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Proteomes 2017, 5(3), 20; doi:10.3390/proteomes5030020

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

1
Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115, USA
2
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
3
Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
4
Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
*
Author to whom correspondence should be addressed.
Received: 7 April 2017 / Revised: 14 July 2017 / Accepted: 27 July 2017 / Published: 1 August 2017
(This article belongs to the Special Issue Computational Proteomics)
View Full-Text   |   Download PDF [7608 KB, uploaded 1 August 2017]   |  

Abstract

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. View Full-Text
Keywords: bioinformatics software; mass spectrometry; quantification; results distribution; API; application programming interface; SQLite bioinformatics software; mass spectrometry; quantification; results distribution; API; application programming interface; SQLite
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Ficarro, S.B.; Alexander, W.M.; Marto, J.A. mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data. Proteomes 2017, 5, 20.

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