Literature DB >> 16403790

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data.

Mikko Katajamaa1, Jarkko Miettinen, Matej Oresic.   

Abstract

SUMMARY: New additional methods are presented for processing and visualizing mass spectrometry based molecular profile data, implemented as part of the recently introduced MZmine software. They include new features and extensions such as support for mzXML data format, capability to perform batch processing for large number of files, support for parallel processing, new methods for calculating peak areas using post-alignment peak picking algorithm and implementation of Sammon's mapping and curvilinear distance analysis for data visualization and exploratory analysis. AVAILABILITY: MZmine is available under GNU Public license from http://mzmine.sourceforge.net/.

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Year:  2006        PMID： 16403790     DOI： 10.1093/bioinformatics/btk039

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  210 in total

1.  msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies.

Authors:  Berend Hoekman; Rainer Breitling; Frank Suits; Rainer Bischoff; Peter Horvatovich
Journal:  Mol Cell Proteomics       Date:  2012-02-07       Impact factor: 5.911

2.  Retention time alignment of LC/MS data by a divide-and-conquer algorithm.

Authors:  Zhongqi Zhang
Journal:  J Am Soc Mass Spectrom       Date:  2012-04       Impact factor: 3.109

3.  An efficient data format for mass spectrometry-based proteomics.

Authors:  Anuj R Shah; Jennifer Davidson; Matthew E Monroe; Anoop M Mayampurath; William F Danielson; Yan Shi; Aaron C Robinson; Brian H Clowers; Mikhail E Belov; Gordon A Anderson; Richard D Smith
Journal:  J Am Soc Mass Spectrom       Date:  2010-07-07       Impact factor: 3.109

4.  Global metabolic profiling procedures for urine using UPLC-MS.

Authors:  Elizabeth J Want; Ian D Wilson; Helen Gika; Georgios Theodoridis; Robert S Plumb; John Shockcor; Elaine Holmes; Jeremy K Nicholson
Journal:  Nat Protoc       Date:  2010-06       Impact factor: 13.491

5.  HPLC/APCI-FTICR-MS as a tool for identification of partial polar mutagenic compounds in effect-directed analysis.

Authors:  Mahmoud Bataineh; Urte Lübcke-von Varel; Heiko Hayen; Werner Brack
Journal:  J Am Soc Mass Spectrom       Date:  2010-02-12       Impact factor: 3.109

Review 6.  Characterizing proteins of unknown function: orphan cytochrome p450 enzymes as a paradigm.

Authors:  F Peter Guengerich; Zhongmei Tang; S Giovanna Salamanca-Pinzón; Qian Cheng
Journal:  Mol Interv       Date:  2010-06

7.  PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools.

Authors:  Sean O'Callaghan; David P De Souza; Andrew Isaac; Qiao Wang; Luke Hodkinson; Moshe Olshansky; Tim Erwin; Bill Appelbe; Dedreia L Tull; Ute Roessner; Antony Bacic; Malcolm J McConville; Vladimir A Likić
Journal:  BMC Bioinformatics       Date:  2012-05-30       Impact factor: 3.169

Review 8.  Mass spectrometry-based metabolomics.

Authors:  Katja Dettmer; Pavel A Aronov; Bruce D Hammock
Journal:  Mass Spectrom Rev       Date:  2007 Jan-Feb       Impact factor: 10.946

Review 9.  After the feature presentation: technologies bridging untargeted metabolomics and biology.

Authors:  Kevin Cho; Nathaniel G Mahieu; Stephen L Johnson; Gary J Patti
Journal:  Curr Opin Biotechnol       Date:  2014-05-06       Impact factor: 9.740

Review 10.  Lipidomic analysis of cerebrospinal fluid by mass spectrometry-based methods.

Authors:  Benoit Colsch; Alexandre Seyer; Samia Boudah; Christophe Junot
Journal:  J Inherit Metab Dis       Date:  2014-12-09       Impact factor: 4.982
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