Proteomic

Abacus is a handy, Java based tool specially designed to help users extract and pre-process spectral count data for label-free quantitative proteomic analysis. This program is designed to be used with the Trans-Proteomic Pipeline (TPP). for WindowsAll Platforms: Windows

A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.) Platforms: Windows, Mac, Linux

MALDIPepQuant is a tool to quantify MALDI peptides (SILAC) from Phenyx output. This tool has been developed as a service of the Bioinformatics Core Facility, within a collaboration between the Proteome Informatics Group from the Swiss Institute of Bioinformatics (SIB) and the Biomedical... Platforms: Mac

ProteoConnections is a bioinformatics platform tailored to address the pressing needs of proteomic analyses. Organise identifications, evaluate the the acquired dataset and accelerate biological interpretation using bioinformatics applications. Platforms: *nix

Manual validation of MS/MS driven peptide identification is a critical evaluation process relying on expert knowledge. Following the onset of large-scale proteomic endeavors, manual validation has become a undoable endeavor useful expert knowledge remains unused. The Peptizer platform was... Platforms: Mac

Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs. A... Platforms: Mac