Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine.

ABSTRACT: Deisotoping, or the process of removing peaks in a mass spectrum resulting from the incorporation of naturally occurring heavy isotopes, has long been used to reduce complexity and improve the effectiveness of spectral annotation methods in proteomics. We have previously described MSFragger, an ultrafast search engine for proteomics, that did not utilize deisotoping in processing input spectra. Here, we present a new, high-speed parallelized deisotoping algorithm, based on elements of several existing methods, that we have incorporated into the MSFragger search engine. Applying deisotoping with MSFragger reveals substantial improvements to database search speed and performance, particularly for complex methods like open or nonspecific searches. Finally, we evaluate our deisotoping method o

SUBMITTER: Teo GC 

PROVIDER: S-EPMC8864561 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature