Comparative Analysis of Data-Driven Rescoring Platforms for Improved Peptide Identification in HeLa Digest Samples.

ABSTRACT: Mass spectrometry is a critical tool to understand complex changes in biological processes. Despite significant advances in search engine technology, many spectra remain unassigned. This research evaluates the performance of three rescoring platforms, Oktoberfest, MS²Rescore, and inSPIRE, using MaxQuant output. The results indicated a substantial increase in identifications at the peptide level (40%-53%) and PSM level (64%-67%). However, some peptides were lost due to limitations in processing posttranslational modifications (PTMs)-with up to 75% of lost peptides exhibiting PTMs. Each platform displayed distinct strengths and weaknesses. For instance, inSPIRE performed best in terms of peptide identifications and unique peptides, while MS²Rescore performed better for

SUBMITTER: Castano JD 

PROVIDER: S-EPMC11962579 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature