{"database":"JPOST Repository","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["https://storage.jpostdb.org/JPST002323/files/A549_IAA_LysC_result.zip","https://storage.jpostdb.org/JPST002323/files/BSA_IAA_LysC_result.zip","https://storage.jpostdb.org/JPST002323/files/A549_IAA_LysCTrypsin.zip","https://storage.jpostdb.org/JPST002323/files/A549_IAA_LysC.zip","https://storage.jpostdb.org/JPST002323/files/RecombinantEGFR_T790M_BEA_PRM.zip","https://storage.jpostdb.org/JPST002323/files/A549_BEA_LysC_result.zip","https://storage.jpostdb.org/JPST002323/files/BSA_BEA_LysC.zip","https://storage.jpostdb.org/JPST002323/files/BSA_IAA_LysC.zip","https://storage.jpostdb.org/JPST002323/files/A549_IAA_LysCTrypsin_result.zip","https://storage.jpostdb.org/JPST002323/files/A549_BEA_LysCTrypsin_result.zip","https://storage.jpostdb.org/JPST002323/files/RecombinantEGFR_T790M_IAA_PRM.zip","https://storage.jpostdb.org/JPST002323/files/A549_BEA_LysC.zip","https://storage.jpostdb.org/JPST002323/files/A549_BEA_LysCTrypsin.zip","https://storage.jpostdb.org/JPST002323/files/BSA_BEA_LysC_result.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Yasushi Ishihama"],"species":["Homo Sapiens (human)","Bos Taurus"],"full_dataset_link":["https://repository.jpostdb.org/entry/JPST002323"],"submitter_affiliation":["Kyoto university"],"sample_protocol":[""],"repository":["jPOST"],"data_protocol":[""],"pubmed_abstract":["To improve the coverage in bottom-up proteomics, S-aminoethylation of cysteine residues (AE-Cys) was carried out with 2-bromoethylamine, followed by cleavage with lysyl endopeptidase (Lys-C) or Lys-C/trypsin. A model study with bovine serum albumin showed that the C-terminal side of AE-Cys was successfully cleaved by Lys-C. The frequency of side reactions at amino acids other than Cys was less than that in the case of carbamidomethylation of Cys with iodoacetamide. Proteomic analysis of A549 cell extracts in the data-dependent acquisition mode after AE-Cys modification afforded a greater number of identified protein groups, especially membrane proteins. In addition, label-free quantification of proteins in mouse nonsmall cell lung cancer (NSCLC) tissue in the data-independent acquisition mode after AE-Cys modification showed improved NSCLC pathway coverage and greater reproducibility. Furthermore, the AE-Cys method could identify an epidermal growth factor receptor peptide containing the T790 M mutation site, a well-established lung-cancer-related mutation site that has evaded conventional bottom-up methods. Finally, AE-Cys was found to fully mimic Lys in terms of collision-induced dissociation fragmentation, ion mobility separation, and cleavage by Lys-C/trypsin, except for sulfoxide formation during sample preparation."],"pubmed_title":["Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation."],"pubmed_authors":["Tomioka Ryota R, Tomioka Ayana A, Ogata Kosuke K, Chan Hsin-Ju HJ, Chen Li-Yu LY, Guzman Ulises H UH, Xuan Yue Y, Olsen Jesper V JV, Chen Yu-Ju YJ, Ishihama Yasushi Y"],"name_synonyms":["C, PRSS, Cysteine Hydrochloride, E 920, Zinc Cysteinate, 2-amino-3-sulfanylpropanoic acid, cisteina, L Cysteine, Trypsin/K, E-920, beta-Trypsin, Tripcellim, L-Zystein, L-2-Amino-3-mercaptopropionic acid, L-Cysteine, (R)-2-amino-3-mercaptopropanoic acid, Hcys, beta Trypsin, Cys, 2-Amino-3-mercaptopropionic acid, L-Cystein, Trypure, CYSTEINE, Zystein., FREE CYSTEINE, E920, 2-amino-3-mercaptopropanoic acid, Cystein, Half-Cystine, Half Cystine, (2R)-2-amino-3-mercaptopropanoic acid, (2R)-2-amino-3-sulfanylpropanoic acid"],"pubmed_abstract_synonyms":["Integral Membrane Proteins, dairy cow, Urogastrone Receptor, E 920, 2-bromoethanamine hydrobromide, Laboratory, Aminosaeure, Mus domesticus, AI326280, Surface Proteins, cleavage, Receptors, Amino acid, Non-Small Cell Lung Cancer, LFQ, Membrane-Associated Proteins, Serum, Integral, Tumor, House Mouse, Epidermal Growth Factor Receptor Family Protein, Mutations, peptide, Lung Carcinomas, ErbB-1, Polypeptides, Techniques, peptido, Method, parenchyma of lung, Non-Small-Cell Lung Carcinoma, TGF alpha, 1, 2-amino-3-mercaptopropanoic acid, Cystein, Non-Small Cell Lung Carcinoma, (R*, C, single-organism biosynthetic process, amino acids, A-549, peptides, MUB3_18, K, cisteina, ErbB 1, bromoethyleneamine hydrobromide, alveolar cell carcinoma, Surface, Bos bovis, Tissue, epsilon-diaminocaproic acid, achromobacter beta-lytic protease (blp), Swiss Mice, Non-Small Cell Lung, sulphoxide, procedures, MUB3.18, Epidermal Growth Factor Receptor, Non Small Cell Lung Carcinoma, Epidermal Growth Factor Receptor Kinase, DIA, Bos Tauurus, Proto oncogene c ErbB 1 Protein, oxen, LYS, Lys, Methodological Studies, malignant neoplasm, TGF-alpha, Lysin, sulfoxide, ErbB Receptor, Surface Protein, Membrane Associated Proteins, domestic cow, Malignancies, Half Cystine, house mouse, Membrane Protein, Lzm, Tumors, Carcinoma, Lzp, pulmo, EGF Receptors, Zinc Cysteinate, PRO, Trypsin/K, Aminokarbonsaeure, frequency, R*)-isomer, HER Family Receptors, mouse, lung parenchyma, 2-bromoethylamine hydrobromide, 2-BEA, Procedure, Cys, CYS, alpha-amino carboxylic acids, collisionally activated dissociation, CID, non-small cell lung cancer, Benign, lysyl endoprotease, NCI-A549 cell, simple tissue, Lzm-s1, 2-bromoethanamine, (2R)-2-amino-3-sulfanylpropanoic acid, and GLY protein 2, non-small cell lung carcinoma (disease), Urogastrone, region, neoplasms, Carcinomas, Amino Acid, Acid, Mus musculus, Cell Membrane Protein, and GLY protein 1, Amino acids, mice, Membrane-Associated, erbB 1 Proto Oncogene Protein, Swiss Mouse, TGF-alpha Receptor, Benign Neoplasms, L-Cysteine, Cell Membrane Proteins, erbB-1 Proto-Oncogene Protein, Methodological, alpha, S*)-isomer, beta Trypsin, surveillance, Methodological Study, morbidity, 2-(methylenedioxy)-4-(2-(octylsulfinyl)propyl)benzene, L-Cystein, Non Small Cell Lung, ErbB-1 Receptor, domesticus, Malignant Neoplasms, Cell Line, non-small cell carcinoma of lung, Lysm, Receptor Tyrosine protein Kinase erbB 1, Transforming-Growth Factor alpha, pulmonary, Acetamide, Cells, Acids, Mouse, HER, Polypeptide, lung neoplasm, bovine, c-ErbB-1 Protein, Integral Membrane, Cysteine Hydrochloride, multicellular organismal biosynthetic process., Procedures, Family Receptors, non-small cell lung carcinoma, Transforming Growth Factor alpha, Neoplasms, lung cancer, Aminocarbonsaeure, Benign Neoplasm, L-Zystein, Transforming Growth Factor alpha Receptor, Gene, Non-Small-Cell Lung, alpha-amino acid, non-small cell carcinoma of the lung, Malignant, A549 Cell Lines, c-erbB-1 Protein, c erbB 1 Protein, non-small cell cancer of the lung, method, cattle, House, Membrane-Associated Protein, method used in an experiment, Gene Products, Studies, lung, Mus musculus domesticus, F15E12.6, NSCLC - non-small cell lung cancer, Half-Cystine, Mice, neoplasm, Technique, erbB-1, A549 Cell, Cell Membrane, study, F15E12_6, Malignancy, occurrence, Swiss, L Cysteine, E-920, beta-Trypsin, prevalence, Hcys, Lung Carcinoma, Family Receptor, Study, Neoplasias, NSC-8400, Epidermal Growth Factor-Urogastrone, NSCLC, sulfoxyl, CYSTEINE, piperonyl sulfoxide, Nonsmall Cell Lung Cancer, A549 cell, FREE CYSTEINE, Epidermal Growth Factor Urogastrone, site, peptidos, (2R)-2-amino-3-mercaptopropanoic acid, Receptor Tyrosine-protein Kinase erbB-1, Non-Small-Cell Lung Carcinomas, 2-iodo-, incidence, Proto-oncogene, Cancer, Lyzs, EGF Receptor, A549, Epidermal Growth Factor Receptor Protein Tyrosine Kinase, Malignant Neoplasm, cow, Epidermal Growth Factor Receptor Family Proteins, ErbB, ERBB, Proteins, Cell Lines, Proto-Oncogene Protein, Cell Surface, Cell Surface Protein, alpha-amino acids, A549 Cell Line, isosafrole octyl sulfoxide, Cell, Peptide, Plasma Albumin, polypeptide, MT, CAD, Mus, Bos primigenius taurus, Protein, proteomic analysis, Epidermal Growth Factor Receptor Protein-Tyrosine Kinase, Membrane Proteins, Nonsmall cell lung cancer, Neoplasm, Proto-oncogene c-ErbB-1 Protein, domestic cattle, techniques, Non-small cell lung cancer, HER Family Receptor, outbreaks, Zystein, Cell Surface Proteins, ATCMPG1, MET, ATCMPG2, Membrane Associated Protein, Achromobacter protease I, DDA, primary cancer, PRSS, sulfox-cide, 2-amino-3-sulfanylpropanoic acid, Tripcellim, L-2-Amino-3-mercaptopropionic acid, House Mice, (R)-2-amino-3-mercaptopropanoic acid, ERBB1, Cancers, Amino, Membrane, malignant tumor, 2-Amino-3-mercaptopropionic acid, endemics, Laboratory Mice, achromopeptidase, Protein Gene Products, plan specification, Trypure, Gene Proteins, EGF, Integral Membrane Protein, Albumin, ox, Epidermal Growth Factor, HER Family, E920, protection against, epidemics, Peptid, Lungs, Receptor, non-small cell cancer of lung, Laboratory Mouse, Neoplasia, HER1, methodology, Non-Small-Cell"],"pubmed_title_synonyms":["C, PRSS, Cysteine Hydrochloride, E 920, Zinc Cysteinate, 2-amino-3-sulfanylpropanoic acid, cisteina, L Cysteine, Trypsin/K, E-920, beta-Trypsin, Tripcellim, L-Zystein, L-2-Amino-3-mercaptopropionic acid, L-Cysteine, (R)-2-amino-3-mercaptopropanoic acid, Hcys, beta Trypsin, Cys, 2-Amino-3-mercaptopropionic acid, L-Cystein, Trypure, CYSTEINE, Zystein., FREE CYSTEINE, E920, 2-amino-3-mercaptopropanoic acid, Cystein, Half-Cystine, Half Cystine, (2R)-2-amino-3-mercaptopropanoic acid, (2R)-2-amino-3-sulfanylpropanoic acid"],"description_synonyms":["DER/faint little ball, Forms, Integral Membrane Proteins, E 920, 2-bromoethanamine hydrobromide, Laboratory, AI326280, Aminosaeure, Mus domesticus, Surface Proteins, Elp-B1, der, Elp-1, Amino acid, Non-Small Cell Lung Cancer, Errb1, LFQ, protein, Membrane-Associated Proteins, Serum, Integral, House Mouse, PIG61, Mutations, Lung Carcinomas, Polypeptides, Techniques, peptido, Method, epidermal growth factor-activated receptor activity, AI552599, Non-Small-Cell Lung Carcinoma, Mutations., 2-amino-3-mercaptopropanoic acid, Cystein, Non-Small Cell Lung Carcinoma, protein aggregate, d-egf-r, C, Lung Cancer, amino acids, A-549, peptides, MUB3_18, K, cisteina, bromoethyleneamine hydrobromide, alveolar cell carcinoma, Surface, Tissue, epsilon-diaminocaproic acid, Swiss Mice, Non-Small Cell Lung, Lung Cancers, procedures, MUB3.18, Non Small Cell Lung Carcinoma, DIA, flb, LYS, Lys, Methodological Studies, Lysin, Surface Protein, Membrane Associated Proteins, 9030024J15Rik, D-EGFR, house mouse, Membrane Protein, NISBD2, Lzm, DER1, Lzp, Carcinoma, Lung cancer, Elp, Wa5, l(2)09261, PRO, DEgfr, Trypsin/K, Aminokarbonsaeure, frequency, mouse, Cancer of Lung, 2-bromoethylamine hydrobromide, 2-BEA, Procedure, CYS, Cys, alpha-amino carboxylic acids, CG10079, non-small cell lung cancer, torpedo/egfr, wa2, cancer of lung, NCI-A549 cell, NOS, simple tissue, Lzm-s1, 2-bromoethanamine, (2R)-2-amino-3-sulfanylpropanoic acid, and GLY protein 2, non-small cell lung carcinoma (disease), region, Carcinomas, egfr, Amino Acid, Acid, Mus musculus, Cell Membrane Protein, and GLY protein 1, HD-33, El, Amino acids, mice, DER/EGFR, EGFR, EGfr, EgfR, Membrane-Associated, dEgfr, Swiss Mouse, DER flb, Cell Membrane Proteins, alpha, Methodological, Torpedo/Egfr, beta Trypsin, surveillance, Methodological Study, morbidity, L-Cystein, Non Small Cell Lung, domesticus, Degfr, Cell Line, non-small cell carcinoma of lung, Lysm, Acetamide, DEGFR, cancer of the lung, Cells, l(2)57DEFa, l(2)05351, dEGFR, Acids, Mouse, Polypeptide, DmHD-33, lung neoplasm, Cancer of the Lung, Proteomes, Integral Membrane, Lung, D-Egf, Procedures, non-small cell lung carcinoma, C-erb, Neoplasms, lung cancer, Aminocarbonsaeure, L-Zystein, mor1, Gene, Non-Small-Cell Lung, alpha-amino acid, non-small cell carcinoma of the lung, mENA, protein-containing complex, EK2-6, A549 Cell Lines, non-small cell cancer of the lung, House, Membrane-Associated Protein, c-erbB, EGFr, Egfr, Gene Products, Studies, Mus musculus domesticus, torpedo/Egfr, EGF receptor activity, F15E12.6, TOP, NSCLC - non-small cell lung cancer, Egf-r, Pulmonary Cancer, Mice, Technique, Pulmonary, A549 Cell, Cell Membrane, study, F15E12_6, EGF-R, occurrence, Swiss, E-920, beta-Trypsin, prevalence, LNCR, top, Torpedo/DER, Hcys, Lung Carcinoma, top/flb, Study, NSCLC, Lung Neoplasm, CYSTEINE, l(2)57EFa, Nonsmall Cell Lung Cancer, A549 cell, FREE CYSTEINE, site, peptidos, l(2)57Ea, (2R)-2-amino-3-mercaptopropanoic acid, Non-Small-Cell Lung Carcinomas, 2-iodo-, incidence, Cancer, Elp-B1RB1, Lyzs, Pulmonary Neoplasms, A549, protein complex, TGF-alpha receptor activity, ERBB, dEGFR1, Proteins, Cell Lines, total expressed protein, Cell Surface, Cell Surface Protein, alpha-amino acids, A549 Cell Line, Cell, Peptide, Plasma Albumin, native protein, epidermal growth factor receptor activity, DmelCG10079, Mus, Protein, proteomic analysis, Membrane Proteins, Neoplasm, Nonsmall cell lung cancer, techniques, Non-small cell lung cancer, DER/top, outbreaks, Zystein, Cell Surface Proteins, ATCMPG1, MET, ATCMPG2, Membrane Associated Protein, DDA, PRSS, top/DER, 2-amino-3-sulfanylpropanoic acid, Pulmonary Neoplasm, Tripcellim, L-2-Amino-3-mercaptopropionic acid, House Mice, (R)-2-amino-3-mercaptopropanoic acid, ERBB1, Cancers, wa-2, Amino, Membrane, 2-Amino-3-mercaptopropionic acid, endemics, Laboratory Mice, Protein Gene Products, Trypure, Gene Proteins, Egf, Integral Membrane Protein, EFG-R, Albumin, Errp, Erbb, Der, DER, E920, protection against, epidemics, Peptid, Pulmonary Cancers, transforming growth factor-alpha receptor activity, non-small cell cancer of lung, Laboratory Mouse, DER/torpedo, HER1, methodology, Non-Small-Cell"],"additional_accession":[]},"is_claimable":false,"name":"Extending the coverage of Lys-C/trypsin-based bottom-up proteomics using cysteine S-aminoethylation ","description":"In this study, S-aminoethylation of Cys (AE-Cys) was carried out with 2-bromoethylamine to form pseudo-Lys, which was then digested with Lys-C or trypsin to improve proteome coverage in bottom-up proteomics. A model study with bovine serum albumin showed that the C-terminal side of Cys was successfully cleaved by AE-Cys followed by digestion with Lys-C. The frequency of side reactions to amino acids other than Cys was not as high as that of carbamidomethylation of Cys with iodoacetamide. Proteomic analysis of A549 cell extracts using AE-Cys identified more protein groups, especially membrane proteins, in a data-dependent acquisition mode. In addition, label-free quantification of mouse non-small cell lung cancer (NSCLC) tissue in data-independent acquisition mode showed improved NSCLC pathway coverage and higher reproducibility with AE-Cys. Furthermore, we successfully identified peptides containing the [T790M] mutation site of EGFR by AE-Cys, which has not been reported by conventional bottom-up methods despite its importance as one of the most important lung cancer-related mutation sites.","dates":{"publication":"Wed Sep 27 00:00:00 BST 2023"},"accession":"PXD045433","cross_references":{"TAXONOMY":["9913","9606"],"pubmed":["38287222"]}}