Literature DB >> 24939128

Employing ProteoWizard to Convert Raw Mass Spectrometry Data.

Jerry D Holman1, David L Tabb, Parag Mallick.   

Abstract

After raw data have been captured by mass spectrometers in biological LC-MS/MS experiments, they must be converted from vendor-specific binary files to open-format files for manipulation by most software. This protocol details the use of ProteoWizard software for this conversion, taking format features, coding options, and vendor particularities into account. This protocol will aid researchers in preparing their data for analysis by database search engines and other bioinformatics tools.
Copyright © 2014 John Wiley & Sons, Inc.

Entities:  

Keywords:  LC-MS/MS; database search; mzML; proteomics; raw files

Mesh：

Year:  2014        PMID： 24939128      PMCID： PMC4113728          DOI： 10.1002/0471250953.bi1324s46

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


  7 in total

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Authors:  Mathias Wilhelm; Marc Kirchner; Judith A J Steen; Hanno Steen
Journal:  Mol Cell Proteomics       Date:  2011-09-29       Impact factor: 5.911

2.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

Authors:  J K Eng; A L McCormack; J R Yates
Journal:  J Am Soc Mass Spectrom       Date:  1994-11       Impact factor: 3.109

3.  Comet: an open-source MS/MS sequence database search tool.

Authors:  Jimmy K Eng; Tahmina A Jahan; Michael R Hoopmann
Journal:  Proteomics       Date:  2012-12-04       Impact factor: 3.984

4.  ProteoWizard: open source software for rapid proteomics tools development.

Authors:  Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick
Journal:  Bioinformatics       Date:  2008-07-07       Impact factor: 6.937

5.  A cross-platform toolkit for mass spectrometry and proteomics.

Authors:  Matthew C Chambers; Brendan Maclean; Robert Burke; Dario Amodei; Daniel L Ruderman; Steffen Neumann; Laurent Gatto; Bernd Fischer; Brian Pratt; Jarrett Egertson; Katherine Hoff; Darren Kessner; Natalie Tasman; Nicholas Shulman; Barbara Frewen; Tahmina A Baker; Mi-Youn Brusniak; Christopher Paulse; David Creasy; Lisa Flashner; Kian Kani; Chris Moulding; Sean L Seymour; Lydia M Nuwaysir; Brent Lefebvre; Frank Kuhlmann; Joe Roark; Paape Rainer; Suckau Detlev; Tina Hemenway; Andreas Huhmer; James Langridge; Brian Connolly; Trey Chadick; Krisztina Holly; Josh Eckels; Eric W Deutsch; Robert L Moritz; Jonathan E Katz; David B Agus; Michael MacCoss; David L Tabb; Parag Mallick
Journal:  Nat Biotechnol       Date:  2012-10       Impact factor: 54.908

6.  mzML--a community standard for mass spectrometry data.

Authors:  Lennart Martens; Matthew Chambers; Marc Sturm; Darren Kessner; Fredrik Levander; Jim Shofstahl; Wilfred H Tang; Andreas Römpp; Steffen Neumann; Angel D Pizarro; Luisa Montecchi-Palazzi; Natalie Tasman; Mike Coleman; Florian Reisinger; Puneet Souda; Henning Hermjakob; Pierre-Alain Binz; Eric W Deutsch
Journal:  Mol Cell Proteomics       Date:  2010-08-17       Impact factor: 5.911

7.  A common open representation of mass spectrometry data and its application to proteomics research.

Authors:  Patrick G A Pedrioli; Jimmy K Eng; Robert Hubley; Mathijs Vogelzang; Eric W Deutsch; Brian Raught; Brian Pratt; Erik Nilsson; Ruth H Angeletti; Rolf Apweiler; Kei Cheung; Catherine E Costello; Henning Hermjakob; Sequin Huang; Randall K Julian; Eugene Kapp; Mark E McComb; Stephen G Oliver; Gilbert Omenn; Norman W Paton; Richard Simpson; Richard Smith; Chris F Taylor; Weimin Zhu; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2004-11       Impact factor: 54.908
  7 in total
  78 in total

1.  The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.

Authors:  Keiryn L Bennett; Xia Wang; Cory E Bystrom; Matthew C Chambers; Tracy M Andacht; Larry J Dangott; Félix Elortza; John Leszyk; Henrik Molina; Robert L Moritz; Brett S Phinney; J Will Thompson; Maureen K Bunger; David L Tabb
Journal:  Mol Cell Proteomics       Date:  2015-10-04       Impact factor: 5.911

2.  StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline.

Authors:  Michael R Hoopmann; Jason M Winget; Luis Mendoza; Robert L Moritz
Journal:  J Proteome Res       Date:  2018-02-14       Impact factor: 4.466

3.  Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.

Authors:  Chih-Chiang Tsou; Chia-Feng Tsai; Guo Ci Teo; Yu-Ju Chen; Alexey I Nesvizhskii
Journal:  Proteomics       Date:  2016-07-22       Impact factor: 3.984

4.  N-linked glycosite profiling and use of Skyline as a platform for characterization and relative quantification of glycans in differentiating xylem of Populus trichocarpa.

Authors:  Philip L Loziuk; Elizabeth S Hecht; David C Muddiman
Journal:  Anal Bioanal Chem       Date:  2016-08-04       Impact factor: 4.142

5.  High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio.

Authors:  Vladimir Sarpe; Atefeh Rafiei; Morgan Hepburn; Nicholas Ostan; Anthony B Schryvers; David C Schriemer
Journal:  Mol Cell Proteomics       Date:  2016-07-13       Impact factor: 5.911

6.  Comparison of global metabolite extraction strategies for soybeans using UHPLC-HRMS.

Authors:  Iqbal Mahmud; Sandi Sternberg; Michael Williams; Timothy J Garrett
Journal:  Anal Bioanal Chem       Date:  2017-08-26       Impact factor: 4.142

7.  Proteometabolomics of Melphalan Resistance in Multiple Myeloma.

Authors:  David C Koomen; Joy D Guingab-Cagmat; Paula S Oliveira; Bin Fang; Min Liu; Eric A Welsh; Mark B Meads; Tuan Nguyen; Laurel Meke; Steven A Eschrich; Kenneth H Shain; Timothy J Garrett; John M Koomen
Journal:  Methods Mol Biol       Date:  2019

8.  Chemoproteomic Profiling Uncovers CDK4-Mediated Phosphorylation of the Translational Suppressor 4E-BP1.

Authors:  Dylan C Mitchell; Arya Menon; Amanda L Garner
Journal:  Cell Chem Biol       Date:  2019-05-02       Impact factor: 8.116

9.  Unusual and Highly Bioactive Sesterterpenes Synthesized by Pleurotus ostreatus during Coculture with Trametes robiniophila Murr.

Authors:  Xiao-Ting Shen; Xu-Hua Mo; Li-Ping Zhu; Ling-Ling Tan; Feng-Yu Du; Qian-Wen Wang; Yuan-Ming Zhou; Xiao-Jie Yuan; Bin Qiao; Song Yang
Journal:  Appl Environ Microbiol       Date:  2019-07-01       Impact factor: 4.792

10.  Methods and Challenges for Computational Data Analysis for DNA Adductomics.

Authors:  Scott J Walmsley; Jingshu Guo; Jinhua Wang; Peter W Villalta; Robert J Turesky
Journal:  Chem Res Toxicol       Date:  2019-11-06       Impact factor: 3.739
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