PXD011748

PXD011748 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	DART-ID increases single-cell proteome coverage
Description	Analysis 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.
HostingRepository	MassIVE
AnnounceDate	2018-11-19
AnnouncementXML	Submission_2018-11-19_17:08:45.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Albert Chen
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Acetyl; TMT6plex
Instrument	Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-19 15:36:57	ID requested
⏵ 1	2018-11-19 17:08:46	announced

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).

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

submitter keyword: retention time, bayesian framework, peptide identification, computational, single cell

Contact List

Nikolai Slavov
contact affiliation	Northeastern University
contact email	n.slavov@northeastern.edu
lab head
Albert Chen
contact affiliation	Northeastern University
contact email	chen.alb@husky.neu.edu
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

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://massive.ucsd.edu/MSV000083149