| Name | Description | Author | Documentation | Installation | Source Code Location |
|---|---|---|---|---|---|
| addLoci | A re-implementation of PepGrep (see below) | Barbara Frewen | html documentation | proteome:/mnt/local/bin/addLoci.pl | proteome CVS repository, module "hermie" |
| BiblioSpec | A suite of tools for managing and searching spectrum libraries | Barbara Frewen | html documentation | proteome:/mnt/local/bin/Blib* (e.g. BlibSearch, BlibBuild) | download from here
Noble CVS repository, module "mslib" |
| ChargeCzar | Determines charge state (+2 or +3) of multiply charged MS/MS spectra | Aaron Klammer | html documentation | proteome:/mnt/local/bin/charge_czar | download from here Noble lab CVS repository, module "czar" |
| DTASelect | Assembles peptide identifications into protein identifications | Dave Tabb | pdf manual | proteome:/mnt/local/bin/DTASelect | download from here |
| grab_seqs.py | Utility to extract a set of protein sequences from a fasta file | Greg Finney | usage statement | proteome:/mnt/local/bin/grab_seqs.py | proteome CVS repository, module "gfscripts" |
| Hardklor | An isotope distribution profiler | Mike Hoopmann | html documentation | proteome:/mnt/local/bin/hardklor | proteome CVS reository, module "Hardklor1.0" |
| hermie | Pipeline of mass spectra analysis, from spectra to protein IDs | Barbara Frewen | html documentation | proteome:/mnt/local/bin/hermie | proteome CVS repository, module "hermie" |
| IDCalc | Implementation of the Kubinyi isotope distribution prediction algorithm | Mike MacCoss, maintained jointly with Mike Hoopmann | ? | ? | ? |
| PepGrep | Updates the protein loci information for peptide identifcations in an SQT file given a new fasta database (see also addLoci.pl) | Dave Tabb | none | proteome:/mnt/local/bin/PepGrep | NA |
| PepHype | Creates a FASTA database of reversed, shuffled, or markov-generated protein sequences from an input FASTA file | Greg Finney | Usage statement when run with no arguments | proteome:~gfinney/bin/PepHype/PepHype.py | proteome CVS repository, module "PepHype" |
| percolator | Evaluates SEQUEST peptide-spectrum matches to differentiate between true and false positives | Lukas Kall | html documentation | proteome:/home/lukall/bin/percolator | Noble CVS repository, module "?" |
| RelEx | Quantitative analysis software for comparing the relative abundance between an unlabeled and stable-isotope-labeled peptide | Mike MacCoss | ? | ? | proteome CVS repository, module "RelEx" |
| run_ms2 | Parallelizes the analysis of tandem mass spectra using SEQUEST across a beowulf cluster | Rovshan Sadygov, maintained by Greg Finney | html documentation | proteome:/mnt/local/bin/run_ms_ssh | proteome CVS repository, module "run_ms_ssh" |
| snppep | Generates all single base-pair mutation peptide variants from a nucleotide FASTA file | Greg Finney | Usage statement when run with no arguments | proteome:~gfinney/bin/gfscripts/snppep.py | proteome CVS repository, module "gfscripts" |
| spectacle | Creates annotated spectrum figures | Barbara Frewen | html documentation | proteome:/mnt/local/bin/spectacle.pl | Noble CVS repository, module "?" |
| MakeMS2 | Program that uses the Xcaliber XDKs to extract data from the RAW files | Mike MacCoss, additional features Mike Hoopmann | ? | all insrument computers | download from here
proteome CVS repository, module "MakeMS2" |
| Mercury | An isotope distribution predictor | Alan Rockwwod, Steven Van Orden, Mike Hoopmann | ? | ? | ? |