removes a relatively slowly varying background from a chromatogram For each data point in the chromatogram a window is centered at the corresponding x val...

Page 136: ...opens Figure 6 39 Baseline Subtract Dialog 6 Type a value in minutes in the Subtraction half window 7 If there are multiple traces in the active graph then select Process all overlays otherwise active...

Page 137: ...ct Samples dialog select the samples from the Available list and then click the arrow to move the files to the Selected list Tip To select one sample expand the file click the sample and then click th...

Page 138: ...d then the selected action is used unless the user holds the Shift key to change the option 8 Select the User incremental offset to fan out overlays to spread the overlays apart in the time direction...

Page 139: ...es to the Selected list Tip To select one sample expand the file click the sample and then click the arrow 4 Click OK 5 Click Process Centroid Spectrum The Centroid dialog opens 6 Use the features sho...

Page 140: ...tensity This value is useful because it does not depend only on the intensity of a single data point as do the Intensity and Height features and it is not influenced by the edges of the peak which may...

Page 141: ...one sample expand the file click the sample and then click the arrow 4 Click OK 5 Click File Export Data as Text If spectral data is exported then the Add Zero Intensity Points for Export dialog open...

Page 142: ...igure 6 46 File Menu Options 3 In the Select Samples dialog select the samples from the Available list and then click the arrow to move the files to the Selected list Tip To select one sample expand t...

Page 143: ...kspace to their default values This includes the options described in the previous section as well as processing options Resetting the options only affects the currently logged in Windows user not oth...

Page 144: ...ph Appearance Tab 4 Click the Peak Labeling Finding tab 5 Select Mass Spectra from the list 6 Use the features shown in Figure 6 49 System User Guide SCIEX X500 QTOF System RUO IDV 05 2334 E 144 234 O...

Page 145: ...ass Spectra 7 Select Chromatograms from the list 8 Use the features shown in Figure 6 50 Figure 6 50 Options Dialog Peak Labeling Finding Tab Chromatograms SCIEX X500 QTOF System System User Guide 145...

Page 146: ...to processing options do not apply to dynamically updating spectra Figure 6 51 Options Dialog Auto Processing Tab 11 Click the XIC tab 12 Use the features shown in Figure 6 52 System User Guide SCIEX...

Page 147: ...is not supported in the Analytics workspace Do not group numbers in any text box for example integration parameters or grid for example Results Tables Processing methods include the criteria used to...

Page 148: ...ey do not need to be adjusted individually for every component However no one set of parameters is likely to be ideal for all components so it might be necessary to adjust some of the parameters indiv...

Page 149: ...7 Select the Acceptance Criteria page and then select the acceptance criteria for peak integration accuracy of standards and quality controls and the calculated concentration range for the unknown sam...

Page 150: ...ssions of Results Tables have been tiled either vertically or horizontally then click Views Reset layout to return the Results Tables to their original layout Table 6 15 Right click Menu Description L...

Page 151: ...ternal standard and all of the internal standards are present in these samples at the same concentration then use this option to provide a shortcut for setting the actual concentration field for all i...

Page 152: ...153 About Results Tables on page 150 Acceptance Criteria on page 153 Confidence Traffic Lights on page 154 Add Samples This option adds additional samples to a currently active Results Table 1 With a...

Page 153: ...sample type and then set the Actual Concentration at 0 Blanks Shows only Double Blank samples These are samples with neither internal standards nor analytes Double Blanks Shows only Solvent samples Th...

Page 154: ...l percent difference level defined in the processing method Shows which components meet the unacceptable percent difference level defined in the processing method Shows which confidence parameters are...

Page 155: ...Import 1 Click to save the current dialog settings to a file Use the Import button to import and use these settings This option lets the user switch between different column layouts Export 2 The name...

Page 156: ...able based on the selection Selecting a category helps the user to easily find a column in the Results Table All Columns 10 2 Select or clear the check box in the Visible column as required Table 6 19...

Page 157: ...For the control sample the area ratio for found peaks is always 1 000 Area Ratio of Control Y Shows the distance from the center line of the peak to the back slope divided by the distance from the ce...

Page 158: ...ard in the original processing method Component Index Y Shows the name of the analyte or internal standard This column is always visible in the Results Table In the Column Settings dialog the check bo...

Page 159: ...only Formula Confidence N Shows the single number score that can be used for relative comparison purposes The value is can be updated using data from the Peak Review Formula Finder Results Table Appli...

Page 160: ...nsorted order If the table is sorted based on another column then it can be returned to the original order by sorting on this column This column is always visible in the Results Table In the Column Se...

Page 161: ...of the Analyte and IS subgroups the Qualifier is itself for the Quantifier If the integration changes for either of the Quantifier or the Qualifier peaks then the Ion Ratio is calculated again Can be...

Page 162: ...End Time N Shows the expected retention time for the internal standard associated with the current analyte For internal standards or for analytes without an internal standard the value is set to N A I...

Page 163: ...ithout an internal standard the value is set to N A IS Width at 50 N Shows the level of confidence in the isotope ratio Applicable to qualitative workflows only Isotope Confidence N Identifies the dif...

Page 164: ...cates whether the peak was found by the Enhanced Peak Finder Applicable to qualitative workflows only Non Targeted Peak Y Shows the name of the instrument operator who acquired the sample Operator Nam...

Page 165: ...ive workflows only Retention Time Error N Shows the confidence in the retention time Applicable to qualitative workflows only RT Confidence Y Shows a user specified comment for the sample Sample Comme...

Page 166: ...nt side of the peak where the intensity is at 10 of the peak height Start Time at 10 N Shows the time in minutes along the front side of the peak where the intensity is at 5 of the peak height Start T...

Page 167: ...d Results Table is opened again Note Adjust the column widths and column order using the header row of the Results Table Drag the header border to change the width Drag the column header to another lo...

Page 168: ...sults Table Metric Note The manufacturer assumes no responsibility or contingent liability including indirect or consequential damages after data has been exported from the Analytics workspace Exporti...

Page 169: ...an be determined Correct chromatograms that did not integrate properly ether by adjusting the peak finding parameters or by manually selecting the starting and ending points for integration After a ch...

Page 170: ...ip If the peak has just been modified then revert the peak to the original method by right clicking and then clicking Revert Peak to Original Method View Options In an open Peak Review pane click View...

Page 171: ...eak Review pane Integration parameters Shows the navigation buttons Click the buttons to move between components move between samples or start the slide show Refer to Review Peaks on page 169 Show nav...

Page 172: ...parameters including the expected retention time for all components for the group at once This feature is not useful if the components for the groups do not have the same retention times Adjust the pe...

Page 173: ...eak Review pane 1 In a Peak Review pane click View and then click XIC MS XIC MS MS or XIC MS MS MS The search results are shown below the graphs Figure 6 54 Library Search Results 2 Click the blue arr...

Page 174: ...row again to collapse the table The results shown in the collapsed table are also shown in the Results Table 8 Click to update the Formula Finder Results column in the Results Table with the selected...

Page 175: ...la The results are shown in groups of 40 compounds Use the right arrow to advanced to the next group in the list Use the left arrow to return to the previous group in the list 1 Spectra pane Shows the...

Page 176: ...nts tab of the fragment table pane The remaining panes refresh In the spectra pane red arrows appear at the top and bottom of the matching fragment in blue In the structure pane the components of the...

Page 177: ...sed for the calculations Samples are not used if the corresponding peak could not be integrated or if the Used field has been manually cleared Num Values The average of the used samples Mean The stand...

Page 178: ...ght The Height field of the Results Table is used Calibration Y Value The regression parameter specified for the analyte is used This is either Area or Height for an analyte that does not have a corre...

Page 179: ...not present If neither QC samples nor excluded standard samples are shown then this option is not available and no legend is drawn Show legend When this option is selected the Y axis is expressed as a...

Page 180: ...e sure that the integration was successful 3 Use the Export Calibration command to save a copy of the calibration 4 Create a new Results Table containing samples of unknown concentration 5 Click Impor...

Page 181: ...ber in the table If two columns are selected then the values from the columns are plotted against one another The first of the two columns to be selected contains the x values and the second the y val...

Page 182: ...ponents and the response for the metric for the components is significantly different Use percent Y axis Changes whether the y axis starts at y 0 or at the minimum y value needing to be plotted Start...

Page 183: ...es click the Sessions list and then select another file Tip The user can also select to view all of the Results Tables in the project at the same time Filter Audited Events Using a Keyword Search The...

Page 184: ...iteria Figure 6 57 Filter Audit Trail Events Dialog Description Label Item Use to filter on a specific word or phrase is 1 Use to filter on a partial word or phrase contains 2 Name of the Results Tabl...

Page 185: ...r to reset all of the filter criteria to No filter 7 Click OK to filter the events Tip Click Remove Filter in the Audit Trail Viewer dialog to remove the filter Print the Audit Trail Viewer 1 Open the...

Page 186: ...The specified percentage of the data points with the smallest intensity are assumed to be noise Typical values range from 20 to 60 If small peaks in the presence of larger peaks are not being found th...

Page 187: ...oint with minimum intensity within the subtraction window The exact value of this parameter is not critical provided that it is set at least a few times larger than the expected peak width In Figure 6...

Page 188: ...are assesses changes to the baseline locally around the peak as opposed to calculating the baseline with respect to the entire chromatogram Linear peak baseline The software fits a line between the po...

Page 189: ...e the user is responsible for validating the template 1 Open the docx template The Reporter template editor opens on the right The template editor is automatically populated with the tag information F...

Page 190: ...Change the field type Click inside the tab and then change the attributes as required Change the attributes of the field type Click the Add new tag icon select the Field Type and then select the attri...

Page 191: ...e All the qualitative confidence traffic lights are listed at the beginning of the table All Peaks Qual A report showing the File Information for each analyte and an XIC table for each Blank each Stan...

Page 192: ...ng of the table Positive Hits Qual A report in csv format showing for each sample a section including the File Information Sample Information and Analyte Results Table Qual CSV report A report showing...

Page 193: ...closing the MS Tune workspace Restore the previous settings by selecting the appropriate backup file from the Restore Instrument Data menu Optimize the Detector When the system sensitivity is low use...

Page 194: ...flow 4 Select the correct channel 1 or 2 click Start and then close the window 5 Wait at least 1 minute for the CDS to equilibrate 6 Make sure that the spray is stable 7 Click Next 8 Follow the on sc...

Page 195: ...the MS Tune workspace Restore the previous settings by selecting the appropriate backup file from the Restore Instrument Data menu Contact sciex com request support Tune Q1 High In MS MS experiments...

Page 196: ...ng Procedures list 3 Select a scan type 4 Click Edit Method and then edit the parameters in the Live Window window as required 5 Click Start Restart Method 6 View the data and then adjust the paramete...

Page 197: ...t be helpful in troubleshooting and performing system diagnostics View Logs 1 Open the Event Log workspace 2 Click an item from the list in the left panel to view the logs Print Logs 1 Open the Event...

Page 198: ...alog opens Figure 6 65 Archive Log Dialog 3 In the Archive event log items older than field click the date icon and then select a date 4 Click Archive System User Guide SCIEX X500 QTOF System RUO IDV...

Page 199: ...micals have been used with the system Recommended Maintenance Schedule Table 7 1 provides a recommended schedule for cleaning and maintaining the system Tip Perform maintenance tasks regularly to make...

Page 200: ...ttle Contact the local QMP or FSE Clean As needed Orifice plate front and rear Contact the local QMP or FSE Clean As needed QJet ion guide and IQ0 lens Contact the local QMP or FSE Clean As needed Q0...

Page 201: ...n if system sensitivity degrades Tip Clean the Q0 region regularly to minimize the impact of charging a significant loss of sensitivity of the ions of interest over a short period of time on the quadr...

Page 202: ...th and safety guidelines refer to Chemical Precautions on page 11 Symptoms of Contamination The system might be contaminated if any one of the following is observed Significant loss in sensitivity Inc...

Page 203: ...Practices WARNING Hot Surface Hazard Let the ion source cool for at least 30 minutes before starting any maintenance procedures Surfaces of the ion source and the vacuum interface components become h...

Page 204: ...cleaning solution pour the solution on the wipe or swab Allow only the center area of the wipe to contact the mass spectrometer surface Cut edges can leave fibers behind Tip Wrap the wipe around a the...

Page 205: ...ystem Damage Do not drop anything into the source drain when the ion source is removed Figure 7 2 Source Drain on the Vacuum Interface 1 Deactivate the devices Refer to Deactivate Devices on page 46 2...

Page 206: ...place by three retaining ball catches mounted on the orifice plate Tip If the curtain plate does not immediately separate from the orifice plate then turn the curtain plate slightly less than 90 degr...

Page 207: ...ng solution 3 Wait until the orifice plate is dry 4 Inspect the orifice plate for solvent stains or lint removing any residue with a clean slightly damp lint free wipe Note Persistent spotting or film...

Page 208: ...w the steps in this procedure to empty the bottle 1 Remove the ion source Refer to the ion source Operator Guide 2 Loosen the clamps connecting the hoses to the cap of the source exhaust drain bottle...

Page 209: ...exhaust drain bottle Make sure that the bottle is secured to prevent spillage 4 Connection to the mass spectrometer 1 6 cm 0 625 inch i d 5 Roughing pump vacuum inlet hose 6 Note Source exhaust hose...

Page 210: ...w module is a dimension critical 10 cm length of black tubing that controls the flow rate of the calibrant into the ion source Figure 7 5 Check Valve and Flow Module Description Item To the CDS 1 Chec...

Page 211: ...s the flow module to the probe Inspect the Roughing Pump Oil Level Inspect the sight glass on the roughing pump to verify that the oil is above the minimum level If the oil is below the minimum level...

Page 212: ...ing of components If the mass spectrometer must be stored for a long time or prepared for shipping then contact a SCIEX FSE for decommissioning information To disconnect power from the mass spectromet...

Page 213: ...e of burns Surfaces of the mass spectrometer become hot during operation Prerequisites Shut down the system It is not necessary to vent the system Refer to Shut Down and Vent the System on page 37 Tur...

Page 214: ...trometer 5 Install a short block on each lifting bar and then secure it with a locking pin CAUTION Potential System Damage Make sure that all locking pins are fully inserted to avoid dropping the mass...

Page 215: ...ote The end of the bar with the longest extension past the block must be at the front of the mass spectrometer 7 Repeat step 6 on the left side of the mass spectrometer 8 Install the locking pins in t...

Page 216: ...and then secure them with two locking pins Figure 7 11 Tall Block Installed 10 At the front of the mass spectrometer insert a short rod through the tall blocks 11 Secure the short rods with two lockin...

Page 217: ...ure 7 12 Installing the Locking Pin on the Short Rod Figure 7 13 Lifting Kit Installed X500R System SCIEX X500 QTOF System System User Guide 217 234 RUO IDV 05 2334 E Service and Maintenance Informati...

Page 218: ...allow the system to be taken off and put onto the bench For X500R systems only positions 1 through 9 are required Figure 7 14 Distribution of Operators X500B System 13 With the assistance of one addit...

Page 219: ...l is opened to service the mass spectrometer Figure 7 15 Correctly Installed Clamp Generate a Support Package 1 Open the Configuration workspace 2 Click About in the left panel 3 Under Service and Sup...

Page 220: ...ressure is too high Contact the local QMP or FSE 1 Ambient temperature is too high A system fault has occurred because the QPS exciter module temperature is too high 1 Confirm the fault in the Status...

Page 221: ...en install and optimize an alternate ion source 10 If the O rings are on the ion source then install them on the vacuum interface If they are missing then contact an FSE 11 Troubleshoot the LC system...

Page 222: ...the sample has degraded 3 The sample inlet fittings are leaking The mass spectrometer performance has degraded Turn the corona discharge needle toward the curtain plate and away from the stream of hea...

Page 223: ...alibration Solution for the SCIEX X500R System 5042912 5 100 mL ESI Positive Calibration Solution for the SCIEX X500R System 5 pack 5042916 100 mL ESI Positive Calibration Solution for the SCIEX X500B...

Page 224: ...56 Fragment ion 4 365 1860 227 0496 Fragment ion 5 236 1281 220 1121 Fragment ion 6 195 0652 86 0964 Fragment ion 7 174 0913 58 0651 Fragment ion 8 Table A 5 TOF MS MS Negative Product Ions 403 1122 2...

Page 225: ...738 112 9856 68 9958 1472 7337 1336 7589 1200 7841 1064 8092 928 8344 792 8596 656 8848 2233 9115 2165 9241 1880 6581 1633 9498 1565 9624 1744 6833 1608 7085 Table A 8 TOF MS MS Positive Product Ions...

Page 226: ...Declustering Potentional V 30 22 20 16 15 Collision Energy V 1200 784 792 8596 520 9100 384 9352 248 9604 Fragment Ion 1 1064 809 656 8848 384 9352 248 9604 204 9706 Fragment Ion 2 928 8344 520 9100...

Page 227: ...ontinued 1200 784 792 8 520 9 384 9 248 9 Precurcor Ion m z 248 9604 112 9856 N A N A N A Fragment Ion 8 204 9706 N A N A N A 154 9738 N A N A N A SCIEX X500 QTOF System System User Guide 227 234 RUO...

Page 228: ...lar Ion C33H41N2O9 448 19659 Fragment C23H30NO8 397 21218 Fragment C23H29N2O4 365 18597 Fragment C22H25N2O3 236 12812 Fragment C13H18NO3 195 06519 Fragment C10H11O4 174 09134 Fragment C11H12NO System...

Page 229: ...er number is the Environmentally Friendly Use Period EFUP date and indicates the number of calendar years the product can be in operation Upon the expiration of the EFUP the product must be immediatel...

Page 230: ...sion Hazard Fire Hazard Fragile Fuse Hertz Hz High Voltage Electrical Shock Hazard If the main cover must be removed contact a SCIEX representative to prevent electric shock Hot Surface Hazard Ionizin...

Page 231: ...cturer Personal Injury Hazard Pinch Hazard Pressurized Gas Hazard Protective Earth ground Puncture Hazard Serial number Toxic Chemical Hazard USB 2 0 connection Ultraviolet Radiation Hazard SCIEX X500...

Page 232: ...lt Ampere power VA Volts voltage V WEEE Do not dispose of equipment as unsorted municipal waste Watts W yyyy mm dd Date of manufacture System User Guide SCIEX X500 QTOF System RUO IDV 05 2334 E 232 23...

Page 233: ...OR TIP N TELL INDICATORS ON THE WAYBILL BEFORE ACCEPTING SHIPMENT NOTIFY YOUR LOCAL SCIEX CUSTOMER SUPPORT ENGINEER IMMEDIATELY IMPORTANT RECORD ANY VISIBLE CRATE DAMAGE INCLUDING TRIPPED IMPACT O GR...

Page 234: ...QUIPMENT WARNING Lifting Hazard NINE PERSONS REQUIRED TO LIFT THIS EQUIPMENT X500B Systems WARNING Lifting Hazard TEN PERSONS REQUIRED TO LIFT THIS EQUIPMENT WARNING Lifting Hazard TEN PERSONS REQUIRE...

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