Unifying the analysis of bottom-up proteomics data with CHIMERYS

Avatar
Poster
Voices Powered byElevenlabs logo
Connected to paperThis paper is a preprint and has not been certified by peer review

Unifying the analysis of bottom-up proteomics data with CHIMERYS

Authors

Frejno, M.; Berger, M. T.; Tueshaus, J.; Hogrebe, A.; Seefried, F.; Graber, M.; Samaras, P.; Fredj, S. B.; Sukumar, V.; Eljagh, L.; Bronshtein, I.; Mamisashvili, L.; Schneider, M.; Gessulat, S.; Schmidt, T.; Kuster, B.; Zolg, D. P.; Wilhelm, M.

Abstract

Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such as data-dependent (DDA), data-independent (DIA) or parallel reaction monitoring (PRM), separate software packages employing different analysis concepts are used for peptide identification and quantification, even though the underlying information is principally the same. Here, we introduce CHIMERYS, a novel, spectrum-centric search algorithm designed for the deconvolution of chimeric spectra that unifies proteomic data analysis. Using accurate predictions of peptide retention time, fragment ion intensities and applying regularized linear regression, it explains as much fragment ion intensity as possible with as few peptides as possible. Together with rigorous false discovery rate control, CHIMERYS accurately identifies and quantifies multiple peptides per tandem mass spectrum in DDA, DIA and PRM experiments.

Follow Us on

0 comments

Add comment