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.
slavovLabI have always hated the career building aspects of pursuing an academic career, and yet I do not have good ideas how to sidestep them.
These aspects aren't unique to academia (seem worse in politics) but are particularly incongruous with what inspired many of us to do research.
slavovLab@skryazhi@NSF I strongly dislike invoking "competition with China" as a motivation -- this is misguided on many levels.
It's hard to predict that this will evolve, and I do not know enough to make an informed prediction. It sounds more promising than menacing.
slavovLab@jcjray Indeed, that is the case; one may come up with reasonable arguments for it, e.g., projects & training in labs with strong track records are more likely to be successful.
K99/R00 carries the bias further since it helps postdocs get faculty positions more than the F grants do.