Literature DB >> 18428681

Using BiblioSpec for creating and searching tandem MS peptide libraries.

Barbara Frewen1, Michael J MacCoss.   

Abstract

BiblioSpec is a software package for creating and searching libraries of tandem MS peptide spectra. Library searching provides a quick method for making peptide-spectrum matches by comparing a query spectrum to a collection of reference spectra of known peptide sequence. Pre-assembled libraries for several model organisms can be used as the basis of a search or custom libraries can easily be assembled. The protocols in this unit describe installing BiblioSpec, searching libraries, and creating custom libraries. Copyright 2007 by John Wiley & Sons, Inc.

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Year:  2007        PMID： 18428681     DOI： 10.1002/0471250953.bi1307s20

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  29 in total

1.  MS-viewer: a web-based spectral viewer for proteomics results.

Authors:  Peter R Baker; Robert J Chalkley
Journal:  Mol Cell Proteomics       Date:  2014-03-03       Impact factor: 5.911

2.  Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.

Authors:  Surendra Dasari; Matthew C Chambers; Misti A Martinez; Kristin L Carpenter; Amy-Joan L Ham; Lorenzo J Vega-Montoto; David L Tabb
Journal:  J Proteome Res       Date:  2012-01-27       Impact factor: 4.466

3.  Proteome-wide Interrogation of Small GTPases Regulated by N6-Methyladenosine Modulators.

Authors:  Yen-Yu Yang; Kailin Yu; Lin Li; Ming Huang; Yinsheng Wang
Journal:  Anal Chem       Date:  2020-07-07       Impact factor: 6.986

4.  Spectral Library Searching To Identify Cross-Linked Peptides.

Authors:  Devin K Schweppe; Juan D Chavez; Arti T Navare; Xia Wu; Bianca Ruiz; Jimmy K Eng; Henry Lam; James E Bruce
Journal:  J Proteome Res       Date:  2016-04-28       Impact factor: 4.466

5.  Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.

Authors:  Susan E Abbatiello; Birgit Schilling; D R Mani; Lisa J Zimmerman; Steven C Hall; Brendan MacLean; Matthew Albertolle; Simon Allen; Michael Burgess; Michael P Cusack; Mousumi Gosh; Victoria Hedrick; Jason M Held; H Dorota Inerowicz; Angela Jackson; Hasmik Keshishian; Christopher R Kinsinger; John Lyssand; Lee Makowski; Mehdi Mesri; Henry Rodriguez; Paul Rudnick; Pawel Sadowski; Nell Sedransk; Kent Shaddox; Stephen J Skates; Eric Kuhn; Derek Smith; Jeffery R Whiteaker; Corbin Whitwell; Shucha Zhang; Christoph H Borchers; Susan J Fisher; Bradford W Gibson; Daniel C Liebler; Michael J MacCoss; Thomas A Neubert; Amanda G Paulovich; Fred E Regnier; Paul Tempst; Steven A Carr
Journal:  Mol Cell Proteomics       Date:  2015-02-18       Impact factor: 5.911

6.  A Quantitative Proteome Map of the Human Body.

Authors:  Lihua Jiang; Meng Wang; Shin Lin; Ruiqi Jian; Xiao Li; Joanne Chan; Guanlan Dong; Huaying Fang; Aaron E Robinson; Michael P Snyder
Journal:  Cell       Date:  2020-09-10       Impact factor: 41.582

7.  Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

Authors:  Susan E Abbatiello; D R Mani; Birgit Schilling; Brendan Maclean; Lisa J Zimmerman; Xingdong Feng; Michael P Cusack; Nell Sedransk; Steven C Hall; Terri Addona; Simon Allen; Nathan G Dodder; Mousumi Ghosh; Jason M Held; Victoria Hedrick; H Dorota Inerowicz; Angela Jackson; Hasmik Keshishian; Jong Won Kim; John S Lyssand; C Paige Riley; Paul Rudnick; Pawel Sadowski; Kent Shaddox; Derek Smith; Daniela Tomazela; Asa Wahlander; Sofia Waldemarson; Corbin A Whitwell; Jinsam You; Shucha Zhang; Christopher R Kinsinger; Mehdi Mesri; Henry Rodriguez; Christoph H Borchers; Charles Buck; Susan J Fisher; Bradford W Gibson; Daniel Liebler; Michael Maccoss; Thomas A Neubert; Amanda Paulovich; Fred Regnier; Steven J Skates; Paul Tempst; Mu Wang; Steven A Carr
Journal:  Mol Cell Proteomics       Date:  2013-05-20       Impact factor: 5.911

8.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Authors:  Mingxun Wang; Jeremy J Carver; Vanessa V Phelan; Laura M Sanchez; Neha Garg; Yao Peng; Don Duy Nguyen; Jeramie Watrous; Clifford A Kapono; Tal Luzzatto-Knaan; Carla Porto; Amina Bouslimani; Alexey V Melnik; Michael J Meehan; Wei-Ting Liu; Max Crüsemann; Paul D Boudreau; Eduardo Esquenazi; Mario Sandoval-Calderón; Roland D Kersten; Laura A Pace; Robert A Quinn; Katherine R Duncan; Cheng-Chih Hsu; Dimitrios J Floros; Ronnie G Gavilan; Karin Kleigrewe; Trent Northen; Rachel J Dutton; Delphine Parrot; Erin E Carlson; Bertrand Aigle; Charlotte F Michelsen; Lars Jelsbak; Christian Sohlenkamp; Pavel Pevzner; Anna Edlund; Jeffrey McLean; Jörn Piel; Brian T Murphy; Lena Gerwick; Chih-Chuang Liaw; Yu-Liang Yang; Hans-Ulrich Humpf; Maria Maansson; Robert A Keyzers; Amy C Sims; Andrew R Johnson; Ashley M Sidebottom; Brian E Sedio; Andreas Klitgaard; Charles B Larson; Cristopher A Boya P; Daniel Torres-Mendoza; David J Gonzalez; Denise B Silva; Lucas M Marques; Daniel P Demarque; Egle Pociute; Ellis C O'Neill; Enora Briand; Eric J N Helfrich; Eve A Granatosky; Evgenia Glukhov; Florian Ryffel; Hailey Houson; Hosein Mohimani; Jenan J Kharbush; Yi Zeng; Julia A Vorholt; Kenji L Kurita; Pep Charusanti; Kerry L McPhail; Kristian Fog Nielsen; Lisa Vuong; Maryam Elfeki; Matthew F Traxler; Niclas Engene; Nobuhiro Koyama; Oliver B Vining; Ralph Baric; Ricardo R Silva; Samantha J Mascuch; Sophie Tomasi; Stefan Jenkins; Venkat Macherla; Thomas Hoffman; Vinayak Agarwal; Philip G Williams; Jingqui Dai; Ram Neupane; Joshua Gurr; Andrés M C Rodríguez; Anne Lamsa; Chen Zhang; Kathleen Dorrestein; Brendan M Duggan; Jehad Almaliti; Pierre-Marie Allard; Prasad Phapale; Louis-Felix Nothias; Theodore Alexandrov; Marc Litaudon; Jean-Luc Wolfender; Jennifer E Kyle; Thomas O Metz; Tyler Peryea; Dac-Trung Nguyen; Danielle VanLeer; Paul Shinn; Ajit Jadhav; Rolf Müller; Katrina M Waters; Wenyuan Shi; Xueting Liu; Lixin Zhang; Rob Knight; Paul R Jensen; Bernhard O Palsson; Kit Pogliano; Roger G Linington; Marcelino Gutiérrez; Norberto P Lopes; William H Gerwick; Bradley S Moore; Pieter C Dorrestein; Nuno Bandeira
Journal:  Nat Biotechnol       Date:  2016-08-09       Impact factor: 54.908

9.  Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development.

Authors:  Amol Prakash; Daniela M Tomazela; Barbara Frewen; Brendan Maclean; Gennifer Merrihew; Scott Peterman; Michael J Maccoss
Journal:  J Proteome Res       Date:  2009-06       Impact factor: 4.466

Review 10.  Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies.

Authors:  Can Bruce; Kathryn Stone; Erol Gulcicek; Kenneth Williams
Journal:  Curr Protoc Bioinformatics       Date:  2013-03
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