title: Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands. Electronic address: s.piersma@vumc.nl.
authors.forename: Sander R
authors.initials: SR
authors.lastname: Piersma
authors.affiliation: OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Jaco C
authors.initials: JC
authors.lastname: Knol
authors.affiliation: OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Inge
authors.initials: I
authors.lastname: de Reus
authors.affiliation: Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Mariette
authors.initials: M
authors.lastname: Labots
authors.affiliation: OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Bharath K
authors.initials: BK
authors.lastname: Sampadi
authors.affiliation: OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Thang V
authors.initials: TV
authors.lastname: Pham
authors.affiliation: Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Ishihama
authors.affiliation: Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Henk M W
authors.initials: HM
authors.lastname: Verheul
authors.affiliation: OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands. Electronic address: c.jimenez@vumc.nl.
authors.forename: Connie R
authors.initials: CR
authors.lastname: Jimenez
mesh_terms: D001706:Biopsy; D018938:Caco-2 Cells; D015179:Colorectal Neoplasms / Q000378:metabolism* / Q000473:pathology; D006801:Humans; D009363:Neoplasm Proteins / Q000378:metabolism*; D010750:Phosphoproteins / Q000378:metabolism*; D040901:Proteomics; D015398:Signal Transduction
chemical_list: D009363:Neoplasm Proteins; D010750:Phosphoproteins
keywords: CRC; Colorectal cancer; Label-free; Phosphoproteomics; Single shot; Titanium dioxide