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. 2018 Jul 2;46(W1):W473-W478.
doi: 10.1093/nar/gky353.

xiSPEC: Web-Based Visualization, Analysis and Sharing of Proteomics Data

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Free PMC article

xiSPEC: Web-Based Visualization, Analysis and Sharing of Proteomics Data

Lars Kolbowski et al. Nucleic Acids Res. .
Free PMC article

Abstract

We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments. Highlighting or selecting data points in any view is represented in all other views. Views are interactive scalable vector graphic elements, which can be exported, e.g. for use in publication. xiSPEC allows for re-annotation of spectra for easy hypothesis testing by modifying input data. xiSPEC is freely accessible at http://spectrumviewer.org and the source code is openly available on https://github.com/Rappsilber-Laboratory/xiSPEC.

Figures

Figure 1.
Figure 1.
Overview of xiSPEC workflow. The input for xiSPEC are peak list data and peptide identifications. The user can either upload files directly to the xiSPEC server or select them from the PRIDE repository by providing the PXD accession number. For single spectra analysis data can be provided via HTML form input. Users can save datasets (publicly or password protected) and share them using a unique URL. Results can be exported as SVG for use in publications and presentations.
Figure 2.
Figure 2.
SVG output of xiSPEC’s views for a cross-linked peptide example. (A) Peptide sequence with fragmentation key. Amino acid residues in one-letter code. Lines show matched peptide fragments. Grayed-out residues are not included in currently selected fragment. (B) Annotated mass spectrum. Matched peaks are colored and labeled (though labels of neutral-loss fragments are hidden in this example). (C) and (D) show spectra QC plots. Each point represents a matched peak of the mass spectrum. (C) Fragment match error over peak intensity. (D) Match error over m/z. Coloring (red and blue) is used to differentiate between the two peptides. Neutral-loss fragments are displayed in a lighter color. Yellow highlight is the currently selected fragment (interconnected between all views).
Figure 3.
Figure 3.
xiSPEC feature examples. (A) Settings view. Peptide input data can be modified in the displayed tab. Appearance customization can be done through the ‘appearance’ tab. (B) Changing PSM modification positions. (C) Use of measuring tool in zoomed-in excerpt of spectrum. Measure distance between peaks with automatic calculation and amino-acid residue matching for multiple charge states. (D) Changing cross-linker position.

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