Literature DB >> 15228367

A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.

Xiao-jun Li1, Patrick G A Pedrioli, Jimmy Eng, Dan Martin, Eugene C Yi, Hookeun Lee, Ruedi Aebersold.   

Abstract

We present a software tool for visualizing data obtained from analyzing complex peptide mixtures by liquid chromatography (LC) electrospray ionization (ESI) mass spectrometry (MS). The data are represented as a two-dimensional density plot. For experiments employing collision-induced dissociation (CID), links are embedded in the image to the CID spectra and the corresponding peptide sequences that are represented by the respective feature. The image provides an intuitive method to evaluate sample quality and the performance of an LC-ESI-MS system and can be used to optimize experimental conditions. Local patterns of the image can also be used to identify chemical contaminants and specific peptide features. Therefore, this software tool may have broad application in MS-based proteomics.

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Year:  2004        PMID： 15228367     DOI： 10.1021/ac035375s

Source DB:  PubMed          Journal:  Anal Chem        ISSN： 0003-2700            Impact factor:   6.986


  19 in total

Review 1.  Advances in proteomics data analysis and display using an accurate mass and time tag approach.

Authors:  Jennifer S D Zimmer; Matthew E Monroe; Wei-Jun Qian; Richard D Smith
Journal:  Mass Spectrom Rev       Date:  2006 May-Jun       Impact factor: 10.946

2.  Chromatographic alignment of LC-MS and LC-MS/MS datasets by genetic algorithm feature extraction.

Authors:  Magnus Palmblad; Davinia J Mills; Laurence V Bindschedler; Rainer Cramer
Journal:  J Am Soc Mass Spectrom       Date:  2007-07-26       Impact factor: 3.109

3.  Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.

Authors:  Nils Gehlenborg; Wei Yan; Inyoul Y Lee; Hyuntae Yoo; Kay Nieselt; Daehee Hwang; Ruedi Aebersold; Leroy Hood
Journal:  Bioinformatics       Date:  2009-01-06       Impact factor: 6.937

Review 4.  Visualization of omics data for systems biology.

Authors:  Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Journal:  Nat Methods       Date:  2010-03       Impact factor: 28.547

5.  A rapid, reproducible, on-the-fly orthogonal array optimization method for targeted protein quantification by LC/MS and its application for accurate and sensitive quantification of carbonyl reductases in human liver.

Authors:  Jin Cao; Vanessa Gonzalez-Covarrubias; Vanessa M Covarrubias; Robert M Straubinger; Hao Wang; Xiaotao Duan; Haoying Yu; Jun Qu; Javier G Blanco
Journal:  Anal Chem       Date:  2010-04-01       Impact factor: 6.986

6.  Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks.

Authors:  Jordy J Hsiao; Brandon H Ng; Melinda M Smits; Harryl D Martinez; Rohini J Jasavala; Izumi V Hinkson; Damian Fermin; Jimmy K Eng; Alexey I Nesvizhskii; Michael E Wright
Journal:  Mol Endocrinol       Date:  2015-07-16

7.  A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome.

Authors:  Xiaotao Duan; Rebeccah Young; Robert M Straubinger; Brian Page; Jin Cao; Hao Wang; Haoying Yu; John M Canty; Jun Qu
Journal:  J Proteome Res       Date:  2009-06       Impact factor: 4.466

8.  Proteomic expression profiling of Haemophilus influenzae grown in pooled human sputum from adults with chronic obstructive pulmonary disease reveal antioxidant and stress responses.

Authors:  Jun Qu; Alan J Lesse; Aimee L Brauer; Jin Cao; Steven R Gill; Timothy F Murphy
Journal:  BMC Microbiol       Date:  2010-06-01       Impact factor: 3.605

9.  'Brukin2D': a 2D visualization and comparison tool for LC-MS data.

Authors:  Dimosthenis Tsagkrasoulis; Panagiotis Zerefos; George Loudos; Antonia Vlahou; Marc Baumann; Sophia Kossida
Journal:  BMC Bioinformatics       Date:  2009-06-16       Impact factor: 3.169

10.  Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

Authors:  Navdeep Jaitly; Anoop Mayampurath; Kyle Littlefield; Joshua N Adkins; Gordon A Anderson; Richard D Smith
Journal:  BMC Bioinformatics       Date:  2009-03-17       Impact factor: 3.169
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