All the software tools we have developed are open source and can be used freely by anyone. We simply ask that you either cite this website or the particular publication where the tool was first used. For Perl scripts the usage is described in commented text in the beginning of each file.
- PCP-SILAC, scripts, instructions and sample data for informatics treatment of PCP-SILAC data.
- finalList, a tool that takes as input a non-redundant list of peptides identified in a project and compiles a non-redundant list of proteins identified. It will also subtract any peptides coming from a FASTA library of contaminants.
- transORF, a tool that takes a FASTA nucleotide file and predicts all open reading frames in all six translation frames. The output is a FASTA amino acid file. This tool is useful for creating a protein library for database searching (where a good prediction is unavailable) if you don’t want to (or can’t) search your MS/MS spectra against a nucleotide library.
- JProteomics2014, Development of a computation framework for the analysis of protein correlation profiling and spatial proteomics experiments 2014
- Attachments to paper Scott et al Molecular System Biology (2017):