PXD001468-2

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.
3	2024-10-22 04:21:27	announced	2024-10-22: Updated project metadata.

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

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/2015/06/PXD001468

PRIDE project URI

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