{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":56,"searchCount":5},"additional":{"omics_type":["Other"],"submitter":["Piersma SR, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Homo_sapiens_viruses, Human"],"submitter_mail":["s.piersma@vumc.nl"],"publication":["25841592"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014775","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014764","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014776","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014765","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014766","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014777","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014778","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014767","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014768","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014757","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014758","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014769","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014780","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014770","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014760","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014771","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014772","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014761","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014762","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014773","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014774","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014763"],"submitter_affiliation":["OncoProteomics Laboratory, VU University Medical Center, Amsterdam"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["Robust phosphopeptide enrichment methods with minimal fractionation are required to profile signaling network analysis in cancer cell lines and tissues. We assessed performance of single-shot LC-MS/MS label-free phosphoproteomics using TiOx-based phosphopeptide enrichment and report phosphopeptide identification reproducibility (75.8%), depth of identification (6014-6150 phosphopeptides) and reproducibility of label-free quantification (CV 17.8%). Subsequently, we have profiled the baseline global phosphorylation of 8 colorectal cancer (CRC) cell lines representing different CRC prognostic subtypes. Global single-shot phosphoproteomics can distinguish CRC subtypes previously identified by transcriptomics and identifies signaling proteins and processes associated with the CCS3 poor prognosis subtype. Data are available via ProteomeXchange with identifiers PXD001546 and PXD001550.","Label-free single-shot phosphoproteomics is a mature workflow that can be used for global quantitative profiling of biological cell lines and tissues to map signaling networks in comparative analyses. Here we show the feasibility of label-free profiling of CRC cell lines at sample input levels compatible with clinical samples such as tumor biopsies. This article is part of a Special Issue entitled: HUPO 2014.","Robust phosphopeptide enrichment methods with minimal fractionation are required to profile signaling network analysis in cancer cell lines and tissues. We assessed performance of single-shot LC-MS/MS label-free phosphoproteomics using TiOx-based phosphopeptide enrichment and report phosphopeptide identification reproducibility (75.8%), depth of identification (6014-6150 phosphopeptides) and reproducibility of label-free quantification (CV 17.8%). Subsequently, we have profiled the baseline global phosphorylation of 8 colorectal cancer (CRC) cell lines representing different CRC prognostic subtypes. Global single-shot phosphoproteomics can distinguish CRC subtypes previously identified by transcriptomics and identifies signaling proteins and processes associated with the CCS3 poor prognosis subtype. Data are available via ProteomeXchange with identifiers PXD001546 and PXD001550.Label-free single-shot phosphoproteomics is a mature workflow that can be used for global quantitative profiling of biological cell lines and tissues to map signaling networks in comparative analyses. Here we show the feasibility of label-free profiling of CRC cell lines at sample input levels compatible with clinical samples such as tumor biopsies. This article is part of a Special Issue entitled: HUPO 2014.","<h4>Unlabelled</h4>Robust phosphopeptide enrichment methods with minimal fractionation are required to profile signaling network analysis in cancer cell lines and tissues. We assessed performance of single-shot LC-MS/MS label-free phosphoproteomics using TiOx-based phosphopeptide enrichment and report phosphopeptide identification reproducibility (75.8%), depth of identification (6014-6150 phosphopeptides) and reproducibility of label-free quantification (CV 17.8%). Subsequently, we have profiled the baseline global phosphorylation of 8 colorectal cancer (CRC) cell lines representing different CRC prognostic subtypes. Global single-shot phosphoproteomics can distinguish CRC subtypes previously identified by transcriptomics and identifies signaling proteins and processes associated with the CCS3 poor prognosis subtype. Data are available via ProteomeXchange with identifiers PXD001546 and PXD001550.<h4>Biological significance</h4>Label-free single-shot phosphoproteomics is a mature workflow that can be used for global quantitative profiling of biological cell lines and tissues to map signaling networks in comparative analyses. Here we show the feasibility of label-free profiling of CRC cell lines at sample input levels compatible with clinical samples such as tumor biopsies. This article is part of a Special Issue entitled: HUPO 2014."],"pubmed_title":["Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines."],"pubmed_authors":["Piersma Sander R SR,Knol Jaco C JC,de Reus Inge I,Labots Mariette M,Sampadi Bharath K BK,Pham Thang V TV,Ishihama Yasushi Y,Verheul Henk M W HM,Jimenez Connie R CR,","Piersma Sander R SR, Knol Jaco C JC, de Reus Inge I, Labots Mariette M, Sampadi Bharath K BK, Pham Thang V TV, Ishihama Yasushi Y, Verheul Henk M W HM, Jimenez Connie R CR"],"name_synonyms":["biological signaling, signalling process, signaling process, Line, Cell Lines, cell line cell, cell_line, cell line., free, Cell, signalling, single organism signaling, Lines"],"description_synonyms":["LC-MS2, liquid chromatography tandem mass spectroscopy, DLD-1, APR, data, biological signaling, OG12X, Large Bowel Carcinoma, Malignant Neoplasm, Colorectal Cancer, Procedures, LRP, SCRIB1, LC-MS/MS, Cell Lines, Phosphorylations, Cancer of Large Intestine, APOER, cell_line, 6330543G17Rik, Procedure, Large Intestine Carcinoma, Cell, phosphorylation, LC-MS-MS, Colorectal, LC/MS/MS, CD91, Method, LC-MSMS, Studies, Line, TGFBR5, Carcinoma of Large Intestine, CRC, Crc, techniques, Colorectal Cancers, malignant tumour, Large Bowel Cancer, Lines, Carcinoma of Large Bowel, network topology analysis, Cancer of Large Bowel, LCMSMS, Large Intestine Cancer, Identification, NOXA, Scrb1, Tissue, malignant neoplasia, cell line cell, Identifications (Psychology), CRIB, Methodological, procedures, Cancers, Methodological Study, malignant tumor, SHOT, free, cell line, OG12, signalling, Study, SCRIB1., A2MR, Methodological Studies, signalling process, liquid chromatography-tandem mass spectroscopy, vartul, signaling process, LRP1A, liquid chromatography tandem mass spectrometry, Og12x, mKIAA0147, Malignant Colorectal Neoplasm, Prx3, IGFBP3R, AI118201, methodology, single organism signaling, Cancer"],"pubmed_title_synonyms":["biological signaling, signalling process, signaling process, Line, Cell Lines, cell line cell, cell_line, cell line., free, Cell, signalling, single organism signaling, Lines"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, projections, biological signaling, OG12X, Large Bowel Carcinoma, Colorectal Cancer, Procedures, lamellae, Gene, CCS-3, Prognostic Factors, 6330543G17Rik, Large Intestine Carcinoma, process of organ, phosphorylation, LC-MS-MS, eEF1A-1, protrusion, lamella, Colorectal, EEF-1, PTI1, Method, LC-MSMS, Studies, Line, Gene Products, HNGC - 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File: QE2_130117_OPL1013_TiOx_CRC_DLD1_3_130125023714.mzml. Published as part of J Proteomics. 2015 Apr 1. pii: S1874-3919(15)00103-7  . From the Abstract: {{i}} Robust phosphopeptide enrichment methods with minimal fractionation are required to profile signaling network analysis in cancer cell lines and tissues. We assessed performance of single-shot LC-MS/MS label-free phosphoproteomics using TiOx-based phosphopeptide enrichment and report phosphopeptide identification reproducibility (75.8%), depth of identification (6014-6150 phosphopeptides) and reproducibility of label-free quantification (CV 17.8%). Subsequently, we have profiled the baseline global phosphorylation of 8 colorectal cancer (CRC) cell lines representing different CRC prognostic subtypes ... {{/i}}","dates":{"submission":"2015-04-17"},"accession":"GPM32320014765","cross_references":{"pubmed":["25841592"],"Pride":["PXD001550"],"pride":[],"Pride Archive":["PXD001550"]}}