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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


No version available


  • person_outline Andrew Keller

Publication for Trans-Proteomic Pipeline

TPP citations


Potential molecular mechanisms of overgrazing induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data

BMC Plant Biol
PMCID: 5941328
PMID: 29739327
DOI: 10.1186/s12870-018-1304-7
call_split See protocol

[…] mzXML data was then matched with the Swiss-Prot/TrEMBL database (release-2015_07) ( [, ] using the PeptideProphet tool in Trans-Proteomic Pipeline software ( []. The matching results were obtain using pepXMLTab software. The following search parameter settings were used: peptide tolerance, ± […]


Spatiotemporal distribution of small ubiquitin‐like modifiers during human placental development and in response to oxidative and inflammatory stress

PMCID: 5924830
PMID: 29468681
DOI: 10.1113/JP275288
call_split See protocol

[…] converted to the mzXML format using Proteowizard open source software (Kessner et al. ), then searched using X!Tandem (Craig & Beavis, ) against Human RefSeq Version 45. Data were analysed using the trans‐proteomic pipeline (TPP) (Pedrioli, ) via the ProHits 2.0.0 software suite (Liu et al. ). Cytoskeleton IDs of the keratin, tubulin and actin families were added up for comparison (data not shown […]


FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell Derived Cardiac Progenitors

Stem Cell Reports
PMCID: 5768897
PMID: 29249665
DOI: 10.1016/j.stemcr.2017.11.008

[…] tatic modification for cysteines, at least one tryptic terminus, and two missed cleavage sites. Statistical analysis of the data, including peptide and protein identification, was performed using the Trans-Proteomic Pipeline v4.3 (TPP; Seattle Proteome Center) including PeptideProphet and ProteinProphet (). Peptides and proteins were detected and quantified at a confidence score of >1.3 using the […]


RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1

PMCID: 5666606
PMID: 29030483
DOI: 10.15252/embj.201796525
call_split See protocol

[…] lected (relative collision energy ~35%). Proteins were identified by searching the data against Swiss‐Prot human database (January 9th 2013) appended with decoy (reverse) sequences using the X!Tandem/Trans‐Proteomic Pipeline software suite (Pedrioli, ). All peptides and proteins with a PeptideProphet (Keller et al, ) and ProteinProphet (Nesvizhskii et al, ) probability score of >0.8 (false discove […]


A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host pathogen interactions

Sci Rep
PMCID: 5591248
PMID: 28887440
DOI: 10.1038/s41598-017-10059-w

[…] ein database comprising 2,891 proteins in a target-decoy approach. Static and variable modifications were considered according to the sample characteristics.The search results were processed with the Trans-Proteomic Pipeline (TPP, version 4.6) including PeptideProphet, iProphet, and ProteinProphet–. Per experiment a PSM FDR threshold was applied to maintain a constant FDR. The build named S. aureu […]


Integrative analysis for the discovery of lung cancer serological markers and validation by MRM MS

PLoS One
PMCID: 5570484
PMID: 28837649
DOI: 10.1371/journal.pone.0183896

[…] were fixed modification of carbamidomethylation at cysteine (+ 57.02 Da) and variable modification of oxidation at methionine (+ 15.99 Da). Peptide assignment and validation were performed using the Trans-Proteomic Pipeline (TPP, version 4.0, The SEQUEST search output was used as an input for TPP analyses. The MS/MS spectra acquired from plasma samples were analyze […]


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

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