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PXD001468-3

PXD001468 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
DescriptionLess 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:21:27.085.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJoel Chick
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonomethylated 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
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog 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.
32024-10-22 04:21:27announced2024-10-22: Updated project metadata.
Publication List
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]
Keyword List
ProteomeXchange project tag: deep learning, benchmarking, machine learning, immunopeptidomics
curator keyword: Technical, Biomedical
submitter keyword: Sequest, Large scale, modifications,Proteomics
Contact List
Steven P Gygi
contact affiliationHarvard medical school, Department of Cell Biology
contact emailsteven_gygi@hms.harvard.edu
lab head
Joel Chick
contact affiliationHarvard Medical School
contact emailchick.joel@gmail.com
dataset submitter
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Dataset FTP location
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PRIDE project URI
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