PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors
Abstract
Accurate and comprehensive peptide precursor ions are crucial to tandem mass-spectrometry-based peptide identification. An identification engine can derive great advantages from the search space reduction enabled by credible and detailed precursors. Furthermore, by considering multiple precursors per spectrum, both the number of identifications and the spectrum explainability can be substantially improved. Here, we introduce PepPre, which detects precursors by decomposing peaks into multiple isotope clusters using linear programming methods. The detected precursors are scored and ranked, and the high-scoring ones are used for subsequent peptide identification. PepPre is evaluated both on regular and cross-linked peptide data sets and compared with 11 methods. The experimental results show that PepPre achieves a remarkable increase of 203% in PSM and 68% in peptide identifications compared to instrument software for regular peptides and 99% in PSM and 27% in peptide pair identifications for cross-linked peptides, surpassing the performance of all other evaluated methods. In addition to the increased identification numbers, further credibility evaluations evidence the reliability of the identified results. Moreover, by widening the isolation window of data acquisition from 2 to 8 Th, with PepPre, an engine is able to identify at least 64% more PSMs, thereby demonstrating the potential advantages of wide-window data acquisition.
Usage
- PepPre will generate the isotopic pattern vectors (IPV) on the first run, and it may cost minutes.
Release
PepPre 1.3.0
🎉 Our paper “PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors” has been accepted by Journal of Proteome Research!- add experimental features for global peptide precursor analysis.
- support .mes input, which is a binary format and is much faster than text-based formats.
- able to split output into batches to support large data from instrument such as Astral.
- support .pf2 output, which is commonly used by software from pFind Team.
- improved UI.
PepPre 1.2.0
- improved UI.
PepPre 1.1.1
- change path for saving configuration.
PepPre 1.1.0
- embed `PepPepView` which can display deisotoped precursor ions and corresponding identification.
- adjust arguments of CLI interface.
PepPre 1.0.3
- the version is not publicly released.
- internal changes.
- adjust file type filtering of input data.
- adjust ext of output file: export as `{file_name}.precursor.[csv|tsv]` if `csv` or `tsv` is selected.
PepPre 1.0.2
- internal changes.
- show logo in ui.
PepPre 1.0.1
- internal changes.
- fix input file type detection.
PepPre 1.0.0
Citation
BibTeX
@article{Tarn2024PepPre,
author = {Ching Tarn and Yu-Zhuo Wu and Kai-Fei Wang},
title = {PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors},
journal = {Journal of Proteome Research},
doi = {10.1021/acs.jproteome.3c00293},
url = {https://doi.org/10.1021/acs.jproteome.3c00293},
year = {2024},
type = {Journal Article}
}