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of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University"],"cell_type":["CL:0000034 stem cell, CL:0000057 fibroblast"],"repository":["GPMDB"],"pubmed_abstract":["Proteome analyses of human induced pluripotent stem cells (iPSC) were carried out on a liquid chromatography-tandem mass spectrometry system using meter-scale monolithic silica-C18 capillary columns without prefractionation. Tryptic peptides from five different iPSC lysates and three different fibroblast lysates (4 μg each) were directly injected onto a 200 cm long, 100 μm i.d. monolithic silica-C18 column and an 8-h gradient was applied at 500 nL/min at less than 20 MPa. We identified 98,977 nonredundant tryptic peptides from 9510 proteins (corresponding to 8712 genes), including low-abundance protein groups (such as 329 protein kinases) from triplicate measurements within 10 days. The obtained proteome profiles of the eight cell lysates were categorized into two groups, iPSC and fibroblast, by hierarchical cluster analysis. Further quantitative analysis based on an exponentially modified protein abundance index approach combined with UniProt keyword enrichment analysis revealed that the iPSC group contains more \"transcription regulation\"-related proteins, while the fibroblast group contained more \"transport\"-related proteins. Our results indicate that this simplified one-shot proteomics approach with long monolithic columns is advantageous for rapid, deep, sensitive, and reproducible proteome analysis."],"pubmed_title":["Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC-MS/MS analysis with meter-scale monolithic silica columns."],"pubmed_authors":["Yamana Ryota R,Iwasaki Mio M,Wakabayashi Masaki M,Nakagawa Masato M,Yamanaka Shinya S,Ishihama Yasushi Y,","Yamana Ryota R, Iwasaki Mio M, Wakabayashi Masaki M, Nakagawa Masato M, Yamanaka Shinya S, Ishihama Yasushi Y"],"name_synonyms":["deep, scale tissue, OG12X, Homo sapients, human being, scale, determination, plant peltate hair, Humo sapiens, 6330543G17Rik, peltate hair., Homo sapiense, man, Homo sapines, SHOT, human, OG12, metre, Homo spaiens, Homo spiens, \"human\" EXACT genbank_common_name [], Homo sapien, iPSC, Homo sapience, Homo sapian, Homo sampiens, Homo sapians, m, chemical analysis, assay, Homo sapeins, iPS cell, Og12x, scales, Home sapiens, Proteomes, Prx3"],"description_synonyms":["liquid chromatography tandem mass spectroscopy, Rrp40p, scale tissue, human being, capillary vessel., Fibroblast-Derived IPS Cell, Slf, IPS, peltate hair, Somatomedin-C, Fibroblast Derived IPS Cells, FPH2, hiPSC, Homo sapiense, electronic data file, IPS Cells, body system, LC-MS-MS, PCH1B, metre, Homo spaiens, RRP40, bA3J10.7, Homo sapien, AL024248, Homo sapians, hRrp-40, LC-MSMS, B1, system, iPS cell, Fibroblast-Derived IPS Cells, Homo sapients, anatomical systems, LCMSMS, plant peltate hair, somatomedin-C, SF, Cal1l, Kitl, man, Mast cell growth factor, Human Induced Pluripotent Stem Cells, Homo sapience, AA409961, IGF1, Homo sampiens, m, D1, Mechano growth factor, P11, Ca[1], Soluble KIT ligand, blood capillary, Sl, Home sapiens, PTHB1, LC-MS2, CAL12, IGF-I, data, 42C, steel factor, p10, hematopoietic growth factor KL, Exosome component 3, p11, LC-MS/MS, somatomedin, Cell, sKITLG, LC/MS/MS, Experiment, CAL1L, iPSC, Fibroblast Derived Induced Pluripotent Stem Cells, Homo sapian, C18, mechano growth factor, computer data file, Ribosomal RNA-processing protein 40, CLP11, Homo sapeins, connected anatomical system, scales, Igf-1, IPS Cell, SHEP7, mast cell growth factor, scale, Stem cell factor, Fibroblast-Derived IPS, Humo sapiens, STAT5, Fibroblast-Derived, Homo sapines, ANX2LG, ANX2L, human, organ system, stem cell factor, Homo spiens, KL-1, \"human\" EXACT genbank_common_name [], GP11, liquid chromatography-tandem mass spectroscopy, MGF, c-Kit ligand, Cells, Fibroblast-Derived Induced Pluripotent Stem Cells, KITLG, liquid chromatography tandem mass spectrometry, SCF, Proteomes"],"pubmed_title_synonyms":["deep, scale tissue, OG12X, Homo sapients, human being, scale, determination, plant peltate hair, Humo sapiens, 6330543G17Rik, peltate hair., Homo sapiense, man, Homo sapines, SHOT, human, OG12, metre, Homo spaiens, Homo spiens, \"human\" EXACT genbank_common_name [], Homo sapien, iPSC, Homo sapience, Homo sapian, Homo sampiens, Homo sapians, m, chemical analysis, assay, Homo sapeins, iPS cell, Og12x, scales, Home sapiens, Proteomes, Prx3"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, scale tissue, transcription, OG12X, human being, Materials, Fibroblast-Derived IPS Cell, determination, IPS, peltate hair, number, Fibroblast Derived IPS Cells, Gene, hiPSC, 6330543G17Rik, Homo sapiense, IPS Cells, body system, presence, LC-MS-MS, metre, Polypeptides, solute:solute exchange, Homo spaiens, Homo sapien, sensitive, Homo sapians, LC-MSMS, B1, Gene Products, system, transcription regulator activity, Low, Kinase, Disease Clustering, Analysis, iPS cell, Fibroblast-Derived IPS Cells, Microscopic polyarteritis, me75, Homo sapients, anatomical systems, LCMSMS, Genetic, Analyses, cell, plant peltate hair, long, min, chemical analysis., proteins, primary dermal fibroblast, man, D17Mit170, ATP-protein phosphotransferase, T1, Human Induced Pluripotent Stem Cells, DNA-dependent, column, Homo sapience, Homo sampiens, m, D1, blood capillary, Home sapiens, Prx3, PTHB1, LC-MS2, Disease, cellular transcription, cou, mouse embryonic fibroblast, DNA-dependent transcription, Proteins, LC-MS/MS, Tl3, Cistrons, Tl2, Cell, results, polypeptide, count in organism, LC/MS/MS, capillary vessel, Lr, iPSC, count, Fibroblast Derived Induced Pluripotent Stem Cells, single-organism transport, Homo sapian, C18, Protein, chemical analysis, Genetic Materials, Homo sapeins, connected anatomical system, scales, Hypersensitivity angiitis, IPS Cell, Cluster Analyses, Genetic Material, deep, Clusterings, scale, Kinases, Fibroblast-Derived IPS, Humo sapiens, Fibroblast-Derived, Homo sapines, SHOT, human, OG12, Micropolyangiitis, organ system, Protein Gene Products, Disease Clusterings, Gene Proteins, Homo spiens, \"human\" EXACT genbank_common_name [], Cluster, Material, liquid chromatography-tandem mass spectroscopy, Clustering, Cells, Fibroblast-Derived Induced Pluripotent Stem Cells, Bra, liquid chromatography tandem mass spectrometry, small molecule transport, Cistron, regulation, assay, quantitative, Og12x, Protein Kinase, Proteomes, Fibroblast, MPA, presence or absence in 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archive~1","varsite~0"],"reanalysis_count":["0"],"submitter_keywords":["Resource Reanalysis"],"citation_count_scaled":["0.0"],"reanalysis_count_scaled":["0.0"],"view_count_scaled":["0.006477483035163479"],"download_count_scaled":["0.0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"Rapid and Deep Profiling of Human Induced Pluripotent Stem Cell Proteome by One-shot NanoLC-MS MS Analysis with Meter-scale Monolithic Silica Columns","description":"PXD ID: PXD000071. Experiment: 120206ry_aHDF1419-P10_3, data file: 120206ry_aHDF1419-P10_3_1-120206ry011.mgf. Data published as part of J Proteome Res. 2013 Jan 4;12(1):214-21 [[PubMed]]. From the Abstract: {{i}}Proteome analyses of human induced pluripotent stem cells (iPSC) were carried out on a liquid chromatography-tandem mass spectrometry system using meter-scale monolithic silica-C18 capillary columns without prefractionation ...{{/i}}","dates":{"submission":"2013-02-10"},"accession":"GPM11210010668","cross_references":{"pubmed":["23210603"],"Pride":["PXD000071"],"pride":[],"Pride Archive":["PXD000071"]}}