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.
Highlights
Adaptation of false-discovery statistics and peptide-to-protein parsimony rules enable straightforward compilation of large-scale mass spectrometry experiments to a simple list of peptides, proteins, and associated quantification values
Results mzStudio was developed in our lab to provide a centralized framework to interactively visualize, annotate, and integrate sequence assignment and other features of mass spectrometry data across instrument manufacturers, platforms, and search engines (Figure 1)
Consistent with our design philosophy for our broader multiplierz project, mzStudio provides direct access to native mass spectrometry data files without the need for conversion to auxiliary file formats; all supported vendors and instrument platforms are listed in Supplementary Table S1
Summary
Adaptation of false-discovery statistics and peptide-to-protein parsimony rules enable straightforward compilation of large-scale mass spectrometry experiments to a simple list of peptides, proteins, and associated quantification values. While some details will continue to evolve, the field has undoubtedly reached a point where the expression of a large number of proteins can be confidently measured in many biological systems based on assignment of unmodified tryptic peptide sequences and their parsimonious mapping to protein groups or other identifiers This approach provides a global view of the proteome and can reveal how constituent components may respond to biological perturbation. These effects can be visualized with simple heat-map graphics, and the underlying lists of quantified proteins can be distributed in standard spreadsheet files. Interrogating mass spectrometry data at this level of functional resolution requires a dynamic and interactive visualization framework on which researchers can experiment with novel hypotheses for peptide sequences and associated modifications
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