Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/PXD002931_community_annotated.sdrf.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082515_23917_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082515_23919_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082515_23920_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082415_23915_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082415_23912_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082415_23913_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082515_23921_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082415_23916_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082515_23918_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082415_23914_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082515_23922_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/082415_23911_HG_v.RAWftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19601_082415_23914_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19619_082515_23917_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19597_082415_23915_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19621_082515_23921_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19598_082415_23911_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19607_082415_23912_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19618_082515_23920_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19622_082515_23922_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19620_082515_23919_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19623_082515_23918_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19599_082415_23916_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/19600_082415_23913_HG_v.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/serum_PTM_revision_Rme.slcftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/serum_PTM_revision_Rme.redundant.blibftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/Serum_PTM_revision.blibftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/serum_PTM_revision_Rme.blibftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/Serum_PTM_revision.slcftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD002931/Serum_PTM_revision.redundant.blibprimary200OKHONGBO GUBlood SerumPooled serum samples were difested by trypsin and peptides were subject to sequencial enrichment using lysine acetylation and arginine mono-methylation antibodies followed by LC-MS/MSPrideHongbo GuPARTIALCell Signaling Technology26635363 Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC. Quantitative profiling of post-translational modifications by immunoaffinity enrichment and LC-MS/MS in cancer serum without immunodepletion. Mol Cell Proteomics. 2015 Dec 3. pii: mcp.O115.052266Cell Signaling Technologyhongbo.gu@cellsignal.comAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryAcute LeukemiaBreast CancerNon-small Cell Lung CarcinomaPtmCancer serumhttps://www.ebi.ac.uk/pride/archive/projects/PXD002931Raw data was searched by Sequest and identified peptides were quantified by label-free quantificationProteomicsHomo Sapiens (human)hongbo.gu@cellsignal.comTechnicalBiomedicalUnited StatesA robust method was developed and optimized for enrichment and quantitative analysis of posttranslational modifications (PTMs) in serum/plasma samples by combining immunoaffinity purification and LC-MS/MS without depletion of abundant proteins. The method was used to survey serum samples of patients with acute myeloid leukemia (AML), breast cancer (BC), and nonsmall cell lung cancer (NSCLC). Peptides were identified from serum samples containing phosphorylation, acetylation, lysine methylation, and arginine methylation. Of the PTMs identified, lysine acetylation (AcK) and arginine mono-methylation (Rme) were more prevalent than other PTMs. Label-free quantitative analysis of AcK and Rme peptides was performed for sera from AML, BC, and NSCLC patients. Several AcK and Rme sites showed distinct abundance distribution patterns across the three cancer types. The identification and quantification of posttranslationally modified peptides in serum samples reported here can be used for patient profiling and biomarker discovery research.Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion.Gu Hongbo H, Ren Jian Min JM, Jia Xiaoying X, Levy Tyler T, Rikova Klarisa K, Yang Vicky V, Lee Kimberly A KA, Stokes Matthew P MP, Silva Jeffrey C JCCarcinomas, Carcinoma, Procedures, non-small cell lung carcinoma, Blood, Non-Small Cell Lung Cancer, pooled, Non-Small Cell Lung, Methodological, Non-Small-Cell Lung, non-small cell carcinoma of the lung, Procedure, Blood Serum, Serum, Methodological Study, Non Small Cell Lung Carcinoma, Lung Carcinoma, Non Small Cell Lung, plan specification, non-small cell lung cancer, Study, non-small cell cancer of the lung, non-small cell carcinoma of lung, Lung Carcinomas, method, Techniques, NSCLC, Experiment, Client., Methodological Studies, Patient, Method, Clients, method used in an experiment, Nonsmall Cell Lung Cancer, Studies, Non-Small-Cell Lung Carcinoma, NSCLC - non-small cell lung cancer, Non-small cell lung cancer, Non-Small Cell Lung Carcinoma, non-small cell cancer of lung, Non-Small-Cell Lung Carcinomas, non-small cell lung carcinoma (disease), Technique, Serums, Non-Small-CellSvc, Polypeptides, Bru, Col4a-1, peptido, Raw, peptides, label, free., Peptid, peptidos, Del(8)44H, Polypeptide, Peptideliquid chromatography tandem mass spectroscopy, LC-MS2, primary cancer, LCMSMS, Malignant Neoplasm, Malignancy, Neoplasms, number, LC-MS/MS, Benign Neoplasm, Blood., Benign Neoplasms, Cancers, Tumor, Blood Serum, Serum, Malignant, presence, malignant tumor, LC-MS-MS, Malignant Neoplasms, Neoplasias, count in organism, LC/MS/MS, MT, Benign, malignant neoplasm, liquid chromatography-tandem mass spectroscopy, LC-MSMS, Neoplasm, liquid chromatography tandem mass spectrometry, Malignancies, Neoplasia, Serums, Cancer, Tumorsliquid chromatography tandem mass spectroscopy, LC-MS2, Pfeiffer's disease (disorder), Lysine Hydrochloride, DL-Arginine Acetate, Blood, acetylation, Arginine Hydrochloride, LC-MS/MS, 2-Amino-5-guanidinovaleric acid, L Isomer, arginine, Monohydrate, Mononucleosis, 2-amino-5-guanidinopentanoic acid, Blood Serum, Serum, Arginin, L-Isomer, antibodies, DL Arginine Acetate, Peptide, L-(+)-arginine, Polypeptides, Lysine Acetate, LC/MS/MS, Mono, peptido, (2S)-2-amino-5-(carbamimidamido)pentanoic acid, L-Isomer Arginine, Acetate, Harg, LC-MSMS, lysine, Hydrochloride, 2, Kissing disease, Lysine, L Arginine, methylation, Arg, L-Lysine, L Lysine, L-Arginine, Gammaherpesviral mononucleosis (disorder), (S)-2-amino-5-guanidinopentanoic acid, PRSS, LCMSMS, peptides, K, (2S)-2-amino-5-guanidinopentanoic acid, (S)-2-Amino-5-guanidinovaleric acid, beta-Trypsin, Tripcellim, R, epsilon-diaminocaproic acid, Acetylations, pooled, Arginine, Monohydrate DL-Arginine Acetate, Glandular Fever, mononucleosis, alpha, beta Trypsin, infectious mononucleosis, Trypure, LYS, glandular fever, Infectious Mononucleosis, Pfeiffer's disease, liquid chromatography-tandem mass spectroscopy, Lysin, Monocytic angina, Filatov's disease, L-Arg, monocytic angina, liquid chromatography tandem mass spectrometry, Peptid, peptidos, LC-MS-MS., Polypeptide, Glandular fever, Gammaherpesviral mononucleosis, 6-diaminohexanoic acid, Enisyl, 2-amino-5-(carbamimidamido)pentanoic acid, Methylations, Serums, L-Argininliquid chromatography tandem mass spectroscopy, malignant tumor of the breast, Biological Markers, Viral Marker, Surrogate Endpoints, Activity, determination, Lysine Hydrochloride, PHGDHD, acute non lymphoblastic leukemia, Myeloid, Laboratory, DL-Arginine Acetate, supply, Blood, Ack-1, Biochemical, mammary neoplasm, Non-Small Cell Lung Cancer, Monohydrate, Endpoint, Human Mammary Neoplasms, Mononucleosis, Serum, Tumor, phosphorylation, A10, Lung Carcinomas, Polypeptides, Techniques, Laboratory Markers, Lysine Acetate, phosphoglyceric acid dehydrogenase activity, SerA, SERA, peptido, "neoplasm of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:126926005], Method, Biological, Non-Small-Cell Lung Carcinoma, 2, cancer of the breast, Non-Small Cell Lung Carcinoma, Arg, Research Activity, Laboratory Research, L Lysine, 3-phosphoglyceric acid dehydrogenase activity, Priorities, BC, Mammary Neoplasms, malignant neoplasm of breast, Fresh Frozen Plasmas, Fresh Frozen, (S)-2-amino-5-guanidinopentanoic acid, LCMSMS, peptides, K, alveolar cell carcinoma, Acute Myeloblastic Leukemia, (S)-2-Amino-5-guanidinovaleric acid, Human Mammary Carcinomas, R, epsilon-diaminocaproic acid, Arginine, NLS, Non-Small Cell Lung, purification, Monohydrate DL-Arginine Acetate, mononucleosis, 4930479N23, NLS1, amlcr1, Non Small Cell Lung Carcinoma, free, aml1, phosphoglycerate oxidoreductase activity, 3-phosphoglycerate:NAD+ 2-oxidoreductase activity, XAML, isolation and purification, Immune, LYS, glandular fever, Markers, Methodological Studies, Ack, ACK, cancer of breast, SerA 3PG dehydrogenase activity, malignant neoplasm, Lysin, Viral Markers, Cdgip, ANLL, Malignancies, Gammaherpesviral mononucleosis, 2610009E16Rik, Research Priority, mammary cancer, Breast Malignant Neoplasms, plasma, ACK-1, acute myelogenous, Tumors, L-Arginin, PGAD, LC-MS2, Carcinoma, Frozen Plasma, Viral, "breast neoplasm" EXACT [MTH:120], Surrogate Endpoint, acetylation, LC-MS/MS, Arginine Hydrochloride, arginine, Research Priorities, Biochemical Markers, Procedure, Blood Serum, Arginin, Plasmas, Biologic Marker, PGDH, non-small cell lung cancer, Benign, Marker, PGDH activity, lysine, NOS, Malignant Neoplasm of Breast, non-small cell lung carcinoma (disease), evi-1, Carcinomas, L-Arginine, Research and Development, ParaT, Acute myelogenous leukemia, End Points, Myeloblastic, susceptibility to, PDG, Acute Myeloid Leukemia, Benign Neoplasms, Methodological, alpha, Immunologic, "mammary neoplasm" RELATED [], Laboratory Marker, Methodological Study, Non Small Cell Lung, infectious mononucleosis, Malignant Neoplasms, Activities, non-small cell carcinoma of lung, Patient, acute myeloid leukemia (AML), breast cancer, Biochemical Marker, liquid chromatography-tandem mass spectroscopy, label, Breast Tumors, aml-1, Filatov's disease, Breast Malignant Tumors, Polypeptide, lung neoplasm, ACK1, Ack1, cancer, Fresh, primary breast cancer, Pfeiffer's disease (disorder), Procedures, Fresh Frozen Plasma, Clinical Markers, non-small cell lung carcinoma, glycerate 3-phosphate dehydrogenase activity, Clinical Marker, Neoplasms, lung cancer, number, Benign Neoplasm, 2-Amino-5-guanidinovaleric acid, L Isomer, Gene, Mammary Cancers, Non-Small-Cell Lung, non-small cell carcinoma of the lung, Malignant, presence, 3PHP reductase activity, LC-MS-MS, Human, L-(+)-arginine, Surrogate End Points, non-small cell cancer of the lung, Surrogate Markers, method, Breast Malignant Tumor, Mono, alpha-phosphoglycerate dehydrogenase activity, acute non lymphoblastic leukaemia, (2S)-2-amino-5-(carbamimidamido)pentanoic acid, Pyk1, isolation, Breast Tumor, Harg, PGD, method used in an experiment, LC-MSMS, Studies, Gene Products, "mammary tumor" EXACT [CSP2005:2016-0671], breast tumor, acute myeloid, NSCLC - non-small cell lung cancer, Lysine, 3-phosphate dehydrogenase activity, Technique, D-3-phosphoglycerate:NAD+ oxidoreductase activity, acute myeloid leukaemia (AML), Gammaherpesviral mononucleosis (disorder), Runx-1, Biomarker, Blood Plasma, Human Mammary, Leukemia, Clinical, Malignancy, Research, Mammary Neoplasm, distribution, Mammary Carcinoma, Biological Marker, Acetylations, Lung Carcinoma, pebp2ab, Research Activities., Cancer of the Breast, Study, Neoplasias, NSCLC, Immunologic Markers, Infectious Mononucleosis, Malignant Tumor of Breast, Pfeiffer's disease, Clients, Mammary, Mammary Cancer, Blood Plasmas, p21cdc42Hs, Nonsmall Cell Lung Cancer, L-Arg, peptidos, Development and Research, Breast, mammary tumor, Non-Small-Cell Lung Carcinomas, Immunologic Marker, Methylations, 2-amino-5-(carbamimidamido)pentanoic acid, Biologic, Cancer, leukemia, HEL-S-113, Breast Carcinoma, Human Mammary Neoplasm, Breast Carcinomas, Malignant Neoplasm, Proteins, alpha-KG reductase activity, Serum Markers, Phosphorylations, End Point, 2-amino-5-guanidinopentanoic acid, "breast tumor" EXACT [NCI2004_11_17:C2910], L-Isomer, 3PGDH, DL Arginine Acetate, Client, Peptide, Immune Marker, AML, Breast Malignant Neoplasm, Frozen Plasmas, count in organism, LC/MS/MS, Priority, MT, Mammary Carcinomas, L-Isomer Arginine, Acetate, D-3-phosphoglycerate dehydrogenase activity, Surrogate End Point, chemical analysis, Protein, D- and L-HGA, Neoplasm, Nonsmall cell lung cancer, Hydrochloride, Human Mammary Carcinoma, Kissing disease, 3-PGDH, L Arginine, methylation, supply and distribution, Non-small cell lung cancer, aml1-evi-1, cbfa2, L-Lysine, Biologic Markers, Plasma, aml, Breast Neoplasm, primary cancer, Serum Marker, distinct, Xaml1, Surrogate, glycerate-1, alphaKG reductase activity, (2S)-2-amino-5-guanidinopentanoic acid, Endpoints, portion of plasma, Glandular Fever, patient, Cancers, malignant tumor, Surrogate Marker, plan specification, Protein Gene Products, 3-phosphoglycerate dehydrogenase activity, Gene Proteins, Acute, 3-phospho-D-glycerate:NAD+ 2-oxidoreductase activity, Breast Cancer, Monocytic angina, liquid chromatography tandem mass spectrometry, protection against, monocytic angina, Cancer of Breast, Peptid, assay, Glandular fever, non-small cell cancer of lung, 6-diaminohexanoic acid, Enisyl, Serums, Neoplasia, breast, Non-Small-Cell, Immune Markersposttranslational amino acid modification, posttranslational modification, posttranslational protein modification, PTM, post-translational amino acid modification., Blood Serum, Serum, post-translational modification, Serums, BloodfalseSerum PTM Identification_Technical TriplicatesA technical triplicate experiment was performed to validate the robustness of the method using pooled serum of non-small cell lung cancer 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