MS-Dictionary

Download   Publications 
Contact: Sangtae Kim [sak008 (at) ucsd.edu]

Summary

Database search tools identify peptides by matching tandem mass spectra against a protein database. We study an alternative approach when all plausible de novo interpretations of a spectrum (spectral dictionary) are generated and then quickly matched against the database. We present a new MS-Dictionary algorithm for efficiently generating spectral dictionaries and demonstrate that MS-Dictionary can identify spectra that are missed in the database search. We argue that MS-Dictionary enables proteogenomic searches in six-frame translation of genomic sequences that may be prohibitively time-consuming for existing database search approaches. We show that such searches allow one to correct sequencing errors and find programmed frameshifts.


Download

Contact Author.

Publications

Spectral Dictionaries: Integrating De Novo Peptide Sequencing with Database Search of Tandem Mass Spectra.
Sangtae Kim, Nitin Gupta and Pavel Pevzner.
Submitted.

 

Latest Releases

ProteoSAFe

1.2.4

GenoMS

2012.01.10

Inspect, MS-Alignment

2012.01.09

Meta-SPS

2013.04.30

MixDB

2011.12.06

MS-Clustering

2011.03.27

MS-Dictionary

2007.11.30

MS-GappedDictionary

2011.06.15

MS-GeneratingFunction

2010.10.14

MS-GFDB

2012.06.07

MS-GF+

2013.04.10

M-SPLIT

2011.06.05

PepNovo

2012.04.23

Spectral Networks

Sept 2007

UniNovo

2013.03.10

Copyright Notice

 

Media Coverage


Nonribosomal Peptide Dereplication and Sequencing (Scientific American, Genetic Engineering News, Natural Products Industry Insider and Genome Web Daily News)

A powerful tool for PTM discovery (Jan 2008, Journal of Proteome research, Vol 7. Issue 1)

From spectral networks to shotgun sequencing (June 2007, Nature Methods, Vol. 4 No. 6)

Identifying peptides without a database (May 2007, Journal of Proteome Research)

UCSD Computer Scientist Wins Young Investigator Award, Research on Snake Venom Proteins Highlighted (Nov 2006, UCSD)