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PXD011748

PXD011748 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDART-ID increases single-cell proteome coverage
DescriptionAnalysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. Identifying proteins by LC-MS/MS proteomics, however, remains challenging for lowly abundant samples, such as the proteomes of single mammalian cells. To increase the identification rate of peptides in such small samples, we developed DART-ID. This method implements a data-driven, global retention time (RT) alignment process to infer peptide RTs across experiments. DART-ID then incorporates the global RT-estimates within a principled Bayesian framework to increase the confidence in correct peptide-spectrum-matches. Applying DART-ID to hundreds of samples prepared by the Single Cell Proteomics by Mass Spectrometry (SCoPE-MS) design increased the peptide and proteome coverage by 30 - 50% at 1% FDR. The newly identified peptides and proteins were further validated by demonstrating that their quantification is consistent with the quantification of peptides identified from high-quality spectra. DART-ID can be applied to various sets of experimental designs with similar sample complexities and chromatography conditions, and is freely available online.
HostingRepositoryMassIVE
AnnounceDate2018-11-19
AnnouncementXMLSubmission_2018-11-19_17:08:45.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterAlbert Chen
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListOxidation; Acetyl; TMT6plex
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-11-19 15:36:57ID requested
12018-11-19 17:08:46announced
Publication List
Chen A, Franks, A & Slavov, N. DART-ID increases single-cell proteome coverage. (submitted).
Chen A, Franks A & Slavov N. DART-ID increases single-cell proteome coverage. biorXiv, DOI: 10.1101/399121. PLOS Comp Bio (submitted).
Keyword List
submitter keyword: retention time, bayesian framework, peptide identification, computational, single cell
Contact List
Nikolai Slavov
contact affiliationNortheastern University
contact emailn.slavov@northeastern.edu
lab head
Albert Chen
contact affiliationNortheastern University
contact emailchen.alb@husky.neu.edu
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location