xiSPEC

xiSPEC visualizes and annotates mass spectrometry spectra to support analysis of proteomics and cross-linking experiments by reading mzML and mzIdentML files.

Key Features:

• Standard-compliant file formats: Supports mzML and mzIdentML as defined by the Proteomics Standards Initiative (PSI).
• Data input flexibility: Accepts uploaded files and can load datasets from the PRIDE repository in supported formats.
• Advanced visualization: Provides three interconnected views—annotated mass spectrum, peptide sequence fragmentation key, and quality-control error plots of matched fragments—rendered as scalable vector graphics (SVG).
• Re-annotation of spectra: Enables modification and re-annotation of peptide-spectrum matches for hypothesis testing and iterative analysis.
• Export functionality: Exports visualizations as SVG files for incorporation into figures and presentations.

Scientific Applications:

• Proteomics data inspection: Facilitates examination and interpretation of peptide-spectrum matches in standard proteomics datasets.
• Cross-linking mass spectrometry: Supports visualization and analysis of cross-linking experiments and cross-linked peptide identifications.
• Quality control and error analysis: Enables assessment of matched fragment mass errors via QC plots.
• Hypothesis testing and iterative validation: Supports re-annotation workflows for testing identification hypotheses and validating assignments.

Methodology:

Parses mzML and mzIdentML files (PSI standards), loads datasets from uploads or the PRIDE repository, renders spectra and related views as SVG, and permits re-annotation of spectra.