Bumbershoot Software

MS-MS Proteomics Research Tools

 

        I.    Introduction

                     i.        About Bumbershoot Software

                    ii.        About the authors

     II.    Documentation

                     i.        Desktop Interface

a.    BumberDash

                    ii.        Sequence Tagging

a.    DirecTag

b.    TagRecon

c.    DBTagIndexer

                   iii.        Database Searching

a.    DBReverser

b.    MyriMatch

                  iv.        Spectral Library Searching

a.    Pepitome

                   v.        Validating Results

a.    IDPicker

b.    DBValidate

c.    TagValidate

                  vi.        Assessing MS/MS Spectrum Quality

a.    ScanRanker

                 vii.        Assessing LC-MS/MS Run Quality

a.    QuaMeter

 

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 Vanderbilt University Medical Center.  He has worked in the field of proteome informatics since 1996, gaining his Ph.D. in the laboratory of John Yates, III.  His work includes DTASelect, a proteomics data mining tool used by many laboratories, and GutenTag, a system for inferring partial sequences from tandem mass spectra as a way to identify them.

 

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.