TPP Tutorials

You can find tutorials for various TPP tools here, including installation guides.


Windows installation
Installation of TPP on Windows systems (applicable to all versions since 5.2.0)
Linux installation
Installation recipes for a handful of Linux flavors and TPP versions
Docker installation
Running TPP on Linux via Docker instead of performing a local installation

Search and Validation

Conversion, Search, and Visualization
Starting with Thermo raw files, convert to mzML format and search with Comet and X!Tandem, followed by examination of results with Pep3D and the PepXMLViewer
PSM Validation
Use PeptideProphet to validate Comet search results
Peptide Validation
Use iProphet to validate peptide sequences from PeptideProphet results
Protein Validation
Use ProteinProphet to generate a validated protein list from PeptideProphet or iProphet results
PTM Localization
Use PTMProphet to validate and localize PTM sites
DIA Analysis
Use Disco to generate pseudo-MS2 spectra, and search with Comet
Cross-linking Analysis
Use Kojak to search and validate a cross-linking experiment
Open-mass Searching with MSFragger
Use MSFragger and TPP to process ISB18 data with an open-mass search and Castor Bean Proteome Entrapment
Spectral Library Searching
Use SpectraST to search a SILAC dataset using spectral libraries as a reference
Analyze Multiple Ions from Chimeric Spectra
Use reSpect to identify multiple peptide ions in spectra


Isotopic Peptide and Protein Quantitation
Use ASAPRatio and XPRESS to analyze a SILAC dataset
Isobaric Peptide and Protein Quantitation
Use Libra to analyze an iTraq-8 dataset
Label-Free Protein Quantitation
Use StPeter to perform label-free quant in a sample dataset

Other Tools

Spectral Library Creation
Use SpectraST in build mode to create a spectral library from validated search results
PEFF Database Indexing
Use ProteoMapper tools to index a database in PEFF format and map peptide sequences, including fuzzy matching

External Resources

Explore some of the many features of PeptideAtlas
ProteoMapper Web
Learn to use the ProteoMapper on-line utility at PeptideAtlas
Explore some of the many features of SRMAtlas