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PTM-Invariant Peptide Identification. An open search tool.

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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:

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}
}