PIPI

PTM-Invariant Peptide Identification. An open search tool.

Executable file

Download PIPI.zip from https://github.com/fcyu/PIPI/releases/latest.

How to use it

Requirement:

• Java 1.8.
• With Percolator installed.

How to compile from source

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

Usage

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

An example of the result file

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

Explanations

1. scan_num: Scan number (start from 1) of the spectrum.
2. peptide: Identified peptide sequence.
3. charge: Precursor charge.
4. theo_mass: Theoretical neutral mass of the identified peptide sequence.
5. exp_mass: Observed neutral mass of the spectrum.
6. abs_ppm: Absolute PPM between theo_mass and exp_mass.
7. 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.
8. protein_ID: Protein accession from the fasta file.
9. score: Identification score. It's similar to XCorr.
10. delta_c_n: The relative difference between the top score and the second best score.
11. percolator_score: Percolator score reported by Percolator.
12. posterior_error_prob: Percolator error probability reported by Percolator.
13. q_value: q-value (used as FDR in the community) estimated by Percolator.
14. 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.
15. MGF_title: MGF title if the input spectral file is in MGF format.
16. labelling: N14 or N15 labelling.
17. isotope_correction: The number of C13 isotope correction. Only applicable to mzXML format.
18. 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.

Cite

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}
}