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 greatly benefit from the search space reduction hinted by credible and detailed precursors. Additionally, both the number of identifications and the spectrum explainability can be increased by considering multiple precursors per spectrum. Here, we propose 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 the following peptide identification. PepPre is evaluated both on regular and cross-linked peptides datasets, and compared with 11 methods in this paper. The experimental results show that PepPre achieves 203% more PSM and 68% more peptide identifications than instrument software for regular peptides, and 99% more PSM and 27% more peptide pair identifications for cross-linked peptides, which also outperforms all other evaluated methods. In addition to the increased identification numbers, further credibility evaluation evidence that the identifications are credible. Moreover, by widening the isolation window of data acquisition from 2 Th to 8 Th, the engine is able to identify at least 64% more PSMs with PepPre, demonstrating the potential advantages of large isolation windows.
Usage
- Please try PepFeat if you want to detect peptide features from LC-MS map.
- PepPre will generate the isotopic pattern vectors (IPV) on the first run, and it may cost minutes.
Release
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
Q&A
-
macOS says: “PepPre.app” is damaged and can’t be opened. You should move it to the Trash.
Please run `sudo xattr -r -d com.apple.quarantine [path/to/PepPre.app]` in terminal. -
Windows Security stops the software and deletes the .exe file.
The software is packaged using PyInstaller, and can be detected as virus by mistake on Windows (see the issue). Please restore the deleted file from `Protection History`, and Windows Security should not stop or delete it again. Otherwise, please add the software to white list. You can also package the software from source yourself.
Source
Example Data
Citation
BibTeX
@article{Tarn2023PepPre,
author = {Ching Tarn and Yu-Zhuo Wu and Kai-Fei Wang},
title = {PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors},
year = {2023},
doi = {10.1101/2023.05.13.540645},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2023/05/14/2023.05.13.540645},
eprint = {https://www.biorxiv.org/content/early/2023/05/14/2023.05.13.540645.full.pdf},
journal = {bioRxiv}
}