MassIVE MSV000083149

Complete Public PXD011748

DART-ID increases single-cell proteome coverage


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


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


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.

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