PXD001546

PXD001546 is an original dataset announced via ProteomeXchange.

Title	Reproducibility of label-free single-shot phosphoproteomics applied to CRC cell lines
Description	There is a need for robust phosphopeptide enrichment methods to allow signaling network analysis in cancer cell lines and tissues with minimal fractionation. With recent instrument developments thousands of unique phosphopeptides can be detected by single-shot LC-MS/MS. However, successful phosphoproteomics experiments still rely on efficient phosphopeptide enrichment from a tryptic digest prior to LC-MS/MS analysis. Here we describe a performance assessment of HAMMOC (hydroxyl acid modified metal affinity chromatography) (Sugiyama MCP2007, Kyono, JPR 2008) combined with single shot label-free quantitation at 500 µg peptide input level. In a triplicate analysis we observe good phosphopeptide identification reproducibility (75.8%), depth of identification (6014-6150 phosphopeptides) and reproducibility of label-free quantification (CV 17.8%, Pearson r 0.87-0.98) by single-shot LC-MS/MS.
HostingRepository	PRIDE
AnnounceDate	2015-04-15
AnnouncementXML	Submission_2015-04-15_02:48:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-11-27 03:46:53	ID requested
⏵ 1	2015-04-15 02:48:01	announced

Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR, Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines. J Proteomics, 127(Pt B):247-58(2015) [pubmed]

curator keyword: Biomedical, Technical

submitter keyword: Human, CRC, colorectal cancer, label-free, single-shot, phosphoproteomics

Connie Ramona Jimenez
contact affiliation	OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact email	c.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliation	OncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact email	s.piersma@vumc.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/04/PXD001546

PRIDE project URI

• PRIDE
  1. PXD001546
     1. Label: PRIDE project
     2. Name: Reproducibility of label-free single-shot phosphoproteomics applied to CRC cell lines