{"id":24557991,"url":"https://github.com/fcyu/pipi","last_synced_at":"2025-04-19T04:15:22.927Z","repository":{"id":87811164,"uuid":"66186393","full_name":"fcyu/PIPI","owner":"fcyu","description":"PTM-Invariant Peptide Identification. 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An open search tool.\n\n## Executable file\nDownload `PIPI.zip` from https://github.com/fcyu/PIPI/releases/latest.\n\n## How to use it\nRequirement: \n- Java 1.8.\n- With [Percolator](https://github.com/percolator/percolator/releases) installed.\n\n\n## How to compile from source\nDownload and install JDK 8 from https://www.oracle.com/java/technologies/downloads/#java8\n\nDownload Maven from https://maven.apache.org/download.cgi\n\nInstall ProteomicsLibrary library:\n```\ngit clone https://github.com/fcyu/ProteomicsLibrary.git\ncd ProteomicsLibrary\nmvn install\n```\n\nDownload and compile PIPI:\n```\ngit clone https://github.com/fcyu/PIPI.git\ncd PIPI\nmvn package\n```\n\n\n## Usage\n```\njava -Xmx64g -jar PIPI.jar \u003cparameter_file\u003e \u003cspectra_file\u003e\n```\n- ```\u003cparameter_file\u003e```: Parameter file. Can be downloaded along with PIPI. There are detailed explanations for the parameters in the file.\n- ```\u003cspectra_file\u003e```: Spectra file (mzXML or mgf).\n\nexample: ```java -Xmx25g -jar PIPI.jar parameter.def data.mzXML```\n\n## An example of the result file\n\n| 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 |\n|----------|----------------------------------------|--------|-----------|----------|----------|----------|-------------------------------------------|----------|-----------|------------------|----------------------|----------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|-----------|--------------------|-------------------------------------|\n| 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                            |\n\n### Explanations\n1. `scan_num`: Scan number (start from 1) of the spectrum.\n2. `peptide`: Identified peptide sequence.\n3. `charge`: Precursor charge.\n4. `theo_mass`: Theoretical neutral mass of the identified peptide sequence.\n5. `exp_mass`: Observed neutral mass of the spectrum.\n6. `abs_ppm`: Absolute PPM between `theo_mass` and `exp_mass`.\n7. `A_score`: AScore based on the paper \"[A probability-based approach for high-throughput protein phosphorylation analysis and site localization](https://doi.org/10.1038/nbt1240)\". In the original algorithm, it only considers phosphorylation. PIPI considers all modifications.\n8. `protein_ID`: Protein accession from the fasta file.\n9. `score`: Identification score. It's similar to XCorr.\n10. `delta_c_n`: The relative difference between the top score and the second best score.\n11. `percolator_score`: Percolator score reported by Percolator.\n12. `posterior_error_prob`: Percolator error probability reported by Percolator.\n13. `q_value`: q-value (used as FDR in the community) estimated by Percolator.\n14. `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.\n15. `MGF_title`: MGF title if the input spectral file is in MGF format.\n16. `labelling`: N14 or N15 labelling.\n17. `isotope_correction`: The number of C13 isotope correction. Only applicable to mzXML format.\n18. `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.\n\n## Cite\nYu, F., Li, N., \u0026 Yu, W. (2016). PIPI: PTM-Invariant Peptide Identification Using Coding Method. Journal of Proteome Research, 15(12), 4423-4435.\n```\n@article{yu2016pipi,\n  title={PIPI: PTM-Invariant Peptide Identification Using Coding Method},\n  author={Yu, Fengchao and Li, Ning and Yu, Weichuan},\n  journal={Journal of Proteome Research},\n  volume={15},\n  number={12},\n  pages={4423--4435},\n  year={2016},\n  publisher={ACS Publications},\n  doi={10.1021/acs.jproteome.6b00485}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffcyu%2Fpipi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffcyu%2Fpipi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffcyu%2Fpipi/lists"}