MS-MS Proteomics Research Tools
i. About Bumbershoot Software
ii. About the authors
i. Desktop Interface
ii. Sequence Tagging
iii. Database Searching
iv. Spectral Library Searching
v. Validating Results
vi. Assessing MS/MS Spectrum Quality
vii. Assessing LC-MS/MS Run Quality
Bumbershoot is a collection of tools created in the Tabb laboratory at the Vanderbilt University Mass Spectrometry Research Center. The identification of peptides can be carried out by many available algorithms including Sequest, Mascot, X!Tandem, and many others. The “MyriMatch” software is designed to conduct this operation on multi-core processors and clusters of computers with high accuracy and throughput. Identification of peptides, however, is not the only step in proteome informatics. Separation of correct identifications from those that are falsely identified is also a challenging problem that we have opted to resolve through the use of reversed database searching. We provide the dbReverser tool to create sequence databases that include each protein in both normal and reversed orientations. The IDPicker tool that evaluates the identifications produced through such databases to find thresholds that produce confident identifications with a user-specified false positive rate. We offer these tools publicly with source code in the hopes that others will find them useful in their present forms and add features from which others can benefit.
David Tabb is an assistant professor in the
Departments of Biomedical Informatics and Biochemistry at
Matthew Chambers is a programmer / analyst in the Tabb laboratory. He achieved a BS degree in Computer Science from Rensselaer Polytechnic Institute, focusing on the development of efficient algorithms for video game design. Matthew joined the Tabb group in 2005.