Don t miss a thing on your peptide mapping journey How to get full coverage peptide maps using high resolution accurate mass spectrometry

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Ezra Harrell
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1 Don t miss a thing on your peptide mapping journey How to get full coverage peptide maps using high resolution accurate mass spectrometry Kai Scheffler, PhD BioPharma Support Expert,LSMS Europe The world leader in serving science

glycosylation, deamidation, sulfation, oxidation disulfide bridge analysis distinguishing Leu/Ile, Asp/isoAsp Mass

2 Outline What is the exact goal of the analysis? sequence elucidation/verification sequence variant analysis, amino acid substitution analysis of modifications: glycosylation, deamidation, sulfation, oxidation disulfide bridge analysis distinguishing Leu/Ile, Asp/isoAsp Mass spectrometry portfolio: which instrument is applicable? Method setup: what is the most suitable method? MS methods: what are the critical parameters? how do they influence the success of the analysis? 2

MS Portfolio for BioPharma Characterization Thermo Scientific Ion Trap LC-MS

Exactive Plus Orbitrap Mass Spectrometer Full MS only (HCD fragmentation, no

mass spectrometers Full MS only Full MS with dd MS 2 (HCD) Thermo Scientific LTQ

detection) Full MS with dd MS 2 (CID, HCD, ETD) MSn Thermo Scientific Orbitrap

3 MS Portfolio for BioPharma Characterization Thermo Scientific Ion Trap LC-MS systems Full MS with dd MS 2 (CID, HCD, ETD) MSn PERFORMANCE Thermo Scientific Exactive Plus Orbitrap Mass Spectrometer Full MS only (HCD fragmentation, no precursor selection) Thermo Scientific Q Exactive hybrid quadrupole- Orbitrap mass spectrometers Full MS only Full MS with dd MS 2 (HCD) Thermo Scientific LTQ Orbitrap XL Hybrid Ion Trap- Orbitrap Mass Spectrometer Full MS only (OT detection) Full MS with dd MS 2 (CID, HCD, ETD) MSn Thermo Scientific Orbitrap Fusion Tribrid Mass Spectrometers Full MS only (OT detection) Full MS with dd MS 2 (CID, HCD, ETD) MSn VALUE 3

4 MS Portfolio for BioPharma Characterization Analysis type Thermo Scientific Ion Trap LC-MS systems Full MS with dd MS 2 (CID, HCD, ETD) MSn PERFORMANCE Thermo Scientific Exactive Plus Orbitrap Mass Spectrometer Full MS only (HCD fragmentation, no precursor selection) Thermo Scientific Q Exactive hybrid quadrupole- Orbitrap mass spectrometers Full MS only Full MS with dd MS 2 (HCD) Thermo Scientific LTQ Orbitrap XL Hybrid Ion Trap- Orbitrap Mass Spectrometer Full MS only (OT detection) Full MS with dd MS 2 (CID, HCD, ETD) MSn Thermo Scientific Orbitrap Fusion Tribrid Mass Spectrometers Full MS only (OT detection) Full MS with dd MS 2 (CID, HCD, ETD) MSn Peptde mapping/sequence confirmation Sequence variant analysis Analysis of PTMs and other modifications Disulfide bond analysis low res, low mass accuracy Full MS only Confirmation of expected ones only Confirmation of expected ones only Confirmation of expected ones only VALUE 4

5 MS Portfolio for BioPharma Characterization Analysis type Thermo Scientific Ion Trap LC-MS systems Full MS with dd MS 2 (CID, HCD, ETD) MSn PERFORMANCE Thermo Scientific Exactive Plus Orbitrap Mass Spectrometer Full MS only (HCD fragmentation, no precursor selection) Thermo Scientific Q Exactive hybrid quadrupole- Orbitrap mass spectrometers Full MS only Full MS with dd MS 2 (HCD) Thermo Scientific LTQ Orbitrap XL Hybrid Ion Trap- Orbitrap Mass Spectrometer Full MS only (OT detection) Full MS with dd MS 2 (CID, HCD, ETD) MSn Thermo Scientific Orbitrap Fusion Tribrid Mass Spectrometers Full MS only (OT detection) Full MS with dd MS 2 (CID, HCD, ETD) MSn Peptde mapping/sequence confirmation Sequence variant analysis Analysis of PTMs and other modifications Disulfide bond analysis low res, low mass accuracy ETD enabled systems only Full MS only Confirmation of expected ones only Confirmation of expected ones only Confirmation of expected ones only VALUE ETD enabled systems only 5

6 Before you setup, refine and start the MS method, you need to ensure you have an optimized LC-MS setup: Method Setup Calibration Source settings: probe position in the source housing (probe depth, x/y position) source voltage gas flows (sheath/aux gas) optimized for LC flow rate S-lens 6

7 Peptide Mapping Method Setup Method 1: Full MS scans only Method 2: Full MS scans with data dependent MS 2 scans 7

8 Peptide Mapping Method Setup Method 1: Full MS scans only Method 2: Full MS scans with data dependent MS 2 scans Sequence confirmation based on intact accurate precursor masses Confirmation of known and expected modifications Confirmation of disulfide bridges Critical parameters: Mass range AGC target setting Fill time 8

9 Peptide Mapping Method Setup Method 1: Full MS scans only Sequence confirmation based on intact accurate precursor masses Confirmation of known and expected modifications Confirmation of disulfide bridges Critical parameters: Mass range AGC target setting Fill time Method 2: Full MS scans with data dependent MS 2 scans Sequence confirmation based on intact accurate precursor masses and MS 2 spectra Confirmation of known and expected modifications and identification of unknowns Confirmation of disulfide bridges and identification of unknowns Critical parameters: Mass range Charge state range AGC target setting MS + MS 2 Maximum injection time MS/MS 2 Fixed first mass (MS 2 ) Intensity threshold TopN Collision energy (NCE) 9

Peptide Mapping Method Setup Method 1: Full MS scans only Sequence confirmation based on intact accurate precursor masses Confirmation of known and expected modifications Confirmation of disulfide

10 Peptide Mapping Method Setup Method 1: Full MS scans only Sequence confirmation based on intact accurate precursor masses Confirmation of known and expected modifications Confirmation of disulfide bridges Critical parameters: Mass range AGC target setting Fill time For Exactive MS series the MS method setup and data acquisition can be done via Thermo Scientific Xcalibur Software and/or Thermo Scientific Chromeleon Chromatography Data System Software Method 2: Full MS scans with data dependent MS 2 scans Sequence confirmation based on intact accurate precursor masses and MS 2 spectra Confirmation of known and expected modifications and identification of unknowns Confirmation of disulfide bridges and identification of unknowns Critical parameters: Mass range Charge state range AGC target setting MS + MS 2 Maximum injection time MS/MS 2 Fixed first mass (MS 2 ) Intensity threshold TopN Collision energy (NCE) 1

11 Critical Parameter 1: Mass Range Parameter relates to the mass range for monitoring intact precursor ions (m/z) Suggested to be set to - m/z for peptide mapping Suggested LC-MS setup is running without a trap column and starting the MS method without a delay time 11

12 Critical Parameter 1: Mass Range Parameter relates to the mass range for monitoring intact precursor ions (m/z) Suggested to be set to - m/z for peptide mapping Suggested LC-MS setup is running without a trap column and starting the MS method without a delay time 12

Suggested LC-MS setup is running without a trap column and starting the MS method

13 Critical Parameter 1: Mass Range Parameter relates to the mass range for monitoring intact precursor ions (m/z) Suggested to be set to - m/z for peptide mapping Suggested LC-MS setup is running without a trap column and starting the MS method without a delay time Include singly charged ions for fragmentation (do not tick exclude box) 13

Critical Parameters 2 & 3: AGC Target Setting MS + MS 2 / Maximum Inject Time AGC target values depend on the particular instrument used: AGC target Exactive Q Exactive Hybrid OT OT Fusion/Lumos Full

14 Critical Parameters 2 & 3: AGC Target Setting MS + MS 2 / Maximum Inject Time AGC target values depend on the particular instrument used: AGC target Exactive Q Exactive Hybrid OT OT Fusion/Lumos Full MS 1-3e6 3e6 3e6 2e5/4e5 MS 2 OT --- 1e5 1e5 5e4/1e5 MS 2 IT e4 1e4/1e4 Optimal max. inject times need to be in accordance with: TopN set in the method Gradient length Sample amount injected Max. Inject time Exactive Q Exactive Hybrid OT OT Fusion/Lumos Full MS 5- ms 5- ms 5- ms 5- ms MS 2 OT ms 15- ms 15- ms MS 2 IT ms - ms 14

15 Critical Parameter 4: TopN with N=? RT: RT: Time (min) NL: 4.31E8 Base Peak F: ms MS 11.1 NL: 5.86E Time (min).151 min = 9.1 sec 15

16 Critical Parameter 4: TopN with N=? RT: RT: Time (min) NL: 4.31E8 Base Peak F: ms MS 11.1 NL: 5.86E Time (min).151 min = 9.1 sec 16

17 Critical Parameter 4: TopN with N=? RT: RT: Time (min) ddtop5 Method Full MS + 5 MS 2 scans per scan cycle Resolution settings : 7k/17,5 k Max. inject time ms NL: 4.31E8 Base Peak F: ms MS 11.1 NL: 5.86E Time (min).151 min = 9.1 sec 17

18 Critical Parameter 4: TopN with N=? RT: RT: Time (min) ddtop5 Method Full MS + 5 MS 2 scans per scan cycle Resolution settings : 7k/17,5 k Max. inject time ms NL: 4.31E8 Base Peak F: ms MS 11.1 NL: 5.86E8 9 Full MS scans 8x5= MS 2 scans 49 scans total in 9.1 sec with an average MS 2 injection time of 159 ms 1 9 NL: 7.88E Time (min).151 min = 9.1 sec 18

Critical Parameter 4: TopN with N=? RT: 5.81 -.54 # 3655-375 RT: 1.95-11.9 AV: 9 NL: 7.1E7 11.7 T: FTMS + p ESI Full lock ms [.-.] 14.79 9 x1 x5 x5 639.2792 13.55 15.22 z=2 12.16 7 8.9 9.61 13.45 14.

19 Critical Parameter 4: TopN with N=? RT: # RT: AV: 9 NL: 7.1E T: FTMS + p ESI Full lock ms [.-.] x1 x5 x z= z= Relative Abundance NL: 4.31E8 Base Peak F: ms MS z=2 z= z= z=2 z=? z=? z=? z=? z=? z=? Time (min) RT: m/z 11.1 NL: 5.86E8 NL: 7.88E ddtop5 Method Full MS + 5 MS 2 scans per scan cycle Resolution settings : 7k/17,5 k Max. inject time ms 9 Full MS scans 8x5= MS 2 scans 49 scans total in 9.1 sec with an average MS 2 injection time of 159 ms Time (min).151 min = 9.1 sec 19

Estimation of Top N For the decisions on what N exactly shoud needs to be considered the average chromatographic peak width at the base and calculate the time available for each scan cycle to

if the peak width is 7 secs aiming at 6 full MS scans, the resulting the cycle time should not exceed 1.15 sec, and can fit one full MS scan + 5 MSMS scans with ms max. inject time.

20 Estimation of Top N For the decisions on what N exactly shoud needs to be considered the average chromatographic peak width at the base and calculate the time available for each scan cycle to obtain at least ~6 Full MS scans over the peak. How many MSMS-scans can fit in every scan cycle to stay within the calculated max. cycle time will depend on the maximum injection time set. E.g. if the peak width is 7 secs aiming at 6 full MS scans, the resulting the cycle time should not exceed 1.15 sec, and can fit one full MS scan + 5 MSMS scans with ms max. inject time A ddtop5 method has been proven as a very good standard method for peptide mapping on all Q Exative MS instruments and only requires modification if extended max. injection times are required sec 7sec 6

21 Critical Parameter 5: Intensity Threshold TIC Time (min) z= z= z=2 Full MS spectrum z= z= m/z 21

22 Critical Parameter 5: Intensity Threshold TIC Time (min) z= m/z z= z= z=2 Full MS spectrum z= z= m/z 22

23 Critical Parameter 5: Intensity Threshold TIC Time (min) z= m/z z= z= z=2 Full MS spectrum z= z= m/z z= z= z= z= m/z 23

Critical Parameter 5: Intensity Threshold TIC 4.84 4.86 4.88 4.9 4.92 Time (min) 682.

24 Critical Parameter 5: Intensity Threshold TIC Time (min) z= m/z intensity threshold charge state peptide match: on/off/preferred dynamic exclusion z= z= z=2 Full MS spectrum z= z= m/z z= z= z= z= m/z 24

25 Critical Parameter 6: Fixed First Mass C-trap HCD cell Quadrupole 25

Critical Parameter 6: Fixed First Mass C-trap HCD cell Quadrupole Scan range: last mass 15 first mass Leaving the first mass open will automatically adjust the mass range based on m/z of the

26 Critical Parameter 6: Fixed First Mass C-trap HCD cell Quadrupole Scan range: last mass 15 first mass Leaving the first mass open will automatically adjust the mass range based on m/z of the precursor ensuring that also high mass fragments ions are captured. Setting a fixed first mass is suggested only when certain low mass ions are desired for monitoring, e.g. 4 (oxonium ions) or for denovo sequencing aiming e.g. at the Lys/Arg y 1 ions at m/z 147/

27 Critical Parameter 4: Fixed First Mass - Set to 1 m/z FTMS + p ESI d Full ms @hcd27. [1.-3.] y z=? z=? m/z y FTMS + p ESI d Full ms @hcd27. [ ] m/z y z=? FTMS + p ESI d Full ms @hcd27. [ ] m/z z=? z=? z=?

28 Critical Parameter 4: Fixed First Mass Set to Auto Adjust FTMS + p ESI d Full ms @hcd28. [ ] m/z FTMS + p ESI d Full ms @hcd28. [ ] m/z FTMS + p ESI d Full ms2 1399,5@hcd28. [ ] m/z 28

29 Critical Parameter 4: Fixed First Mass Set to Auto Adjust FTMS + p ESI d Full ms @hcd28. [ ] m/z FTMS + p ESI d Full ms @hcd28. [ ] m/z FTMS + p ESI d Full ms2 1399,5@hcd28. [ ] m/z 29

30 Reviewing ox ox Identified Modifications ox ox 3

31 Peptide Mapping with Short and Long Separation Times Thermo Scientific Vanquish UHPLC Platform coupled to a Thermo Scientific Q Exactive HF MS min gradient.4 ml min -1 bar 3 min gradient.4 ml min -1 bar Heavy Chain Light Chain % Sequence coverage obtained for Rituximab Light and Heavy Chain min gradient.6 ml min bar min gradient 1. ml min bar min gradient 1.1 ml min bar Time [min] 31

78 6.97 9.43 5.47 5. 7.44 9.82 4.2 5.55 5.83 14.64 2.73 1.59 13.22 8.63 19.56 5 min gradient 1.

6 ml min -1 85 bar min gradient.4 ml min -1 bar 3 min gradient.

Gradient Time 3 min min 13 min 8 min 5 min Modification Abundance σ Light Chain Q1+NH3 loss 91.95% 91.

52%.51%.58% -.51%.3% Heavy Chain M34+Oxidation 1.64% 1.54% 1.73% 1.42% 1.45%.13% Heavy Chain N31+A1GF 4.

9% 1.2% 1.2% -.98%.5% Heavy Chain N31+A2GF 37.88% 37.11% 38.59%.48% 43.12% 2.

36% 1.5%.21% Heavy Chain N31+A2S1GF.83%.86% - - -.2% Heavy Chain N31+A2S1G1F 2.

32 Peptide Mapping with Short and Long Separation Times Thermo Scientific Vanquish UHPLC Platform coupled to a Thermo Scientific Q Exactive HF MS Heavy Chain Light Chain min gradient 1.1 ml min bar 8 min gradient 1. ml min bar min gradient.6 ml min bar min gradient.4 ml min -1 bar 3 min gradient.4 ml min -1 bar Time [min] % Sequence coverage obtained for Rituximab Light and Heavy Chain Gradient Time 3 min min 13 min 8 min 5 min Modification Abundance σ Light Chain Q1+NH3 loss 91.95% 91.17% 89.69% 9.93% 26.57% 28.% Heavy Chain ~Q1+NH3 loss 99.62% 99.67% 99.61% 99.68% 99.69%.4% Heavy Chain N33+Deamidation.52%.51%.58% -.51%.3% Heavy Chain M34+Oxidation 1.64% 1.54% 1.73% 1.42% 1.45%.13% Heavy Chain N31+A1GF 4.32% 4.42% 3.83% 3.52% 3.38%.46% Heavy Chain N31+A1G1F 1.87% 1.91% 1.72% 3.32% 1.46%.73% Heavy Chain N31+A2G 1.9% 1.2% 1.2% -.98%.5% Heavy Chain N31+A2GF 37.88% 37.11% 38.59%.48% 43.12% 2.41% Heavy Chain N31+A2G1F 42.6% 41.89% 43.42% 43.% 43.35%.75% Heavy Chain N31+A2G2F 1.23% 1.17% 9.81% 1.36% 1.5%.21% Heavy Chain N31+A2S1GF.83%.86% % Heavy Chain N31+A2S1G1F 2.14% Heavy Chain N31+A3Sg1G 1.3% Heavy Chain N31+M5 1.61% 1.59% 1.66% 1.87% 1.86%.14% Heavy Chain N31+Unglycos..54%.9%.76%.83%.97%.16% Heavy Chain G45+Lys 3.57% 3.56% 3.92% 3.% 3.15%.28% median.19% 32

33 Identified Deamidation of Peptide VVSVLTVHQDWLN*GK R=323 R=336 z=2 z= ppm R=322 z= ppm 95.1 R=3297 z=2 measured R=332 z= R=2792 z= R=33 z= m/z NL: 2.51E6 RT min NL: 1.87E6 RT min R=3 z=2 Intact peptide precursor simulated m/z NL: 8.26E3 c 83 h 134 n 22 o 23 +H : C 83 H 136 N 22 O 23 p (gss, s /p : ) Chrg 2 R : 3 NL: 8.26E3 unmodified peptide measured spectrum simulated MS 2 spectrum unmodified peptide c 83 h 133 n 21 o 24 +H : C 83 H 135 N 21 O 24 p (gss, s /p : ) Chrg 2 R : 3 deamidated peptide 33

34 Identified Deamidation of Peptide VVSVLTVHQDWLN*GK simulated MS 2 spectrum.6 ppm deamidated peptide measured spectrum.97 ppm 1.5 ppm.14 ppm 34

35 Identified Deamidation of Peptide VVSVLTVHQDWLN*GK.6 ppm.97 ppm 1.5 ppm deamidated peptide measured spectrum.14 ppm 35

36 Disulfide Bridge Analysis 36

37 Sample Analysis by Mass Spectrometry Q Exactive Plus Analysis of reduced (+alkylated) sample Analysis of unreduced sample Method used for both samples: data-dependent Top5 Method: Full MS + top5 MS/MS scans per cycle reduced sample Time (min) unreduced sample Time (min) 37

38 Sample Analysis by Mass Spectrometry Q Exactive Plus Analysis of reduced (+alkylated) sample Analysis of unreduced sample Method used for both samples: data-dependent Top5 Method: Full MS + top5 MS/MS scans per cycle peaks deteced in reduced sample only peaks detected in unreduced sample only reduced sample Time (min) unreduced sample Time (min) 38

39 Disulfide Bridge Analysis - Result Review R e l a t i v e I n t e n s i t y HC:39-43 HC: LC:62-66 HC:39-43 Reduced LC:8-211 LC:14-17 HC:-65 LC:14-17 HC:-65 HC: LC:62-66 HC: LC:8-211 HC: Non-Reduced HC: LC: HC:68-83 HC:51-59 LC: HC:81-87 LC: HC:68-83 LC:19-24 HC:68-76 HC:88-98 LC:189-7 RT (min) HC: HC:68-76 HC: HC: LC:1-18 HC: LC:25-42 HC:31-38 HC: HC:44-5 HC:77-87 LC:62-86 HC: HC: LC:5-61 HC: LC:191-7 HC:44-5 HC: LC:25-42 HC:-3 HC:31-38 HC:51-84 HC: HC: HC: HC: HC: LC: HC: HC: LC:46-49 HC: LC:46-49 LC: HC:66-76 HC: HC:1-19 HC: HC: HC:-11 LC: HC: HC:35-3 HC: LC:46-53 Cysteine containing peptides HC: HC: HC: Expected/confirmed disulfide bridge linked peptides HC:137-15/HC: HC:

Disulfide Bridge Analysis - Result Review R e l a t i v e I n t e n s i t y 95 9 85 75 7 65 55 5 45

HC:217-221 LC:62-66 HC:338-341 LC:8-211 HC:413-417 Non-Reduced HC:413-417 LC:15-169 HC:68-83 HC:51-59

HC:68-76 HC:33-337 HC:33-337 LC:1-18 HC:252-258 LC:25-42 HC:31-38 HC:443-449 HC:44-5 HC:77-87

LC:5-61 HC:259-277 LC:191-7 HC:44-5 HC:278-291 LC:25-42 HC:-3 HC:31-38 HC:51-84 HC:443-449 HC:125-136

HC:1-19 2 1 3 HC:396-412 HC:-11 LC:127-142 HC:226-251 HC:35-3 HC:99-124 LC:46-53 Cysteine containing

40 Disulfide Bridge Analysis - Result Review R e l a t i v e I n t e n s i t y HC:39-43 HC: LC:62-66 HC:39-43 Reduced LC:8-211 LC:14-17 HC:-65 LC:14-17 HC:-65 HC: LC:62-66 HC: LC:8-211 HC: Non-Reduced HC: LC: HC:68-83 HC:51-59 LC: HC:81-87 LC: HC:68-83 LC:19-24 HC:68-76 HC:88-98 LC:189-7 RT (min) HC: HC:68-76 HC: HC: LC:1-18 HC: LC:25-42 HC:31-38 HC: HC:44-5 HC:77-87 HC: HC: HC: LC: HC: LC-HC HC4 HC1 HC2 LC2 LC1 Hinge HC3 LC:62-86 LC:5-61 HC: LC:191-7 HC:44-5 HC: LC:25-42 HC:-3 HC:31-38 HC:51-84 HC: HC: HC: HC: HC: HC: LC:46-49 HC: LC:46-49 LC: HC:66-76 HC: HC: HC: HC:-11 LC: HC: HC:35-3 HC: LC:46-53 Cysteine containing peptides HC: HC: HC: Expected/confirmed disulfide bridge linked peptides HC:137-15/HC: HC:

41 Details for Expected Light Chain S-S-Bond: C134-C194 Light chain amino acid sequence XICs Non-Reduced Precursor isotope pattern Fragment ion coverage maps Reduced No correlating peak present 41

sequence location of scrambled disulfide

42 Details for Unexpected Heavy Chain S-S-Bond: C22-C264 Heavy chain amino acid sequence location of scrambled disulfide bridge in the trastuzumab heavy chain sequence XICs Non-Reduced Precursor isotope pattern Fragment ion coverage maps MS pattern = 1.84 ppm z=5 Reduced No correlating peak present m/z RT (min) 42

43 Benefits of ETD: Distinguising Leu/Ile Based on Diagnostic ETD-HCD MS 3 ions 43

44 Benefits of ETD: Distinguising Leu/Ile Based on Diagnostic ETD-HCD MS 3 ions HCD fragmentation ->MS 3 spectrum ETD MS 2 spectrum Leucine Isoleucine 44

45 What we Learned 45

46 What we Learned 46

47 What we Learned 47

New Mass Spectrometry Tools to Transform Metabolomics and Lipidomics

New Mass Spectrometry Tools to Transform Metabolomics and Lipidomics July.3.13 Ken Miller Vice President of Marketing, Life Sciences Mass Spectrometry 1 The world leader in serving science Omics & the