{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_2_DMSO.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_5_Ac44AzGal.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_3_Ac42AzMan.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_6_Ac44AzGal.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_4_Ac42AzMan.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_1_DMSO.raw"],"Pepxml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_tri_acetylated.pep.pep.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_di_acetylated.pep.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_mono_acetylated.pep.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD016217/190923L_SAM6048_BY19_CF_un_acetylated.pep.xml"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["cwoo@chemistry.harvard.edu"],"submitter":["Christina Woo"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":["Not available"],"submitter_keywords":["Ac44azgal","O-glcnac modifications","Ac42azman","Isotag"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD016217"],"tissue":["Lung","Epithelial Cell"],"sample_protocol":["We treated H1299 cells with either Ac42AzMan (200 μM), Ac44AzGal (200 μM), or DMSO vehicle in duplicate for 16 h. We then subjected the corresponding lysates to CuAAC with a mixture of isotopically-labeled, cleavable biotin tags. After enrichment of the labeled proteins on streptavidin beads and on-bead trypsinolysis, we exulted the directly modified, and therefore isotopically encoded, peptides using weak acid. Subsequent LC-MS/MS analysis using the IsoStamp v2.0 software was then used to look for azido-hexose modification of any Asn, Ser, Thr, or Cys residue."],"repository":["Pride"],"quantification_method":["Not available"],"modification":["iodoacetamide derivatized residue","monohydroxylated residue"],"data_protocol":["The raw data was processed using Proteome Discoverer 2.4 (Thermo Fisher Scientific). For quantitative proteomics, the data was searched against the human-specific SwissProt-reviewed database 2016 (20,152 proteins, downloaded on Aug. 19, 2016). Both HCD and EThcD spectra with a signal-to-noise ratio greater than 1.5 were searched against a database containing the Swissprot 2018 annotated human proteome (20,355 proteins, downloaded on Feb. 21, 2019) and contaminant proteins using Sequest HT and Byonic with a mass tolerance of 10 ppm for the precursor and 0.02 Da for fragment ions with full trypsin digestion, 2 missed cleavages, variable modifications (methionine oxidation, +15.995 Da; carbamidomethylcysteine, +57.021 Da; and others as described below). Intact glycopeptide searches allowed for un-acetylated, mono-acetylated, di-acetylated or tri-acetylated form of unnatural sugars (HexAz0Si, +287.112 Da; HexAz2Si, +289.124 Da; mono-acetylated HexAz0Si, +329.122 Da; mono-acetylated HexAz2Si, + 331.135 Da; di-acetylated HexAz0Si, +371.133 Da; di-acetylated HexAz2Si, +373.145 Da; tri-acetylated HexAz0Si, +413.143 Da; and tri-acetylated HexAz2Si, +415.156 Da) on asparagine, cysteine, serine, and threonine. Glycopeptide spectral assignments passing a false discovery rate of 1% at the spectrum level based on a target decoy database were manually validated for an isotope precursor pattern."],"omics_type":["Proteomics"],"labhead":["Christina Woo"],"instrument_platform":["Orbitrap Fusion Lumos"],"labhead_affiliation":["Department of Chemistry and Chemical Biology, Harvard University"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["cwoo@chemistry.harvard.edu"],"publication":["32411667 Darabedian N, Yang B, Ding R, Cutolo G, Zaro BW, Woo CM, Pratt MR. O-Acetylated Chemical Reporters of Glycosylation Can Display Metabolism-Dependent Background Labeling of Proteins but Are Generally Reliable Tools for the Identification of Glycoproteins. Front Chem. 2020 8:318 10.3389/fchem.2020.00318"],"submitter_affiliation":["Harvard University"],"submitter_country":["United States"],"pubmed_abstract":["Monosaccharide analogs bearing bioorthogonal functionalities, or metabolic chemical reporters (MCRs) of glycosylation, have been used for approximately two decades for the visualization and identification of different glycoproteins. More recently, proteomics analyses have shown that per-O-acetylated MCRs can directly and chemically react with cysteine residues in lysates and potentially cells, drawing into question the physiological relevance of the labeling. Here, we report robust metabolism-dependent labeling by Ac42AzMan but not the structurally similar Ac44AzGal. However, the levels of background chemical-labeling of cell lysates by both reporters are low and identical. We then characterized Ac42AzMan labeling and found that the vast majority of the labeling occurs on intracellular proteins but that this MCR is not converted to previously characterized reporters of intracellular O-GlcNAc modification. Additionally, we used isotope targeted glycoproteomics (IsoTaG) proteomics to show that essentially all of the Ac42AzMan labeling is on cysteine residues. Given the implications this result has for the identification of intracellular O-GlcNAc modifications using MCRs, we then performed a meta-analysis of the potential O-GlcNAcylated proteins identified by different techniques. We found that many of the proteins identified by MCRs have also been found by other methods. Finally, we randomly selected four proteins that had only been identified as O-GlcNAcylated by MCRs and showed that half of them were indeed modified. Together, these data indicate that the selective metabolism of certain MCRs is responsible for S-glycosylation of proteins in the cytosol and nucleus. However, these results also show that MCRs are still good tools for unbiased identification of glycosylated proteins, as long as complementary methods are employed for confirmation."],"pubmed_title":["O-Acetylated Chemical Reporters of Glycosylation Can Display Metabolism-Dependent Background Labeling of Proteins but Are Generally Reliable Tools for the Identification of Glycoproteins."],"pubmed_authors":["Darabedian Narek N, Yang Bo B, Ding Richie R, Cutolo Giuliano G, Zaro Balyn W BW, Woo Christina M CM, Pratt Matthew R MR"],"sample_synonyms":["liquid chromatography tandem mass spectroscopy, DIMETHYL SULFOXIDE, CRL-5803, vitamin B7, determination, Sialic acid-binding Ig-like lectin 1, protein, Strepavidin, peptide, std, Polypeptides, protein polypeptide chains, srybeta, peptido, 5-[(3aS, Biotin, 6aR)-Hexahydro-2-oxo-1H-thieno[3, sry-beta, Software Engineering, NCI-H1299, protein aggregate, Computer Program, SER, sry alpha, LCMSMS, DmelCG6127, peptides, MUB3_18, (3aS, Open, cis-Hexahydro-2-oxo-1H-thieno(3, dimethyl sulphoxide, biotina, Computer Programs and Programming, biotine, proteins, BIOTIN, MUB3.18, ser, Bd, Hermes, biotinum, Dimethylsulfoxid, LC-MS2, Medobiotin, Hexose, DMSO, dimethyli sulfoxidum, dmso, Rombellin, PRO, methylsulfinylmethane, acid, LC-MS/MS, CYS, Source Softwares, 4S, 4-d)imidazole-4-pentanoic acid, Software Tools, (3aS-(3aalpha, Programs, Program, Computer Applications, (CH3)2SO, Computer Applications Software, Computer Applications Softwares, Biotin Ratiopharm, Softwares, 4-d)imidazoline-4-valeric acid, and GLY protein 2, D-Biotin, 1H-Thieno(3, Acid, (methanesulfinyl)methane, and GLY protein 1, Software Applications, Biotine Roche, acide, Source Software, Srybeta, acids, acido, Sheep erythrocyte receptor, Applications, CG17957, liquid chromatography-tandem mass spectroscopy, cis-(+)-Tetrahydro-2-oxothieno[3, CG6127, Sry alpha, Polypeptide, D-(+)-biotin, Biokur, Computer Software Applications, 4-d]imidazol-4-yl)pentanoic acid, Deacura, Biotine, Medebiotin, dimethylsulfoxyde, Gene, sryalpha, Vitamin H, Computer, protein-containing complex, LC-MS-MS, polypeptide chain, mel(3)8, 4beta, LC-MSMS, Gene Products, smooth ER, F15E12.6, 6aalpha))-, Gelfert, Application, S(O)Me2, sulfinylbis(methane), Open Source Softwares, H1299, Biotin Hermes, F15E12_6, Sryalpha, Siglec-1, Coenzyme R, Software Application, sry beta, weak, Open Source Software, Computer Software Application, dimetil sulfoxido, 4-d]imidazole-4-valeric acid, Tools, (+)-cis-Hexahydro-2-oxo-1H-thieno[3, peptidos, Saeure, CG7938, CD169, Applications Software, Open Source, bead, Computer Software, protein complex, Proteins, srya, Roche, Biotin Gelfert, Mischung, 5-(2-oxohexahydro-1H-thieno[3, Cell, 4]imidazole-4-valeric acid, Peptide, sryb, Tool, polypeptide, 6aR)-2-oxohexahydro-1H-thieno[3, LC/MS/MS, Software Tool, cis-Tetrahydro-2-oxothieno(3, 4]imidazoline-4-valeric acid, biotin, native protein, natural protein, 4-d]imidazol-4-yl]pentanoic acid, Protein, chemical analysis, Dimethyl sulfoxide, Software, ATCMPG1, MET, Biodermatin, ATCMPG2., Biotin-Ratiopharm, sry-a, sry-b, Gabunat, Saeuren, DmelCG7938, Engineering, hexahydro-2-oxo-, dimethyl sulfoxide, Rpw, 4)imidazole-4-valeric acid, Protein Gene Products, Computer Programs, Gene Proteins, sry-alpha, CT18858, Applications Softwares, liquid chromatography tandem mass spectrometry, Peptid, assay, dimethyl sulfur oxide, DmelCG17957, sry"],"pubmed_title_synonyms":["biochemical pathways, glicoproteinas, Metabolic Process, O-Glycosylated, C-Glycosylated, Protein Glycosylation, degradation, Process, Processes, protein complex, metabolism resulting in cell growth, Proteins, Metabolic Concepts, Gene, protein, Metabolic Processes, protein-containing complex, Concept, Metabolic Phenomena, Metabolism Concepts, protein polypeptide chains, Glycoprotein, native protein, glycosylation, natural protein, polypeptide chain, Glycosylation, glycoproteins, Metabolism, Protein, Glycosylated Proteins, Phenomena, Gene Products, Concepts, secretion, background, Metabolism Concept, protein aggregate, glycoproteine, Phenomenon, metabolism, Metabolism Phenomena, C-Glycosylated Proteins, Metabolic Phenomenon, glicoproteina, Glykoprotein, multicellular organism metabolic process, N-Glycosylated, Neoglycoproteins., biodegradation, Metabolic, catabolism, N-Glycosylated Proteins, Glycosylated, glycoproteines, Metabolic Concept, metabolic process resulting in cell growth, labeling, proteins, O-Glycosylated Proteins, introduction, Protein Gene Products, Gene Proteins, single-organism metabolic process, biotransformation, Glycosylated Protein, Catabolism, Anabolism, Glykoproteine"],"data_synonyms":["Forms, Bru, Pfeiffer's disease (disorder), human being, 2-amino-4-(methylsulfanyl)butanoic acid, Cysteine Hydrochloride, Raw, ion, Peptidomics, False, number, L Isomer, FBN, Gene, Hasp, Mononucleosis, L-Threonine, protein, precursor, protein-containing complex, presence, 2-Amino-3-hydroxypropionic acid, protein polypeptide chains, L-Isomer Methionine, Drug Tolerance, Methionine, Mono, polypeptide chain, ECTOL1, Gene Products, L-Methionine, 2, Del(8)44H, Half-Cystine, protein aggregate, WMS, Pedameth, Threonin, Gammaherpesviral mononucleosis (disorder), Svc, DL-Asparagine, proportion, asparagina, F, pattern, asparagine, iones, M, L Cysteine, N, L-Asparagine, beta-Trypsin, proteins, mononucleosis, L Threonine, Ratio, ions, man, ASN, Asn, OCTD, Asparagin, 2-amino-4-(methylthio)butanoic acid, glandular fever, 10^[-6], 2-amino-3-hydroxypropanoic acid, Infectious Mononucleosis, Pfeiffer's disease, distribution., ppm, EThcD, Gammaherpesviral mononucleosis, Half Cystine, GPHYSD2, metionina, Racemethionine, drug tolerance, SGS, Signal-To-Noise, ratio, serine, data, DL-Methionine, Zinc Cysteinate, protein complex, immune system tolerance, T5E21.12, Proteins, 2-Amino-4-(methylthio)butyric acid, Ratios, total expressed protein, L-Isomer, ACMICD, count in organism, Serin, native protein, HCD, Immune Tolerance, natural protein, Ionen, 3-Hydroxyalanine, Signal To Noise Ratio, Protein, Immunologic Tolerance, MFS1, Methionin, Kissing disease, methionine, Hmet, Data Base, WMS2, Met, T5E21_12, parent ion, Serine, Col4a-1, Signal-To-Noise Ratios, proportionality, Tripcellim, Glycopeptide, rate, Glandular Fever, L-Cysteine, MASS, 2-amino-3-carbamoylpropanoic acid, beta Trypsin, 4-diamino-4-oxobutanoic acid, human, Sugar, infectious mononucleosis, Protein Gene Products, Gene Proteins, Trypure, Self Tolerance, Tolerance, precursor ion, Ion, Isolation of Nuclei TAgged in specific Cell Types, SSKS, Monocytic angina, Filatov's disease, alpha-amino-gamma-methylmercaptobutyric acid, quotient, 2018, monocytic angina, L Serine, Glandular fever, quantitative, threonine, variable, L-Serine, Liquimeth, Proteomes, presence or absence in organism, Immunological Tolerance"],"description_synonyms":["glicoproteinas, d230, O-Glycosylated, Cysteine Hydrochloride, nucleocytoplasm, C-Glycosylated, Procedures, Peptidomics, NR3C2, Gene, dTAFII250, protein, protein-containing complex, EfW1, O-GLCNAC, dmTAF[[II]]230, protein polypeptide chains, DmelCG7586, Techniques, Glycoprotein, glycosylation, polypeptide chain, Glycosylation, glycoproteins, dmTAF1, Taf230, Method, Gene Products, Tep6, TEP6, Studies, Low, Half-Cystine, glycoproteine, protein aggregate, Technique, C-Glycosylated Proteins, TepVI, TAF250, protoplasm, glicoproteina, Glykoprotein, Taf200, N-Glycosylated, me75, dTAF[[II]]250, TFIID TAF250, protoplast, cel, cell, L Cysteine, glycoproteines, Taf1p, labeling, proteins, procedures, O-Glycosylated Proteins, D17Mit170, T1, anon-28DE, Study, dTAF250, Methodological Studies, dTEPVI, DmTEP6, Half Cystine, Glycosylated Protein, TAF, intracellular, MCR, nuclear receptor subfamily 3 group C member 2, Glykoproteine, Neoglycoproteins, Gene., visualization, dTAF[[II]]230, TAF[[II]]250, cou, Protein Glycosylation, Zinc Cysteinate, protein complex, Proteins, TAF200, MLR, Mlr, l(3)84Ab, TEP6mel, BG:DS00004.13, CG7586, TAFII-250, Procedure, TAF250/230, Tl3, Tl2, Cell, mcr, dTAF230, TAFII250, MR, Lr, native protein, natural protein, p230, Protein, Glycosylated Proteins, Drawings, TAF[[II]]250/230, TFIID, background, techniques, internal to cell, Taf[[II]]250, TAF[[II]]230, N-Glycosylated Proteins, Glycosylated, L-Cysteine, TAF[II]250, Methodological, CG17603, TAF[[II]], Methodological Study, introduction, Protein Gene Products, Gene Proteins, data encoding as image, DmelCG17603, Taf250, NR3C2VIT, alpha-2-Mrp, SR3-5, Bra, HRNT1, TAF230, methodology, TAF1"],"pubmed_abstract_synonyms":["glicoproteinas, biochemical pathways, Metabolic Process, O-Glycosylated, nucleocytoplasm, Metabolic Concepts, protein, Atomkern, SUB, dmTAF[[II]]230, protein polypeptide chains, DmelCG7586, Techniques, Glycoprotein, glycoproteins, DmelCG12298, Method, horsetail nucleus, Tep6, TEP6, Concepts, SCRAMBLED, Metabolism Concept, glycoproteine, protein aggregate, methodology., Phenomenon, KIF20A, 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complex, EfW1, O-GLCNAC, CG12298, glycosylation, polypeptide chain, Glycosylation, dmTAF1, Taf230, Metabolism, Gene Products, Studies, Low, Half-Cystine, nucleo atomico, Metabolism Phenomena, Technique, TAF250, protoplasm, nuclei, Taf200, dTAF[[II]]250, protoplast, cell, L Cysteine, mei-1794, nucleus of CNS, noyau, nucleo, glycoproteines, Metabolic Concept, Taf1p, labeling, O-Glycosylated Proteins, anon-28DE, Study, dTAF250, nucleus, SRF9, TAF, MCR, Glykoproteine, data, TAF[[II]]250, cou, Protein Glycosylation, degradation, protein complex, Proteins, l(3)84Ab, TEP6mel, BG:DS00004.13, Cell, mcr, Concept, Metabolic Phenomena, dTAF230, STRUBBELIG-RECEPTOR FAMILY 9, Metabolism Concepts, Isotope, MR, Lr, native protein, natural protein, nervous system nucleus, p230, Protein, Glycosylated Proteins, Phenomena, TAF[[II]]250/230, TFIID, background, techniques, metabolism, Metabolic Phenomenon, Taf[[II]]250, multicellular organism metabolic process, TAF[[II]]230, biodegradation, Metabolic, N-Glycosylated Proteins, Dub, TAF[II]250, nucleus of neuraxis, neuraxis nucleus, introduction, Protein Gene Products, Gene Proteins, single-organism metabolic process, DmelCG17603, alpha-2-Mrp, Bra, T19D16.8, SCM, HRNT1, methodology, Anabolism, TAF1"],"name_synonyms":["biochemical pathways, glicoproteinas, Metabolic Process, O-Glycosylated, C-Glycosylated, Protein Glycosylation, degradation, Process, Processes, protein complex, metabolism resulting in cell growth, Proteins, Metabolic Concepts, Gene, protein, Metabolic Processes, protein-containing complex, Concept, Metabolic Phenomena, Metabolism Concepts, protein polypeptide chains, Glycoprotein, native protein, glycosylation, natural protein, polypeptide chain, Glycosylation, glycoproteins, Metabolism, Protein, Glycosylated Proteins, Phenomena, Gene Products, Concepts, secretion, background, Metabolism Concept, protein aggregate, glycoproteine, Phenomenon, metabolism, Metabolism Phenomena, C-Glycosylated Proteins, Metabolic Phenomenon, glicoproteina, Glykoprotein, multicellular organism metabolic process, N-Glycosylated, Neoglycoproteins., biodegradation, Metabolic, catabolism, N-Glycosylated Proteins, Glycosylated, glycoproteines, Metabolic Concept, metabolic process resulting in cell growth, labeling, proteins, O-Glycosylated Proteins, introduction, Protein Gene Products, Gene Proteins, single-organism metabolic process, biotransformation, Glycosylated Protein, Catabolism, Anabolism, Glykoproteine"],"additional_accession":[]},"is_claimable":false,"name":"O-Acetylated chemical reporters of glycosylation can display metabolism-dependent background labeling of proteins but are generally reliable tools for the identification of glycoproteins","description":"Monosaccharide analogs bearing bioorthogonal functionalities, or metabolic chemical reporters (MCRs) of glycosylation, have been used for approximately two decades for the visualization and identification of different glycoproteins. More recently, proteomics analyses have shown that per-O-acetylated MCRs can directly and chemically react with cysteine residues in lysates and potentially cells, drawing into question the physiological relevance of the labeling. Here, we report robust cellular labeling by Ac42AzMan but not the structurally-similar Ac44AzGal. However, the levels of background chemical-labeling of cell lysates by both reporters are low and identical. We then characterized Ac42AzMan labeling and found that the vast majority of the labeling occurs on intracellular proteins but that this MCR is not converted to previously characterized reporters of intracellular O-GlcNAc modification. Additionally, we used IsoTag proteomics to show that essentially all of the Ac42AzMan labeling is on cysteine residues. Given the implications this result has for the identification of intracellular O-GlcNAc modifications using MCRs, we then performed a meta-analysis of the potential O-GlcNAcylated proteins identified by different techniques. We found that many of the proteins identified by MCRs have also been found by other methods. Finally, we randomly selected four proteins that had only been characterized as O-GlcNAcylated by MCRs and showed that half of them were indeed 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