TPP pipeline

TPP specifications


Unique identifier OMICS_02449
Name TPP
Alternative name Trans-Proteomic Pipeline
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Andrew Keller <>

Publication for Trans-Proteomic Pipeline

TPP citations

PMCID: 5686074

[…] 1600 m/z. post-acquisition of data, readw was used to convert files to mzxml, which were used to query the human ipi database using the sequest platform. false discovery rate was determined using the trans-proteomic pipeline tpp, with a fdr set at approximately 5%. finally, relative enrichment or depletion in tumor group was normalized to control group., rna was isolated using trizol (life technol […]

PMCID: 5595980

[…] of cysteine residues (+ 57.02 da) was used as fixed modification, whereas methionine oxidation (+ 15.99 da) was set as a variable. peptide lists from both search engines were combined within the trans-proteomic pipeline for further analysis. the ms raw data associated with the present paper are available upon request., in-gel digests were performed as described by huesgen et al.60. […]

PMCID: 5370288

[…] in the orbitrap, with resolution of 30 000 (at m/z 400)., thermo xcalibur native acquisition files (.raw files) were converted to the open file format mzxml via readw.exe, which is available in the trans-proteomic pipeline (tpp) platform ( an open-source computer program, msinspect, was utilized to locate isotopes in the lc-ms data and assemble […]

PMCID: 5270547

[…] seconds was used after 2 repeats of ms2 for a precursor ion. ms2 were collected with 1 microscan and a collision energy of 35%., we performed peptide identification using x! tandem incorporated in a trans-proteomic pipeline (version 4.6 occupy rev 2).56 each raw data file was first converted to mzxml using the msconvert tool incorporated in proteowizard (version 3.0.4205).57 ms/ms scans […]

TPP institution(s)
Institute for Systems Biology, Seattle, WA, USA

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