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Evaluation of different data-driven rescoring platforms to increase peptide identifications in HeLa digest samples

ABSTRACT: Evaluate the performance of different rescoring platforms with the aim of standardizing pipelines within our research group.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jesus Castano

LAB HEAD: Francis Beaudry

PROVIDER: PXD052875 | Pride | 2025-05-07

REPOSITORIES: Pride

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			Action	DRS
	100FDR_msms.txt	Txt
	HeLa_samples09.raw	Raw
	HeLa_samples10.raw	Raw
	checksum.txt	Txt

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Publications

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

Castaño Jesus D JD Beaudry Francis F

Proteomics 20250202 7

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, MS<sup>2</sup>Rescore, 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 p ...[more]

PMID: 39895169

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