Literature DB >> 11780965

Matching peptide mass spectra to EST and genomic DNA databases.

J S Choudhary1, W P Blackstock, D M Creasy, J S Cottrell.   

Abstract

The use of mass spectrometry data to search molecular sequence databases is a well-established method for protein identification. The technique can be extended to searching raw genomic sequences, providing experimental confirmation or correction of predicted coding sequences, and has the potential to identify novel genes and elucidate splicing patterns.

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Year:  2001        PMID： 11780965     DOI： 10.1016/S0167-7799(01)01795-4

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN： 0167-7799            Impact factor:   19.536


  13 in total

1.  Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry.

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2.  Identification of single amino acid polymorphisms in MS/MS spectra of peptides.

Authors:  A L Chernobrovkin; V A Mitkevich; I A Popov; M I Indeikina; E V Ilgisonis; A V Lisitsa; A I Archakov
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3.  A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry.

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Journal:  Genome Res       Date:  2011-07-27       Impact factor: 9.043

4.  A ranking-based scoring function for peptide-spectrum matches.

Authors:  Ari M Frank
Journal:  J Proteome Res       Date:  2009-05       Impact factor: 4.466

5.  Mapping the proteome of barrel medic (Medicago truncatula).

Authors:  Bonnie S Watson; Victor S Asirvatham; Liangjiang Wang; Lloyd W Sumner
Journal:  Plant Physiol       Date:  2003-03       Impact factor: 8.340

6.  An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome.

Authors:  Danny A Bitton; Duncan L Smith; Yvonne Connolly; Paul J Scutt; Crispin J Miller
Journal:  PLoS One       Date:  2010-01-28       Impact factor: 3.240

7.  Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

Authors:  Markus Brosch; Gary I Saunders; Adam Frankish; Mark O Collins; Lu Yu; James Wright; Ruth Verstraten; David J Adams; Jennifer Harrow; Jyoti S Choudhary; Tim Hubbard
Journal:  Genome Res       Date:  2011-04-01       Impact factor: 9.043

8.  Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.

Authors:  Ari M Frank; Matthew E Monroe; Anuj R Shah; Jeremy J Carver; Nuno Bandeira; Ronald J Moore; Gordon A Anderson; Richard D Smith; Pavel A Pevzner
Journal:  Nat Methods       Date:  2011-05-15       Impact factor: 28.547

9.  The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features.

Authors:  Mohamed Helmy; Naoyuki Sugiyama; Masaru Tomita; Yasushi Ishihama
Journal:  Front Plant Sci       Date:  2012-04-02       Impact factor: 5.753

10.  Generation of a predicted protein database from EST data and application to iTRAQ analyses in grape (Vitis vinifera cv. Cabernet Sauvignon) berries at ripening initiation.

Authors:  Joost Lücker; Mario Laszczak; Derek Smith; Steven T Lund
Journal:  BMC Genomics       Date:  2009-01-26       Impact factor: 3.969
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