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PXD001468

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2015-06-03
  • AnnouncementXML: Submission_2015-06-16_12:34:50.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Joel Chick
  • Title: An Ultra-tolerant Database Search Identifies more than 100,000 Modified Peptides
  • Description: Less than half of all MS/MS spectra acquired in shotgun proteomics typically result in a confident peptide match. Here we present an ultra-tolerant Sequest database search that allowed peptide matching even with modifications of unknown masses up to ±500 Da. From an HEK293 cell proteome-wide dataset (9,513 proteins and 396,736 peptides), a ±500-Da search matched an additional 184,000 modified peptides. These were linked to both biological and chemical modifications representing 523 distinct mass bins including phosphorylation, glycosylation, and methylation. We attempted to localize all unknown modification masses to specific regions within a peptide, and known modifications were accurately assigned to the correct amino acids with frequencies often >90%. These data demonstrate that a large fraction of previously unassignable spectra are assignable to peptide sequences with modifications.
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: S-pyridylethyl-L-cysteine; biotinylated residue; iodoacetic acid derivatized residue; farnesylated residue; monohydroxylated residue; acetylated residue; dehydrated residue; carbamoylated residue; phosphorylated residue; (R)-5-oxo-1: 4-tetrahydrothiazine-3-carboxylic acid; amidated residue; monomethylated residue; dihydroxylated residue; homoserine lactone; methylthiolated residue; deamidated residue; carboxylated residue; sulfated residue; iodoacetamide derivatized residue; deaminated residue; homoserine; formylated residue; monosodium salt
  • Instrument: Q Exactive

Dataset History

VersionDatetimeStatusChangeLog Entry
02014-11-06 05:07:06ID requested
12015-06-03 08:02:00announced
22015-06-16 12:34:52announcedUpdated publication reference for PubMed record(s): 26076430.

Publication List

  1. Chick JM, Kolippakkam D, Nusinow DP, Zhai B, Rad R, Huttlin EL, Gygi SP, A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides. Nat Biotechnol, 33(7):743-9(2015) [pubmed]

Keyword List

  1. curator keyword: Biomedical, Technical
  2. submitter keyword: Proteomics, Sequest, Large scale, modifications

Contact List

    Steven P Gygi
    • contact affiliation: Harvard medical school, Department of Cell Biology
    • contact email: steven_gygi@hms.harvard.edu
    • lab head:
    Joel Chick
    • contact affiliation: Harvard Medical School
    • contact email: chick.joel@gmail.com
    • dataset submitter:

Full Dataset Link List

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  2. PRIDE project URI
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