PXD001468

PXD001468 is an original dataset announced via ProteomeXchange.

Title	A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as 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	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:21:27.085.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	monomethylated residue; (R)-5-oxo-1; carboxylated residue; dehydrated residue; biotinylated residue; phosphorylated residue; deaminated residue; acetylated residue; iodoacetic acid derivatized residue; iodoacetamide derivatized residue; deamidated residue; farnesylated residue; dihydroxylated residue; homoserine lactone; S-pyridylethyl-L-cysteine; carbamoylated residue; sulfated residue; methylthiolated residue; amidated residue; homoserine; monosodium salt; monohydroxylated residue; formylated residue
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.

10.1038/nbt.3267;

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]

ProteomeXchange project tag: deep learning, benchmarking, machine learning, immunopeptidomics

curator keyword: Technical, Biomedical

submitter keyword: Sequest, Large scale, modifications,Proteomics

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: A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides