JUMPptm: Integrated software for sensitive identification of post-translational modifications and its application in Alzheimer's disease study.

ABSTRACT:

Background

Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment of modified proteins or peptides. However, recent ultra-deep whole proteome profiling generates millions of spectra in a single experiment, leaving many unassigned spectra, some of which may be derived from PTM peptides.

Methods

Here we present JUMPptm, an integrative computational pipeline, to extract PTMs from unenriched whole proteome. JUMPptm combines the advantages of JUMP, MSFragger and Comet search engines, and includes de novo tags, customized database search and peptide filtering, which iteratively analyzes each PTM by a multi-stage strategy to improve sensitivity and specificity.

Results

We applied JUMPptm to the deep brain

SUBMITTER: Poudel S 

PROVIDER: S-EPMC9957936 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature