Literature DB >> 23292976

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

Anton A Goloborodko1, Lev I Levitsky, Mark V Ivanov, Mikhail V Gorshkov.   

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.

Mesh：

Year:  2013        PMID： 23292976     DOI： 10.1007/s13361-012-0516-6

Source DB:  PubMed          Journal:  J Am Soc Mass Spectrom        ISSN： 1044-0305            Impact factor:   3.109


  15 in total

1.  pymzML--Python module for high-throughput bioinformatics on mass spectrometry data.

Authors:  Till Bald; Johannes Barth; Anna Niehues; Michael Specht; Michael Hippler; Christian Fufezan
Journal:  Bioinformatics       Date:  2012-02-02       Impact factor: 6.937

2.  mzIdentML: an open community-built standard format for the results of proteomics spectrum identification algorithms.

Authors:  Martin Eisenacher
Journal:  Methods Mol Biol       Date:  2011

3.  TOPP--the OpenMS proteomics pipeline.

Authors:  Oliver Kohlbacher; Knut Reinert; Clemens Gröpl; Eva Lange; Nico Pfeifer; Ole Schulz-Trieglaff; Marc Sturm
Journal:  Bioinformatics       Date:  2007-01-15       Impact factor: 6.937

4.  Empirical approach to false discovery rate estimation in shotgun proteomics.

Authors:  Anton A Goloborodko; Corina Mayerhofer; Alexander R Zubarev; Irina A Tarasova; Alexander V Gorshkov; Roman A Zubarev; Mikhail V Gorshkov
Journal:  Rapid Commun Mass Spectrom       Date:  2010-02       Impact factor: 2.419

5.  Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

Authors:  Michael Specht; Sebastian Kuhlgert; Christian Fufezan; Michael Hippler
Journal:  Bioinformatics       Date:  2011-02-16       Impact factor: 6.937

6.  Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition.

Authors:  J L Meek
Journal:  Proc Natl Acad Sci U S A       Date:  1980-03       Impact factor: 11.205

7.  mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data.

Authors:  Martin Strohalm; Daniel Kavan; Petr Novák; Michael Volný; Vladimír Havlícek
Journal:  Anal Chem       Date:  2010-06-01       Impact factor: 6.986

8.  Liquid chromatography at critical conditions: comprehensive approach to sequence-dependent retention time prediction.

Authors:  Alexander V Gorshkov; Irina A Tarasova; Victor V Evreinov; Mikhail M Savitski; Michael L Nielsen; Roman A Zubarev; Mikhail V Gorshkov
Journal:  Anal Chem       Date:  2006-11-15       Impact factor: 6.986

9.  Software platform for rapidly creating computational tools for mass spectrometry-based proteomics.

Authors:  Damon May; Wendy Law; Matt Fitzgibbon; Qiaojun Fang; Martin McIntosh
Journal:  J Proteome Res       Date:  2009-06       Impact factor: 4.466

10.  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
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  41 in total

1.  UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra.

Authors:  Jake Rosenberg; W Ryan Parker; Michael B Cammarata; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2018-04-06       Impact factor: 3.109

2.  2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample.

Authors:  Lindsay Pino; Andy Lin; Wout Bittremieux
Journal:  J Proteome Res       Date:  2019-10-07       Impact factor: 4.466

3.  psims - A Declarative Writer for mzML and mzIdentML for Python.

Authors:  Joshua Klein; Joseph Zaia
Journal:  Mol Cell Proteomics       Date:  2018-12-18       Impact factor: 5.911

4.  Adaptation of Decoy Fusion Strategy for Existing Multi-Stage Search Workflows.

Authors:  Mark V Ivanov; Lev I Levitsky; Mikhail V Gorshkov
Journal:  J Am Soc Mass Spectrom       Date:  2016-06-27       Impact factor: 3.109

5.  Brute-Force Approach for Mass Spectrometry-Based Variant Peptide Identification in Proteogenomics without Personalized Genomic Data.

Authors:  Mark V Ivanov; Anna A Lobas; Lev I Levitsky; Sergei A Moshkovskii; Mikhail V Gorshkov
Journal:  J Am Soc Mass Spectrom       Date:  2018-01-03       Impact factor: 3.109

6.  Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification.

Authors:  Pieter Moris; Joey De Pauw; Anna Postovskaya; Sofie Gielis; Nicolas De Neuter; Wout Bittremieux; Benson Ogunjimi; Kris Laukens; Pieter Meysman
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

7.  The Late S-Phase Transcription Factor Hcm1 Is Regulated through Phosphorylation by the Cell Wall Integrity Checkpoint.

Authors:  Takahiro Negishi; Jiri Veis; David Hollenstein; Mizuho Sekiya; Gustav Ammerer; Yoshikazu Ohya
Journal:  Mol Cell Biol       Date:  2016-01-04       Impact factor: 4.272

Review 8.  Algorithms and design strategies towards automated glycoproteomics analysis.

Authors:  Han Hu; Kshitij Khatri; Joseph Zaia
Journal:  Mass Spectrom Rev       Date:  2016-01-04       Impact factor: 10.946

9.  Advanced Precursor Ion Selection Algorithms for Increased Depth of Bottom-Up Proteomic Profiling.

Authors:  Simion Kreimer; Mikhail E Belov; William F Danielson; Lev I Levitsky; Mikhail V Gorshkov; Barry L Karger; Alexander R Ivanov
Journal:  J Proteome Res       Date:  2016-09-07       Impact factor: 4.466

10.  Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy.

Authors:  Julia A Bubis; Daria S Spasskaya; Vladimir A Gorshkov; Frank Kjeldsen; Aleksandra M Kofanova; Dmitry S Lekanov; Mikhail V Gorshkov; Vadim L Karpov; Irina A Tarasova; Dmitry S Karpov
Journal:  Appl Microbiol Biotechnol       Date:  2020-03-10       Impact factor: 4.813
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