TOF/QTOF Users Meeting. Jim Lau, Agilent Technologies.

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1 TOF/QTOF Users Meeting Jim Lau, Agilent Technologies.

2 Agenda Goal Share Best Practices, Develop Network of Agilent Users Today s Topics: Care and Feeding Agilent LCMS Systems Data Acquisition: Optimize TOF/QTOF for Best Mass Accuracy MassHunter Qual: MFG and MFE for Small and Large Molecule Applications Overview MassProfiler Software MassHunter Bioconfirm Software Questions and Answer Period

3 Care and Feeding of QTOF/TOF (Cont.) Defragment Hard Drives (Weekly) Use Diskeeper to Defragment Drives If Errors Run Check Disk for Errors Program Check LC Components Firmware If older version update LC Firmware

4 Data Acquisition Overview How to Improve Mass Accuracy Optimize Source Parameters: Drying Gas Temperature and Flow; Fragmenter Voltage Optimize Ion Transmission in Quads For Low Mass Analytes < 300 Change Quad Amu Gain to 100 Review How to Calibrate/Tune Q(TOF) Optimize Points Defining a Peak Reduce maximum mass from m/z 3200 to 1700 Increase Acquisition Rate MS (2-4 spectra/s) Causes of High Mass Error (> 3ppm) Saturated Ions Unresolved Ions

5 Optimization of ESI Source Parameters VCap Entrance of the Capillary, 2000 to 4500V (3500V) Dependent on compound and MW Concentrated samples (µg/µl) lower VCap Drying Gas - Dependent on LC flow rate L/sec Gas Temp - Start at high temperature work down oc Skimmer - Voltage on skimmer and lens after capillary 65V Fragmentor- Not Same as QQQ/Quad, Compound Dependent Vary fragmentor/scan (30V steps) 120V to 240V FIA with Injection Program or MultiFragmentor acquis.

6 Vary Fragmentor with FIA Injection Program Multiple Methods or Scan Functions Auto Sampler Injection Program REMOTE Startpulse REPEAT 5 times VALVE bypass DRAW Def Amount from Sample, def. speed, def offset VALVE mainpass WAIT 0.75 min END REPEAT Vary Fragmentor Voltage Right Click in Expt Area and select Add Experiment Vary Fragmentor Voltage by 20-40V per Experiment Acquire Data using Injector Program Determine Optimum Voltage from EIC as a Function of Fragmentor Voltage

7 Extracted Ion Chromatograms: Advanced Tab Fragmentor Setting

8 Review How to Tune and Calibrate the Q(TOF)

9 Entering Calibration and Tuning In Mass Hunter Workstation Data Acquisition, select the Tune Context.

10 Set Instrument State for Calibration Mass Range: Low (1700 m/z), Standard (3200 m/z) or High (20000) Instrument Modes: High Resolution (4GHz) 4GHz (High Resolution disabled) Extended Dynamic Range (2GHz) Minimum Storage Size (1 GHz) Agilent 6520 Advanced showing

11 Calibration 1. Turn on MS. 2. Select Instrument State. 3. Select Bottle B. 4. Press Calibrate. 5. Apply Calibrate weekly. Generates fifth order polynomial to accurately assign masses over entire mass range. Takes seconds.

12 Calibration Result - Mass Calibration Curve The Mass Calibration Curve is generated by selecting the Calibrate button. The calibration curve shows the time-to-mass fit of the polynomial correction across the full mass range. Apply accepts new TOF Mass Coefficients to polynomial mass correction function. Residual Error display often exhibits polynomial wave pattern.

13 Calibration Result - Detailed Residual Plot Detailed Residual Plot shows: uncorrected mass error in ppm (blue diamonds). corrected mass error in ppm (red squares) after applying fifth-order polynomial mass correction. actual calibration curve green line.

14 Optimization for Low Mass Operation 1. Calibrate using the entire mass range (High 3200 m/z). 2. Perform an AutoTune. 3. Instrument State change mass range from 3200 to Deselect higher masses not in new range from mass list. 5. Re-calibrate.

15 Mass Calibration Error Reduced The errors have been reduced. Must have 6 points. No gain with fewer points.

16 Automatic and Manual Tuning Automated tuning for most users Manual tuning for diagnostics and special applications

17 Order of Tuning Choices (Check TOF Tune) If necessary, do (Quick TOF Tune) If necessary, do (TOF Tune) If necessary, do FIRST every few months Initial TOF Tune (Check Quad Tune) If necessary, do (Quad Tune) If necessary, do AT PM time (Yearly) Initial Quad Tune

18 Autotunes TOF and Quad Autotune TOF Autotune steps are displayed while the system tunes.

19 Autotune Report

20 Save Tune File When Changing Context Or, save and load tune files in the Instrument State tab. Make certain to specify correct tune file in acquisition method.

21 September 17th, 2008

22 September 17th, 2008

23 New Makeup Procedure for Reference Solution Changing from Acetonitrile to Methanol Solution 2 ml of HP121 into 98 ml of 95/5 MeOH/Water 0.8 ml of HP921 into 99.2 ml of 95/5 MeOH/Water Using a 500 ml volumetric flask, mix 25 ml of HP121 and 921 into 450 ml of 95/5 MeOH/Water with 0.2% Acetic Acid. Internal Reference Mass Correction Two Ions (1 < m/z 350, second 500 amu higher) (m/z , , , , ) Neb Pressure at 5 psi Better for Negative ion performance and for use with APCI and Multimode sources without changing reference solution.

24 Addition of Negative Ion Reference Ion From Acquisition MS TOF Tab General Tab Ion Polarity Negative Ref Mass Tab Right Click Add Input Mass Input Mass Reference Solution can also be introduced using a Binary or Isocratic with a 100:1 splitter designed by Agilent. Flow rate of LC set at between ml/min and gives very stable flow.

25 My Mass Error is Above 3 ppm What should I do? Check for Interference from Chemical Background Change Chromatography Create Narrow (+/- 10ppm) Extracted Ion Chromatogram with subtraction Check Resolution of Peak in Spectrum Peak List Check for Saturated Peak Peak List or * in Mass Spectrum

26 September 17th, 2008

27 September 17th, 2008

28 September 17th, 2008

29 Poor Mass Accuracy Example Unresolved Peaks Spectrum Peak List 1 Table Resolution Column BPC EIC m/z EIC m/z ppm error

30 Compare Manual versus Automated Analysis Find Compounds by Feature Extraction Manual Spectral Subtraction Automated Spectral Extraction

31 QUALITATIVE ANALYSIS

32 Find Compounds by Formula Find Compounds in analysis by inputting: Formulas separate by, A database with Formulas Worklist Formulas

33 Find Compounds by Formula - Options Input Comma Separated Formulas

34 Find Compounds by Formula: Accurate Mass Database Search Modify default.csv file adding formula, RT and exact mass of compound Results Compound Found in Table

35 Find Compounds by Formula Compounds Found

36 Identify Compounds Search a Database after Find Compounds Generate Formulas after a Find Compounds

37 Example: Characterization of Synthetic Urine Mixture of 72 Compounds MW Daltons, Mixed Classes. Acquire ESI Positive and Negative ion MS and MSMS. First Step: Find Compounds by Molecular Feature. Second Step: Search Compound Table by Metlin & Exact Mass Database. Compare Accurate Mass, Coverage, Dynamic Range.

38 Database Searching Search Mode

39 Automated Compound Search Metlin Database

40 Creating a Database Modify existing database file and save to unique name. MassHunter\Databases\default.csv.

41 Mass Hunter Qual Molecular Formula Generation

42 Molecular Formula Generator

43 Molecular Formula Generation Parameters Pull Down Menu.. Compounds or Spectrum Peaks Adduct Selection Electron State: Even Electron Allows none Add Natural Isotopes with [ ] Limits for Matches using MS, MSMS Mass Error, DBE. DBE can be Negative for Sulfate and Phosphate Compounds.

44 Molecular Formula Generator MS Formula Results MS/MS Formula Results

45 Molecular Formula Generation

46 Allowed Species, Limits and Charge State User Inputs

47 Charge State and Isotope Distribution (B.02.00) New in B Isotope Model: Common Organic Molecules Peptides Unbiased (unique isotope patterns) Charge State: 1 or 2 for small molecule for large molecule

48 Isotope Distribution (Experimental/Theoretical)

49 Cross Score (using MFG with MFE)

50 MFG Overview

51 Molecular Feature Extractor (MFE) How it works Map signals in the 3-dim. space in time and mass at the MS level. IMPORTANT: High resolution in mass and time! Remove areas which only contain noise, and NO signals. Identify all mass signals with a common RT (narrow time window) Combine mass signals with common RT and chemical relation (isotope, adduct, dimer, higher charge state) => Molecular feature or Compound. Create Extracted Compound Chromatograms (ECC) and Compound Mass Spectra from ions associated to a molecular feature (compound) Compound list or Molecular feature list RT m/z Abund

52 Find by Molecular Feature

53 Method Editor MFE (cont.) Extraction Parameters Target Data Type Small Molecule Large Molecule Infusion Peak Filters S/N Profile only Peak Height both

54 Method Editor MFE (cont.)

55 Method Editor MFE (cont.)

56 Method Editor MFE (cont.)

57 Method Editor MFE (cont.)

58 Executed

59 Find Compounds by Molecular Feature x10 6 Cpd 279:+ ECC Scan CoffeeSpiked12.d Counts vs. Acquisition Time (min) Over 280 Compounds Found in Coffee Spiked with Pesticide

60 Compound List Use found compounds for further analysis: Use Molecular Formula Generator on list. Search a Database and match findings Upload the MFE results to Mass Profiler or GeneSpring for analysis.

61 Large Molecule Applications Proteins, Oligonucleotides, Peptides

62 API-Electrospray: Multiply-Charged Data Find Molecular Weight of Intact Protein Multiply charged compounds acquire a range of charge states yielding a series of mass peaks for a single compound. Each mass peak represents a different charge state. Compounds in excess of 100,000 Da may be analyzed. Picomole to femtomole full scan spectra. Useful for obtaining molecular weights

63 Green Fluorescent Protein MW 27 kda - Multiple Charged Envelope

64 Determining Charge State of a Multiply Charged Ion m m Determine Charge State: Assume that a pair of ions at m 1 and m 2 are two charge states of the same ion (n 1 and n 2 ), where n 2 = n 1-1 Assume an adduct ion weight, x. (H+ in this example, mass = 1) Calculate charge state for the second ion n 2. If these peaks are related, it must be an integer. n 2 = (m 1 -x)/(m 2 -m 1 ) = ( )/( ) = 4 n 2 = 4

65 Determining Molecular Weight of a Multiply Charged Ion Calculate Molecular Weight, M Use X = hydrogen = 1.0 M = n 2 (m2-x) 4( ) = Repeat for next pair of peaks in the series n 2 = ( )/( ) = 5 M = 5( ) = The next pair(s) form a coherent set if: They calculate out to an integer charge state in the proper series with earlier pairs The calculated MW is close enough to the MW derived from earlier pairs

66 Deconvolute Myoglobin Open the data file. Integrate the data. Obtain background subtracted peak spectrum. Fill in Deconvolute Method parameters.

67 Deconvolution Parameters Highlight spectrum then Execute Mass Range Expected Mass Range of the Protein. Sets the x-axis of the deconvolution result display. Mass Step Resolution of the deconvoluted protein mass range. Use limited m/z range mass range examined in algorithm. Adduct expected adduct, necessary for proper calculation. Proton,ammonium, potassium, sodium, proton loss. Average mass %peak The % of the peak used for the calculation. Isotope width Automatic, old automatic, specified

68 Deconvolution Result Mass intact protein if it were singly charged.

69 MS Spectrum and Deconvolved Spectrum of Horse Myoglobin x10 6 x Scan ( min, 6 scans) myo.d MS Scan ( sec, 8 scans) myo.d Deconvoluted (1) Deconvolved Spectrum Theoretical: Observed: Error: Da ppm Abundance vs. Mass (amu) Abundance vs. Mass-to-Charge (m/z)

70 Export Data

71 Resolved Charge State Deconvolution Converts Isotopically Resolved Charged States to Singly Charged Spectrum Applications: Surfactants Peptides Oligonucleotide HRES Mode Resolves to +13

72 Large Molecule Molecular Feature Extraction

73 Mass Profiling A Powerful Workflow Mass Profiling: is used to find differences between sample sets originally developed for proteomics/metabolomics can be applied to many analytical problems where finding differences between samples is important is done using statistical analysis Molecular Feature: a discrete molecular entity defined by the combination of RT, mass and response in an LC/MS or GC/MS analysis typically represents a known or unknown compound LC/MS or GC/MS Analysis Find molecular features Compare sample sets Identification Validation GC/MS LC/MS MFE (LC/MS) AMDIS (GC/MS) Mass Profiler GeneSpring MS Spectrum Mill Molecular Formulas DB Search (METLIN) Library Search QQQ MRM GeneSpring MS

74 MassProfiler Dependent on MFE Feature Extraction Don t extract all the compounds only Important ones How to Mine for Gold Generated a Base Peak Chromatogram Input Mass Range of Compounds Exclude Reference Ions Input m/z to 4 decimal places Set window to 20 ppm Run Standards to Determine RT Information

75 Good Quality *.MHD Gives Good Quality Profiler 1. Centroid versus Profile data 2. S/N versus Total Counts Typically use 100 counts Too high may not detect C13 peak Profile S/N 10 First Pass 3. Focused MHD generation Limit Retention Time Limit m/z Range 4. Ion Species (NH 4 If buffer) 5. Check Box if High Salt 6. Check if Free Radicals/Quats

76 Good Quality *.MHD Gives Good Quality Profiler 7. Charge State = 1 to detect only singly charged species 8. Last Tabs only for Display in MassHunter QUAL 9. *.ProPos from Profile 10. *.CentPos from Centroid

77 Find Compounds by Molecular Feature

78 Large Molecule Applications Protein Characterization Software Resolved Charge State Deconvolution Maximum Entropy Software Large Molecule Molecular Feature Extraction Bioconfirm B Peptides, Intact Proteins, Oligonucleotides

79 Mass Profiler B Highlights Impurity Profiling/Differential Analysis Software Graphical Displays Mass vs Retention Time Log2 Ratio (Group1/Group2) vs Retention Time Log2 Abundance Group 2 vs Log2 Abundance Group 1 Unique to Group 1 vs RT and Unique to Group 2 vs RT (New) Feature Identification (NEW) Molecular Formula Generation and AMRT database Single Feature or Batch Processing (summary report) Web Internet Database Searching

80 Mass Profiling Software Processed Processed TIC Processed TIC Group TIC A (Impure) Aligns Data RT, Mass, Abundance Processed Processed TIC Processed TIC Group B TIC (Control) What s Changed? Mass/RT >2 Fold Change What s Unique!! Impurity Control All Data RT/Mass

81 Graphical Displays

82 Mass Profiler Reproducibility of Results Reproducible Retention Time Stability Spread in ChromatographyRT Spread of Peak in Time

83 Mass Profiler Reproducibility of Results Outlier Sample or Feature

84 Blue Unique Group 2 and Red Unique Group 1

85 Mass Profiler The Basics Double Click Mass Profiler Icon 1 for Single Group Comparison 2 for Differential Analysis

86 Mass Profiler Load MHD Files *.MHD Data File Location Select Add then add in the *.MHD files in Groups Holding Down ctrl key select all *.MHD to add Then Select OK

87 Set Up Mass Profiler Method *.mpm is Extension of Mass Profiler Project

88 Mass Profiler Edit Method 1. Limit Mass Range and RT 2. For Small Molecule Apps Multiply Charge Forbidden 3. For Biomolecules Apps Multiply Charged Required 4. Abundance to 0.1 to 0.01% 5. Number of Ions >=2 6. Isotope Pattern Matching

89 Mass Profiler How to Import Exclusion List Sort Table By Height/Volume Right Click on Table Select EXPORT From EXCEL Copy Masses From Table

90 Mass Profiler Exclusion List of Masses Paste List of Masses From Blank Into Exclude Masses

91 Mass Profiler Alignment

92 Mass Profiler Results Filters

93 Mass Profiler Special Case No Replicates For Example without Replicates Min Differential Score MUST be set to ZERO before loading *.MHD Files

94 Feature Identification Set Parameters for MFG

95 Identify Composition of Features Right Click any feature in Graph Right Click any feature in Table

96 Individual Feature Results # Compositions and Database Hits

97 Identification Summary Report

98 Feature Details

99 Exact Mass/Formula Database Searching

100 Export Feature Information

101 Questions and Answers

102 METLIN Personal Metabolite Database Software

103 METLIN Personal Database G6825AA Metabolite-specific database for metabolomics research Database installed on a PC Contains ~15000 compounds Manual and batch searches Query based on monoisotopic mass Customizable Add compounds Assign chromatographic retention times to metabolites Create subset databases Works with other Agilent software Cost: $3759

104 METLIN Personal Database Search Capabilities Manual searches Search on neutral or charged monoisotopic mass User-specified search tolerance Optionally restrict by retention time Molecular formula Compound name Retention time (user defined) Batch and manual mass searches from Agilent products GeneSpring MS MassHunter Qual Mass Profiler

105 METLIN Personal Database Initial View User search mode

106 METLIN Manual Single Mass Search Single mass search settings Active metabolite structure Hyperlinks to Metabolite websites Metabolite search results

107 METLIN Batch Search Load file for batch search Active metabolite structure Active mass Active mass search results

108 METLIN Batch Summary Active metabolite structure Batch summary best metabolite match Exportable list of best metabolite search results

109 Creating a New METLIN Database METLIN is read only and can not be changed Create a new personal database from METLIN

110 Edit Metabolite Database Update Entry Add retention time to existing metabolite

111 METLIN Mass Search With Retention Time Adds Specificity Only 1 metabolite instead of 3!!!! Adding retention time eliminates isobaric metabolites

112 Edit Metabolite Database New Entry Select add new then type new metabolite information

113 METLIN Search from Mass Hunter Qual Identify compounds: search database Specify the METLIN database Set search parameters Manual search options Select ion in spectra Select MFE compound(s) Batch search Automate by Find and Identify Find compounds by MFE Search database Generate formula (optional) Name and CAS number Set Parameters Database and MFG results View detailed results

114 METLIN Searching From Mass Profiler Mass Profiler METLIN searching is virtually the same as METLIN Mass Profiler can optionally add MFG MFG is used to assist METLIN search METLIN results are exportable Database customization is done only in METLIN Retention time changes New compounds New database METLIN search integrated into Mass Profiler

115 Summary Care and Feeding of QTOF/TOF Remember to Defrag Hard Drives Weekly Software updates available Mass Profiler B $3,150 Differential Analysis Software Batch Molecular Formula Generation and Database Searching METLIN Personal Metabolite Database B $3,759 Accurate Mass Retention Time Database (AMRT) Convert *.CSV to MTL Formats User Generated Databases (Plant Extract, Pesticides, AA s)

116 Questions and Answers Thank You

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