PatternLab for proteomics comprises a computational environment for quantitative analysis of proteomic data. Below we find links to its modules. These tools are a result of collaborations between Fiocruz (Laboratory for proteomics and Protein Engineering and Laboratory for Toxinology, Fiocruz - RJ), The Systems Engineering and Computer Science Program from the Federal University of Rio de Janeiro, Proteomics Unit from UFRJ, and the John Yates III lab.
Search Engine Processor (SEPro)
Used for fltering and organising results from ProLuCID, SEQUEST, Spectrum Identification Machine.
PepExplorer: a similarity-driven tool for analyzing de novo sequencing results
Statistically filtering and organising de novo sequencing results.
A simulation to help explain the multi-dimensional protein identification technology procedure.
A software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). SIM-XL introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. SIM-XL is the first tool to support XL data in the mzIdentML format.
DiagnoProt is a tool that finds discriminative mass spectra among different biological conditions and ultimately performs spectral profiling classification of unknown conditions by comparing sets of tandem mass spectra (MS/MS).
Yet another deconvolution algorithm.