PXD008966

PXD008966 is an original dataset announced via ProteomeXchange.

Title	An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies
Description	Phosphorylation-mediated signaling pathways have major implications in cellular regulation and disease. Mass spectrometry-based proteomics is a well-established approach for quantifying thousands of phosphorylation events in a single experiment. However, proteins with roles in signaling pathways are frequently less abundant and phosphorylation is often sub-stoichiometric. As such, the efficient enrichment and subsequent recovery of phosphorylated peptides is vital. To understand better phosphopeptide recovery from enrichment strategies, we designed a peptide internal standard-based assay directed toward sample preparation strategies for mass spectrometry analysis. We coupled mass-differential tandem mass tag (mTMT) reagents (specifically, TMTzero and TMTsuper-heavy), nine mass spectrometry-amenable phosphopeptides (phos9), and peak area measurements from extracted ion chromatograms to determine phosphopeptide recovery. We showcase this mTMT/phos9 recovery assay by evaluating three commercial phosphopeptide enrichment workflows. Our assay provides data on the recovery of phosphopeptides, which complement other metrics, namely the number of identified phosphopeptides and enrichment specificity. Our mTMT/phos9 assay is applicable to any enrichment protocol in a typical experimental workflow irrespective of sample origin or labeling strategy.
HostingRepository	PRIDE
AnnounceDate	2018-12-04
AnnouncementXML	Submission_2019-06-17_03:26:33.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-15 09:33:52	ID requested
1	2018-12-04 08:13:47	announced
⏵ 2	2019-06-17 03:26:34	announced	Updated publication reference for PubMed record(s): 29671274.

Paulo JA, Navarrete-Perea J, Erickson AR, Knott J, Gygi SP, An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. J Am Soc Mass Spectrom, 29(7):1505-1511(2018) [pubmed]

ProteomeXchange project tag: Reference

submitter keyword: TMT super-heavy, TMTsh, TMT0, TMTzero, Lumos, phosphorylation, mTRAQ

Joao A. Paulo
contact affiliation	Cell Biology, Harvard Medical School, USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008966
     1. Label: PRIDE project
     2. Name: An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies