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DART-ID increases single-cell proteome coverage

Albert Chen, View ORCID ProfileAlexander Franks, View ORCID ProfileNikolai Slavov
doi: https://doi.org/10.1101/399121
Albert Chen
Department of Bioengineering, Northeastern University;
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Alexander Franks
Department of Statistics and Applied Probability, UC Santa Barbara
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Nikolai Slavov
Department of Bioengineering, Northeastern University;
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  • For correspondence: nslavov@alum.mit.edu
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 23, 2018.
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DART-ID increases single-cell proteome coverage
Albert Chen, Alexander Franks, Nikolai Slavov
bioRxiv 399121; doi: https://doi.org/10.1101/399121
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DART-ID increases single-cell proteome coverage
Albert Chen, Alexander Franks, Nikolai Slavov
bioRxiv 399121; doi: https://doi.org/10.1101/399121

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