MS/MS Software Solutions

Solutions overview

Proteome Software offers a variety of proteomics, metabolomics, and small molecule mass spectrometry software solutions for handling large-scale, data-rich biological identification or quantitative experiments. We innovate on the leading edge of MS/MS analytics, and our software tools are used in hundreds of laboratories and universities around the world.

Please use the buttons above to browse our mass spectrometry software solutions. Contact us for a free evaluation of any of our products, or to learn more about our scientific software solutions.

Workflow Integration

  • Proteome Software builds major search engine compatibility directly into our programs, including the ability to combine results from different search engines. See our File Compatibility Matrix for a detailed, updated list of compatible file formats.
  • Create and execute custom SQL queries for drilling down into your data.
  • Many of our programs are cross-compatible. Our Scaffold Software Suite employs a sophisticated analysis pipeline, enabling comprehensive data exploration.

Venn Diagrams

Kernel Density Charts


  • Our programs offer many types of quantitation, including label-free for proteomics, metabolomics, as well as iTRAQ, TMT, and SILAC data analysis.
  • Examine differential expression levels using multiple metrics, including spectral counting, precursor intensity, and TIC.
  • Perform advanced quantitation in Scaffold Q+ and Scaffold Q+S with intensity weighting, error estimation, and parametric and non-parametric statistics.
  • View protein and peptide changes in time-course experiments.

Statistical Analysis

Fold Change Significance

Annotated Spectra

Data Validation

  • You can set custom thresholds for your results in order to return optimal confidence, including a range of simple and advanced filtering options.
  • In Scaffold, combine data from multiple search engines and search with X! Tandem (bundled with Scaffold) to broaden and refine your findings.
  • In proteomics, use Scaffold for graphical representations that include Venn diagrams, mass spectra, protein sequences, and fragmentation tables that help you dial into important information.
  • In metabolomics, use Scaffold Elements to validate identifications by examining matches to MS/MS spectra and expected isotopic distributions.

Biological Insight

  • Scaffold includes color-coded and organized GO Term Annotations via any number of GOA databases. You can also define custom gene ontologies and compare GO expression across sample categories with interactive pie and bar charts.
  • Scaffold Elements provides hyperlinks to metabolite reference information such as PubChem, ChemSpider and KEGG.
  • Customize your view to help highlight items of interest by starring, marking, sorting and filtering.

Gene Ontology

Experimental Details

Publish and Share

  • Proteome Software offers Free Viewers for all of our products. This makes sharing your data with anyone simple, even if they do not own any of our software.
  • Publish detailed analysis and search parameters accurately every time.
  • Export any graph, table, or visual into a variety of formats in just a few clicks.

Post-Translational Modifications

  • With Scaffold PTM, you can explore your proteins’ modification sites with the robust site localization probability algorithm, Ascore.
  • Find the motifs that your data exhibit, or define motifs that you suspect exist because of outside implications.
  • Quantify the modifications either by spectral counting or more advanced quantitative methods, if quantitative data has been loaded.

Residues with PTMs

Elements Heat Map

Small Molecule MS (Metabolomics, Lipidomics)

  • Confidently identify analytes using multidimensional search and scoring algorithms with Scaffold Elements.
  • Designate biological and technical replicates for proper statistical interpretation.
  • Discover meaningful trends in your data with hierarchical clustering, heatmaps and quantitative statistics.