Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mas...

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Published in:Journal of the American Society for Mass Spectrometry Vol. 24; no. 2; pp. 301 - 304
Main Authors: Goloborodko, Anton A., Levitsky, Lev I., Ivanov, Mark V., Gorshkov, Mikhail V.
Format: Journal Article
Language:English
Published: New York Springer-Verlag 01.02.2013
Springer Nature B.V
Subjects:
Analytical Chemistry
Application Note
Bioinformatics
Biotechnology
Chemistry
Chemistry and Materials Science
Chromatography, Liquid
Data analysis
Data Mining - methods
Databases, Protein
Documentation
Electrochemical analysis
Internet
Libraries
Mass spectrometry
Organic Chemistry
Packages
Polypeptides
Proteomics
Proteomics - methods
Prototyping
Python
Reproducibility of Results
Software
Source code
Tandem Mass Spectrometry
Data processing
Bioinformatics
Proteomics
ISSN:1044-0305, 1879-1123, 1879-1123
Online Access:Get full text
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Abstract Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics , the source code repository at http://hg.theorchromo.ru/pyteomics , documentation at http://packages.python.org/pyteomics . Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/ . Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com
AbstractList Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.
Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.
Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com [Figure not available: see fulltext.]
Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics , the source code repository at http://hg.theorchromo.ru/pyteomics , documentation at http://packages.python.org/pyteomics . Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/ . Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com
Author Levitsky, Lev I.
Ivanov, Mark V.
Goloborodko, Anton A.
Gorshkov, Mikhail V.
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  surname: Goloborodko
  fullname: Goloborodko, Anton A.
  organization: Department of Physics, Massachusetts Institute of Technology, Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow Institute of Physics and Technology (State University)
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  givenname: Lev I.
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  fullname: Levitsky, Lev I.
  organization: Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow Institute of Physics and Technology (State University)
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  givenname: Mark V.
  surname: Ivanov
  fullname: Ivanov, Mark V.
  organization: Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow Institute of Physics and Technology (State University)
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  givenname: Mikhail V.
  surname: Gorshkov
  fullname: Gorshkov, Mikhail V.
  email: gorshkov@chph.ras.ru
  organization: Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow Institute of Physics and Technology (State University)
BackLink https://www.ncbi.nlm.nih.gov/pubmed/23292976$$D View this record in MEDLINE/PubMed
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Snippet Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data,...
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SubjectTerms Analytical Chemistry
Application Note
Bioinformatics
Biotechnology
Chemistry
Chemistry and Materials Science
Chromatography, Liquid
Data analysis
Data Mining - methods
Databases, Protein
Documentation
Electrochemical analysis
Internet
Libraries
Mass spectrometry
Organic Chemistry
Packages
Polypeptides
Proteomics
Proteomics - methods
Prototyping
Python
Reproducibility of Results
Software
Source code
Tandem Mass Spectrometry
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