Primary Structure Analysis. Automated Evaluation. LC-MS Data Sets
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1 Primary Structure Analysis by Automated Evaluation of LC-MS Data Sets Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 1
2 LC-MS Peptide Mapping Origin of Signals Peptides with and without post-translational modifications Molecules from the chromatographic system Noise Fields of Application Verification of primary structure Assessment of micro-heterogeneity Identification of unexpected variants and contaminations Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 2
3 Identification of Unexpected Molecules Basic Software Requirements Search for peptides expected Removal of signals specific to peptides identified High degree of automation Additional Requirement Efficient and specific removal of chemical background and other noise Lack of Suitable Software Development of MassMap Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 3
4 Example Data - TIC Chromatogram Intensity [a.u.] Characteristics of Data Set 6 5 Tryptic map of IgG1 mab ESI-Tof, resolution 8 (FWHM) LC Solvent: ACN/H 2 O/TFA plus TFA-Fix Time [min] Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 4
5 Mass Spectrum of Example Peak Intensity [a.u.] 15 Signals from Solvent System m/z [amu] Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 5
6 Removal of Signals Originating from Solvent System Nomenclature Signals from solvent system Type1 (background) signals Requirement Removal of Type1 signals must not lead to loss of relevant signals. Type1 Removal by MassMap m/z values of Type1 signals m/z values observed in sufficient number of consecutive scans Testing of IC chromatograms for all Type1 m/z values Features corresponding to chromatographic peaks are not removed Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 6
7 Type1 Signals - Influence on TIC Chromatogram 8 Intensity [a.u.] Original Data Set 4 4 appr..5% 2 2 After Type1 Removal Time [min] Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 7
8 Nonspecific Low Intensity (Type2) Signals Motivation for Removal of Low Intensity Noise Decrease of memory needed for backup and storage Acceleration of computing Removal of Type2 Signals by MassMap Reduction of size of files by a factor of approximately 3 Algorithm implemented does not lead to loss of relevant signals. Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 8
9 Example Peak - Removal of Type2 Signals 2 Intensity [a.u.] Original Data Set 2 After Type2 Removal m/z [amu] Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 9
10 Pepmap-Analysis - Workflow Part 1 LC-MS Data Set (netcdf, MassLynx, Xcalibur) Conversion and Type2/Type1 Removal Corrected Data Set Protein Sequence (ASCII) Creation of lis-file with Data of Molecules Expected (lis-file #1) HC1, , , EVGVQLVKPGGEGSGGSLK HC2, , , LFSFYSCDASGAYWTYMVR HC2_oxM, , , LFSFYSCDASGAYWTYMVR HC3, , , QEPTK HC3_pyE, , , QEPTK HC4, , , LEWVYSYGDGTYPDATISSVK Automated Search for Molecules of lis-file List of Molecules Found and Identification Information Operator Assessment of Automatic Identifications List of Molecules Accepted Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 1
11 Operator Assessment of Automatic Identifications Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 11
12 Pepmap-Analysis - Workflow Part 2 List of Molecules Accepted Removal of Molecular Ions of Molecules Accepted Difference Data Set 1 Creation of fra-file with Fragment and Adduct Ions (fra-file #1) HC27,12 1, , y2 1, , a'5 2, , a'5 2, , c 9 2, , Na 2, , K 2, , NaK 3, , -H2O 3, , Na 3, , K 3, , ACN 3, , NaK Additional Removal of Fragment and Adduct Ions of Molecules Accepted Intensity [a.u.] TIC Corrected Data Set TIC Difference Data Set Time [min] Difference Data Set 2 Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 12
13 Example Peak - Residual Signals 2 Intensity [a.u.] 4 15 Signals Specific to Molecule m/z [amu] Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 13
14 Example Data Set - BIC Chromatograms BIC Chromatograms Background corrected total Ion Current chromatograms 7 Intensity [a.u.] BIC Corrected Data Set Total ion current chromatograms w/o residual Type2 signals 6 5 BIC Difference Data Set 2 Cutoff value calculated for every scan 4 Increase of sensitivity for detection of unexpected molecules Time [min] Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 14
15 Pepmap-Analysis - Workflow Part 3 Difference Data Set 2 Creation of lis-file #2 with Molecules Missing in lis-file #1 7 6 Intensity [a.u.] BIC Corrected Data Set BIC Difference Data Set 3 R1_1, , R1_2, , R1_3, , R1_4, , R1_5, , R1_6, , R1_7, , R1_8, , R1_9, , R1_1, , Analysis of Data Set with lis-file #2 Combination of lis-files and Corresponding Analyses Time [min] lis-file #3 + Difference Data Set 3 Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 15
16 Pepmap-Analysis - Output Data Mass Spectra and Chromatograms TIC/BIC chromatograms including peak lists Mass spectra and ion current chromatograms of molecules identified Text File with ID Information File ready for import into MS Excel Printed Reports Contents configurable Hardcopies of full reports may serve as records of analyses. Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 16
17 Sic-Analysis Motivation for Development Analysis of specific ion current chromatograms is a highly valuable tool for the quantitative assessment of micro-heterogeneity. Quantitative data from pepmap-analyses are only correct for signals w/o cross-talk from other signals. Properties of sic-modules Design comparable to pepmap-modules Higher degree of automation of identification process Simple Workflow Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 17
18 Sic-Analysis - Workflow pepmap-analysis of Data Set Creation of sic-file (Defining SICs) Creation of grp-file (Defining Report Groups ) Number of Report Groups 4 Name of Group, Number of Signals HC_ox_deamide, 32 Name of Signal, Molecule HC2, HC2 HC2_oxM, HC2_oxM HC3, HC3 HC3_pyE, HC3_pyE HC19, HC19 HC19_isoAsp, HC19_deamid HC19_Asp, HC19_deamid HC19_oxM, HC19_oxM Automated Calculation of SICs Operator Evaluation of Signals Other Data Sets HC19_z1_i, 1, , , NLYQMLNSLSK 1, HC19_z1_i-1, 1, , , NLYQMLNSLSK 1,,1 HC19_z2_i, 1, , , NLYQMLNSLSK 2, HC19_z2_i-3, 1, , , NLYQMLNSLSK 2,,1,2,3 HC19_deamid_z1_i-1, 1, , , NLYQMLNSLSK 1,,1 HC19_deamid_z2_i-3, 1, , , NLYQMLNSLSK 2,,1,2,3 Automated Calculation and Evaluation of SICs val-files (Chromatographic and Mass Spectrometric Information for Fully Automated Evaluation) Result of Automated Analysis Operator Assessment of Automatic Analyses with Problems Final Result(s) (Spectra, Chromatograms, Quantitative Information, Reports) Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 18
19 MassMap - Overview Fields of Application Verification of primary structure Testing for unexpected variants and contaminations Quantitative assessment of micro-heterogeneity Applicable for all mixtures of molecules analyzed by GC/LC-MS Valuable tool for research/development, comparability/biosimilarity studies, release testing Status of Development pepmap-modules: Development finished, validation of version 4.1 in progress (end QI/21) sic-modules: Final testing in progress, start of validation QII/21 Additional Information Based on GRAMS/AI (Thermo Electron) Windows OS: NT, XP, Vista, 7 Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 19
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