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pmid:33555887
Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb and Their Use for Developing a Mass Spectral Library.
Qian Dong · Xinjian Yan · Yuxue Liang · Sanford P Markey · Sergey L Sheetlin · Concepcion A Remoroza · William E Wallace · Stephen E Stein
Journal of proteome research · 2021 doi:10.1021/acs.jproteome.0c00823
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Experiment
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Complete file
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Analyses involved both partially reduced and non-reduced samples under neutral and weakly basic conditions followed by nanoflow liquid chromatography tandem mass spectrometry (LC-MS/MS). Spectra of peptides containing disulfide bonds are identified by both MS1 ion and MS2 fragment ion data in order to completely map all the disulfide linkages in the NISTmAb. This led to the detection of 383 distinct disulfide-linked peptide ions, arising from fully tryptic cleavage, missed cleavage, irregular cleavage, complex Met/Trp oxidation mixtures, and metal adducts. Fragmentation features of disulfide bonds under low-energy collision dissociation were examined. These include (1) peptide bond cleavage leaving disulfide bonds intact; (2) disulfide bond cleavage, often leading to extensive fragmentation; and (3) double cleavage products resulting from breakages of two peptide bonds or both peptide and disulfide bonds. Automated annotation of various complex MS/MS fragments enabled the identification of disulfide-linked peptides with high confidence. Peptides containing each of the nine native disulfide bonds were identified along with 86 additional disulfide linkages arising from disulfide bond shuffling. The presence of shuffled disulfides was nearly completely abrogated by refining digest conditions. A curated spectral library of 702 disulfide-linked peptide spectra was created from this analysis and is publicly available for free download. Since all IgG1 antibodies have the same constant regions, the resulting library can be used as a tool for facile identification of \"hard-to-find\" disulfide-bonded peptides. Moreover, we show that one may identify such peptides originating from IgG1 proteins in human serum, thereby serving as a means of monitoring the completeness of protein reduction in proteomics studies. 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"section[19]/table-wrap[1]#tbl2", "version": null, "note": "Disulfide-Linked Peptides Detected for Each of the Nine Native Disulfide Linkages Obtained from the Triplicate LC–MS/MS Analyses of the 18 h NISTmAb Digest Partially Reduced with TCEP and Alkylated with IAMg,h", "structure": {"pmcid": "PMC9278810", "section_index": 19, "section_title": "Identification of Native (Expected) NISTmAb Disulfide Linkages", "row_count": 61, "column_count": 8}, "table": {"label": "Table 2", "caption": "Disulfide-Linked Peptides Detected for Each of the Nine Native Disulfide Linkages Obtained from the Triplicate LC–MS/MS Analyses of the 18 h NISTmAb Digest Partially Reduced with TCEP and Alkylated with IAMg,h", "rows": [["bond name", "position in protein", "class", "missed cleaved sites", "peptide sequence", "mass", "charge", "absolute abund."], ["1a VH", "HC22-HC97", "tryptic 25%", "0", "eESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_VTNMDPADTATYYCAR", "5431.587", "4,5,6", "3.6 × 1010"], ["missed cleav.", "1", "eESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_VTNMDPADTATYYCARD", "8213.882", "5,6,7", "9.3 × 1010"], ["MIFNFYFDVWGQGTTVTVSSASTK"], ["2", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_VTNMDPADTATYYCARDMI", "9381.511", "6,7", "8.6 × 1009"], ["FNFYFDVWGQGTTVTVSSASTKGPSVFPLAPSSK"], ["2", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIRQPPGK_SS_VTNMDPADTATYYC", "8721.163", "5,6,7,8", "3.2 × 1009"], ["ARDMIFNFYFDVWGQGTTVTVSSASTK"], ["3", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_DTSKNQVVLKVTNMDPADT", "9326.501", "6,7,8", "2.3 × 1009"], ["ATYYCARDMIFNFYFDVWGQGTTVTVSSASTK"], ["3", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIRQPPGK_SS_VTNMDPADTATYYC", "9888.792", "7,8", "8.3 × 1008"], ["ARDMIFNFYFDVWGQGTTVTVSSASTKGPSVFPLAPSSK"], ["semi- tryptic", "0", "ESGPALVKPTQTLTLTCTFSGF_SS_VTNMDPADTATYYCAR", "4085.906", "4,5", "2.4 × 1009"], ["0", "ESGPALVKPTQTLTLTCTFSGFSL_SS_VTNMDPADTATYYCAR", "4286.022", "3", "3.4 × 1008"], ["", "", "", "", "", "", "", ""], ["2a CH1", "HC147-HC203", "tryptic 94%", "0", "eSTSGGTAALGCLVK_SS_DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV", "7916.919", "5,6,7,8", "1.8 × 1011"], ["VTVPSSSLGTQTYICNVNHKPSNTK"], ["missed cleav.", "1", "fSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSS", "7898.909", "5,6", "4.4 × 1009"], ["LGTQTYICNVNHKPSNTK"], ["1", "STSGGTAALGCLVK_SS_DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTV", "8259.11", "6,7", "4.8 × 1008"], ["PSSSLGTQTYICNVNHKPSNTKVDK"], ["semi- tryptic", "0", "STSGGTAALGCLVK_SS_SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT", "6869.428", "5,6,7", "4.5 × 1009"], ["YICNVNHKPSNTK"], ["0", "STSGGTAALGCLVK_SS_TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ", "7069.544", "6", "1.8 × 1009"], ["TYICNVNHKPSNTK"], ["0", "STSGGTAALGCLVK_SS_SLSSVVTVPSSSLGTQTYICNVNHKPSNTK", "4409.221", "5,6", "3.3 × 1008"], ["0", "STSGGTAALGCLVK_SS_SVVTVPSSSLGTQTYICNVNHKPSNTK", "4122.073", "4,5,6", "2.2 × 1008"], ["0", "STSGGTAALGCLVK_SS_SSVVTVPSSSLGTQTYICNVNHKPSNTK", "4209.105", "4,5", "1.4 × 1008"], ["0", "STSGGTAALGCLVK_SS_TVPSSSLGTQTYICNVNHKPSNTK", "3836.904", "4,5", "9.3 × 1007"], ["", "", "", "", "", "", "", ""], ["3a CH2", "HC264-HC324", "tryptic 96%", "0", "eTPEVTCVVVDVSHEDPEVK_SS_CK", "2328.098", "2,3,4,5", "2.5 × 1011"], ["missed cleav.", "2", "TPEVTCVVVDVSHEDPEVK_SS_VVSVLTVLHQDWLNGKEYKCK", "4537.287", "4,5,6,7", "6.6 × 1009"], ["3", "TPEVTCVVVDVSHEDPEVK_SS_VVSVLTVLHQDWLNGKEYKCKVSNK", "4965.526", "5,6", "1.5 × 1009"], ["1", "TPEVTCVVVDVSHEDPEVK_SS_EYKCK", "2748.299", "4,5", "9.4 × 1008"], ["1", "TPEVTCVVVDVSHEDPEVK_SS_CKVSNK", "2756.336", "4,5", "2.8 × 1008"], ["semi- tryptic", "0", "TPEVTCVVVDVSHED_SS_CK", "1874.839", "4", "5.1 × 1008"], ["0", "TPEVTCVVVDVSH_SS_CK", "1630.77", "2", "4.7 × 1008"], ["0", "TPEVTCVVVD_SS_CK", "1307.61", "2,3", "3.4 × 1008"], ["", "", "", "", "", "", "", ""], ["4a CH3", "HC370-HC428", "tryptic 99%", "0", "eNQVSLTCLVK_SS_WQQGNVFSCSVMHEALHNHYTQK", "3844.824", "3,4,5,6,7", "9.9 × 1010"], ["semi- tryptic", "0", "NQVSLTCLVK_SS_VFSCSVMHEALHNHYTQK", "3231.563", "4,5", "7.6 × 1007"], ["", "", "", "", "", "", "", ""], ["5b VL", "LC23- LC87", "tryptic 92%", "0", "VTITCSASSR_SS_FSGSGSGTEFTLTISSLQPDDFATYYCFQGSGYPFTFGGGTK", "5446.46", "4,5", "1.4 × 1010"], ["missed cleav.", "1", "DIQMTQSPSTLSASVGDRVTITCSASSR_SS_FSGSGSGTEFTLTISSLQPDDFATYYCFQ", "7320.344", "5", "1.0 × 1009"], ["GSGYPFTFGGGTK"], ["2", "VTITCSASSR_SS_FSGSGSGTEFTLTISSLQPDDFATYYCFQGSGYPFTFGGGTKVEIKR", "6071.851", "5,6", "2.0 × 1008"], ["", "", "", "", "", "", "", ""], ["6b CL", "LC133-LC193", "tryptic 66%", "0", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "3555.749", "3,4,5", "1.2 × 1011"], ["missed cleav.", "1", "SGTASVVCLLNNFYPR_SS_HKVYACEVTHQGLSSPVTK", "3820.903", "3,4,5,6,7", "6.2 × 1010"], ["2", "SGTASVVCLLNNFYPR_SS_ADYEKHKVYACEVTHQGLSSPVTK", "4427.168", "5,6", "6.0 × 1008"], ["semi- tryptic", "0", "SGTASVVCLLNNFYPR_SS_VYACEVTH", "2658.257", "4", "4.5 × 1007"], ["", "", "", "", "", "", "", ""], ["7c H-L", "HC223-LC213", "missed cleav.", "1", "SCDKTHTC(CAM)PPC(CAM)PAPELLGGPSVFLFPPKPK_SS_GEC", "3467.639", "3,4,5,6,7", "2.6 × 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"30"]], "row_count": 16, "column_count": 9, "numeric_cells": 70, "header_rows": 1, "locator": "section[22]/table-wrap[1]#tbl4"}}, {"id": "asset:table:pmid:33555887:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1089f8a516002a20d6de9172744614f95ebcb24c4a1a17fa9f33f9732f4a84bc", "bytes": 4346, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[27]/table-wrap[1]#tbl3", "version": null, "note": "Fragment Ion Annotation in an FT-CID MS/MS Spectrum of the Charge 3+ Disulfide-Linked Peptide, SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTKa", "structure": {"pmcid": "PMC9278810", "section_index": 27, "section_title": "Overview of Different Types of Fragments Observed", "row_count": 56, "column_count": 9}, "table": {"label": "Table 3", "caption": "Fragment Ion Annotation in an FT-CID MS/MS Spectrum of the Charge 3+ Disulfide-Linked Peptide, SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTKa", "rows": [["class", "group", "cleavage site", "m/z", "mass error in ppm", "assignment of fragment", "charge", "sequence", "percent abundance"], ["intact disulfide bond fragment", "1a", "single C-N cleavage in either peptide", "985.8223", "1.1", "y9", "3", "CLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "5.5"], ["1075.204", "1.9", "y12-NH3", "3", "SVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "18.5"], ["1080.879", "1.4", "y12", "3", "SVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "25.4"], ["1131.5491", "2.2", "b(2)16-H2O", "3", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVT", "10.2"], ["1308.6421", "1", "b9-H2O", "2", "SGTASVVCL_SS_VYACEVTHQGLSSPVTK", "6.4"], ["1312.1265", "1", "b(2)8-H2O", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTH", "19.5"], ["1321.1309", "0.3", "b(2)8", "2", "SGTASVVCLLNNFYPR_SS_ YACEVTH", "32.8"], ["1385.1595", "0.2", "b(2)9", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQ", "47"], ["1413.6871", "4.6", "b11-H5NO", "2", "SGTASVVCLLN_SS_VYACEVTHQGLSSPVTK", "19.9"], ["1431.2117", "0.4", 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