MassIVE MSV000083149

Complete Public PXD011748

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. [doi:10.25345/C5KW3W] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: retention time ; bayesian framework ; peptide identification ; computational ; single cell

Contact

Principal Investigators: Nikolai Slavov, Northeastern University, USA
Submitting User: blahoink

Publications

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).

Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Proteins:
Protein Accessions (reported):
Peptides:
Variant Peptides:
PSMs:
 
FTP Download Browse Results
 
FTP Download Link (click to copy):

- Dataset Reanalyses


+ Dataset History


Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.
Number of distinct protein accessions reported by originally submitted search results.