Quantifying compartment-associated variations of protein abundance in proteomics data.

ABSTRACT: Quantitative mass spectrometry enables to monitor the abundance of thousands of proteins across biological conditions. Currently, most data analysis approaches rely on the assumption that the majority of the observed proteins remain unchanged across compared samples. Thus, gross morphological differences between cell states, deriving from, e.g., differences in size or number of organelles, are often not taken into account. Here, we analyzed multiple published datasets and frequently observed that proteins associated with a particular cellular compartment collectively increase or decrease in their abundance between conditions tested. We show that such effects, arising from underlying morphological differences, can skew the outcome of differential expression analysis. We propose a method to

SUBMITTER: Parca L 

PROVIDER: S-EPMC6056770 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature