Treffer: jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

Title:
jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats
Authors:
GRISS, Johannes, REISINGER, Florian, HERMJAKOB, Henning, ANTONIO VIZCAINO, Juan
Source:
Proteomics (Weinheim. Print). 12(6):795-798
Publisher Information:
Weinheim: Wiley-VCH, 2012.
Publication Year:
2012
Physical Description:
print, 16 ref
Original Material:
INIST-CNRS
Subject Terms:
Biochemistry, molecular biology, biophysics, Biochimie, biologie moléculaire, biophysique, Sciences biologiques et medicales, Biological and medical sciences, Sciences biologiques fondamentales et appliquees. Psychologie, Fundamental and applied biological sciences. Psychology, Biochimie analytique, structurale et metabolique, Analytical, structural and metabolic biochemistry, Protéines, Proteins, Divers, Miscellaneous, Etalon, Standard, Marco, Norme, Standards, Norma, Protéomique, Proteomics, Proteómica, Spectrométrie masse, Mass spectrometry, Espectrometría masa, Bioinformatics, Data standard, Java, MS data processing, Proteomics standards initiative
Document Type:
Fachzeitschrift Article
File Description:
text
Language:
English
Author Affiliations:
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
Department of Medicine I, Medical University of Vienna, Vienna, Austria
ISSN:
1615-9853
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=25778990
Rights:
Copyright 2015 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Analytical, structural and metabolic biochemistry
Accession Number:
edscal.25778990
Database:
PASCAL Archive

Weitere Informationen

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/.