An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.

ABSTRACT:

Background

Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed to avoid this, including the generation of reduced transcriptome-informed protein databases, which only contain proteins whose transcripts are detected in the sample-matched transcriptome. These were found to increase peptide identification sensitivity. Here, we present a detailed evaluation of this approach.

Results

We establish that the increased sensitivity in peptide identification is in fact a statistical artifact, directly resulting from

SUBMITTER: Fancello L 

PROVIDER: S-EPMC9208142 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature