PXD001468

PXD001468 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2015-06-03
AnnouncementXML	Submission_2015-06-16_12:34:50.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joel Chick
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

Revision	Datetime	Status	ChangeLog Entry
0	2014-11-06 05:07:06	ID requested
1	2015-06-03 08:02:00	announced
⏵ 2	2015-06-16 12:34:52	announced	Updated publication reference for PubMed record(s): 26076430.

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]

curator keyword: Biomedical, Technical

submitter keyword: Proteomics, Sequest, Large scale, modifications

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

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PRIDE project URI

• PRIDE
  1. PXD001468
     1. Label: PRIDE project
     2. Name: An Ultra-tolerant Database Search Identifies more than 100,000 Modified Peptides