PTM-Invariant Peptide Identification. An open search tool.
Download PIPI.zip from https://github.com/fcyu/PIPI/releases/latest.
Requirement:
- Java 1.8.
- With Percolator installed.
Download and install JDK 8 from https://www.oracle.com/java/technologies/downloads/#java8
Download Maven from https://maven.apache.org/download.cgi
Install ProteomicsLibrary library:
git clone https://github.com/fcyu/ProteomicsLibrary.git
cd ProteomicsLibrary
mvn install
Download and compile PIPI:
git clone https://github.com/fcyu/PIPI.git
cd PIPI
mvn package
java -Xmx64g -jar PIPI.jar <parameter_file> <spectra_file>
<parameter_file>: Parameter file. Can be downloaded along with PIPI. There are detailed explanations for the parameters in the file.<spectra_file>: Spectra file (mzXML or mgf).
example: java -Xmx25g -jar PIPI.jar parameter.def data.mzXML
| scan_num | peptide | charge | theo_mass | exp_mass | abs_ppm | A_score | protein_ID | score | delta_C_n | percolator_score | posterior_error_prob | q_value | other_PTM_patterns | MGF_title | labelling | isotope_correction | MS1_pearson_correlation_coefficient |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1436 | nESEDKPEIEDVGSDEE(129.043)EE(-0.948)Kc | 3 | 2320.008 | 2320.011 | 1.361049 | 13.02612 | NP_001017963.2;NP_005339.3;XP_011535020.1 | 5.106351 | 0.000121 | 2.69477 | 7.21E-06 | 0.002299 | nESEDKPEIEDVGSDEEE(129.043)E(-0.948)Kc-4.9165;nESEDKPEIEDVGSDEE(129.043)E(-0.948)EKc-4.8888;nESEDKPEIEDVGSDE(129.043)EEE(-0.948)Kc-4.8815;nESEDKPEIEDVGSDEE(-0.948)EE(129.043)Kc-4.6991 | N14 | 0 | 0.897093 |
scan_num: Scan number (start from 1) of the spectrum.peptide: Identified peptide sequence.charge: Precursor charge.theo_mass: Theoretical neutral mass of the identified peptide sequence.exp_mass: Observed neutral mass of the spectrum.abs_ppm: Absolute PPM betweentheo_massandexp_mass.A_score: AScore based on the paper "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". In the original algorithm, it only considers phosphorylation. PIPI considers all modifications.protein_ID: Protein accession from the fasta file.score: Identification score. It's similar to XCorr.delta_c_n: The relative difference between the top score and the second best score.percolator_score: Percolator score reported by Percolator.posterior_error_prob: Percolator error probability reported by Percolator.q_value: q-value (used as FDR in the community) estimated by Percolator.other_PTM_patterns: The second best to the fifth best modification patterns corresponding to the identified peptide sequence. There is an identification score following each pattern.MGF_title: MGF title if the input spectral file is in MGF format.labelling: N14 or N15 labelling.isotope_correction: The number of C13 isotope correction. Only applicable to mzXML format.MS1_pearson_correlation_coefficient: The similarity between the observed MS1 isotope pattern and the theoretical isotope pattern. The range is from 0 to 1. Only applicable to mzXML format.
Yu, F., Li, N., & Yu, W. (2016). PIPI: PTM-Invariant Peptide Identification Using Coding Method. Journal of Proteome Research, 15(12), 4423-4435.
@article{yu2016pipi,
title={PIPI: PTM-Invariant Peptide Identification Using Coding Method},
author={Yu, Fengchao and Li, Ning and Yu, Weichuan},
journal={Journal of Proteome Research},
volume={15},
number={12},
pages={4423--4435},
year={2016},
publisher={ACS Publications},
doi={10.1021/acs.jproteome.6b00485}
}