Literature DB >> 18806791

Building consensus spectral libraries for peptide identification in proteomics.

Henry Lam1, Eric W Deutsch, James S Eddes, Jimmy K Eng, Stephen E Stein, Ruedi Aebersold.   

Abstract

Spectral searching has drawn increasing interest as an alternative to sequence-database searching in proteomics. We developed and validated an open-source software toolkit, SpectraST, to enable proteomics researchers to build spectral libraries and to integrate this promising approach in their data-analysis pipeline. It allows individual researchers to condense raw data into spectral libraries, summarizing information about observed proteomes into a concise and retrievable format for future data analyses.

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Year:  2008        PMID： 18806791      PMCID： PMC2637392          DOI： 10.1038/nmeth.1254

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  28 in total

1.  Data analysis--the Achilles heel of proteomics.

Authors:  Scott D Patterson
Journal:  Nat Biotechnol       Date:  2003-03       Impact factor: 54.908

2.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

Review 3.  The ABC's (and XYZ's) of peptide sequencing.

Authors:  Hanno Steen; Matthias Mann
Journal:  Nat Rev Mol Cell Biol       Date:  2004-09       Impact factor: 94.444

Review 4.  Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.

Authors:  Rovshan G Sadygov; Daniel Cociorva; John R Yates
Journal:  Nat Methods       Date:  2004-12       Impact factor: 28.547

5.  Using annotated peptide mass spectrum libraries for protein identification.

Authors:  R Craig; J C Cortens; D Fenyo; R C Beavis
Journal:  J Proteome Res       Date:  2006-08       Impact factor: 4.466

6.  Development and validation of a spectral library searching method for peptide identification from MS/MS.

Authors:  Henry Lam; Eric W Deutsch; James S Eddes; Jimmy K Eng; Nichole King; Stephen E Stein; Ruedi Aebersold
Journal:  Proteomics       Date:  2007-03       Impact factor: 3.984

7.  Optimization and testing of mass spectral library search algorithms for compound identification.

Authors:  S E Stein; D R Scott
Journal:  J Am Soc Mass Spectrom       Date:  1994-09       Impact factor: 3.109

8.  Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach.

Authors:  Wei-Jun Qian; Matthew E Monroe; Tao Liu; Jon M Jacobs; Gordon A Anderson; Yufeng Shen; Ronald J Moore; David J Anderson; Rui Zhang; Steve E Calvano; Stephen F Lowry; Wenzhong Xiao; Lyle L Moldawer; Ronald W Davis; Ronald G Tompkins; David G Camp; Richard D Smith
Journal:  Mol Cell Proteomics       Date:  2005-03-07       Impact factor: 5.911

9.  The critical evaluation of a comprehensive mass spectral library.

Authors:  P Ausloos; C L Clifton; S G Lias; A I Mikaya; S E Stein; D V Tchekhovskoi; O D Sparkman; V Zaikin; D Zhu
Journal:  J Am Soc Mass Spectrom       Date:  1999-04       Impact factor: 3.262

10.  Methods for peptide identification by spectral comparison.

Authors:  Jian Liu; Alexander W Bell; John J M Bergeron; Corey M Yanofsky; Brian Carrillo; Christian E H Beaudrie; Robert E Kearney
Journal:  Proteome Sci       Date:  2007-01-16       Impact factor: 2.480
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  102 in total

1.  Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets.

Authors:  Kang Ning; Damian Fermin; Alexey I Nesvizhskii
Journal:  Proteomics       Date:  2010-07       Impact factor: 3.984

2.  Formation of y + 10 and y + 11 ions in the collision-induced dissociation of peptide ions.

Authors:  Lisa E Kilpatrick; Pedatsur Neta; Xiaoyu Yang; Yamil Simón-Manso; Yuxue Liang; Stephen E Stein
Journal:  J Am Soc Mass Spectrom       Date:  2011-12-08       Impact factor: 3.109

3.  Proteomic analysis of the androgen receptor via MS-compatible purification of biotinylated protein on streptavidin resin.

Authors:  Ryan J Austin; Heidi M Smidansky; Carly A Holstein; Deborah K Chang; Angela Epp; Neil C Josephson; Daniel B Martin
Journal:  Proteomics       Date:  2011-12-12       Impact factor: 3.984

Review 4.  Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions.

Authors:  Paola Picotti; Ruedi Aebersold
Journal:  Nat Methods       Date:  2012-05-30       Impact factor: 28.547

5.  Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides.

Authors:  Andrew Keller; Samuel L Bader; Ulrike Kusebauch; David Shteynberg; Leroy Hood; Robert L Moritz
Journal:  Mol Cell Proteomics       Date:  2015-12-24       Impact factor: 5.911

6.  Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification.

Authors:  Nathan P Manes; Jessica M Mann; Aleksandra Nita-Lazar
Journal:  J Vis Exp       Date:  2015-08-17       Impact factor: 1.355

7.  Library dependent LC-MS/MS acquisition via mzAPI/Live.

Authors:  James T Webber; Manor Askenazi; Scott B Ficarro; Max A Iglehart; Jarrod A Marto
Journal:  Proteomics       Date:  2013-05       Impact factor: 3.984

8.  Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.

Authors:  Eric W Deutsch; David Shteynberg; Henry Lam; Zhi Sun; Jimmy K Eng; Christine Carapito; Priska D von Haller; Natalie Tasman; Luis Mendoza; Terry Farrah; Ruedi Aebersold
Journal:  Proteomics       Date:  2010-03       Impact factor: 3.984

9.  Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers.

Authors:  Carly A Sherwood; Ashley Eastham; Lik Wee Lee; Jenni Risler; Olga Vitek; Daniel B Martin
Journal:  J Proteome Res       Date:  2009-09       Impact factor: 4.466

10.  MaRiMba: a software application for spectral library-based MRM transition list assembly.

Authors:  Carly A Sherwood; Ashley Eastham; Lik Wee Lee; Amelia Peterson; Jimmy K Eng; David Shteynberg; Luis Mendoza; Eric W Deutsch; Jenni Risler; Natalie Tasman; Ruedi Aebersold; Henry Lam; Daniel B Martin
Journal:  J Proteome Res       Date:  2009-10       Impact factor: 4.466
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