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mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data

Although not yet truly ‘comprehensive’, modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide seq...

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Detalles Bibliográficos
Autores principales: Ficarro, Scott B., Alexander, William M., Marto, Jarrod A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620537/
https://www.ncbi.nlm.nih.gov/pubmed/28763045
http://dx.doi.org/10.3390/proteomes5030020
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author Ficarro, Scott B.
Alexander, William M.
Marto, Jarrod A.
author_facet Ficarro, Scott B.
Alexander, William M.
Marto, Jarrod A.
author_sort Ficarro, Scott B.
collection PubMed
description Although not yet truly ‘comprehensive’, modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed. Here, we introduce mzStudio, an open-source Python module built on our multiplierz project. This desktop application provides a highly-interactive graphical user interface (GUI) through which scientists can examine and annotate spectral features, re-search existing PSMs to test different modifications or new spectral matching algorithms, share results with colleagues, integrate other domain-specific software tools, and finally create publication-quality graphics. mzStudio leverages our common application programming interface (mzAPI) for access to native data files from multiple instrument platforms, including ion trap, quadrupole time-of-flight, Orbitrap, matrix-assisted laser desorption ionization, and triple quadrupole mass spectrometers and is compatible with several popular search engines including Mascot, Proteome Discoverer, X!Tandem, and Comet. The mzStudio toolkit enables researchers to create a digital provenance of data analytics and other evidence that support specific peptide sequence assignments.
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spelling pubmed-56205372017-10-03 mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data Ficarro, Scott B. Alexander, William M. Marto, Jarrod A. Proteomes Article Although not yet truly ‘comprehensive’, modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed. Here, we introduce mzStudio, an open-source Python module built on our multiplierz project. This desktop application provides a highly-interactive graphical user interface (GUI) through which scientists can examine and annotate spectral features, re-search existing PSMs to test different modifications or new spectral matching algorithms, share results with colleagues, integrate other domain-specific software tools, and finally create publication-quality graphics. mzStudio leverages our common application programming interface (mzAPI) for access to native data files from multiple instrument platforms, including ion trap, quadrupole time-of-flight, Orbitrap, matrix-assisted laser desorption ionization, and triple quadrupole mass spectrometers and is compatible with several popular search engines including Mascot, Proteome Discoverer, X!Tandem, and Comet. The mzStudio toolkit enables researchers to create a digital provenance of data analytics and other evidence that support specific peptide sequence assignments. MDPI 2017-08-01 /pmc/articles/PMC5620537/ /pubmed/28763045 http://dx.doi.org/10.3390/proteomes5030020 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ficarro, Scott B.
Alexander, William M.
Marto, Jarrod A.
mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data
title mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data
title_full mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data
title_fullStr mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data
title_full_unstemmed mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data
title_short mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data
title_sort mzstudio: a dynamic digital canvas for user-driven interrogation of mass spectrometry data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620537/
https://www.ncbi.nlm.nih.gov/pubmed/28763045
http://dx.doi.org/10.3390/proteomes5030020
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