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IsoMatchMS

R package for matching and visualizing isotope profiles with trelliscope displays. This package includes support for:

PSpecteR_Logo

  • Intact proteomics

  • Proteoforms (those with known post-translational modifications and unknown mass shifts)

  • Digested proteomics

  • Glycomics (using molecular formula)

  • Adducts of different masses

  • Any biomolecules with a known molecular formula (lipids, metabolites, etc.)

How it works

  1. All MS1 peaks from an MS data file (XML-based or ThermoFisher raw) are summed together. Alternatively, a pre-summed spectra can be used.

  2. The summed spectra is noise filtered, with recommended values provided for top-down proteomics, bottom-up proteomics, and small molecules (glycomics).

  3. Isotope profiles are calculated based the on provided molecular formulas (small molecule identification) or ProForma strings (proteomics). These ProForma strings can include any modifications, either known (e.g. Acetyl, Oxidation), or unknown (e.g. a numeric mass shift).

  4. The isotope profiles are matched to the mass spectra, ranked from high to low quality with Pearson correlation. Results are visualized with an interactive trelliscope display.

To install

devtools::install_github("PNNL-HubMAP-Proteoform-Suite/IsoMatchMS")

To get started, read our vignette

Example displays

Example trelliscope displays can be seen here

If some panels do not load through github.io, try git cloning the example repo, clicking the docs folder, selecting the display you'd like to open, and then clicking the index.html file.

Here is the command to copy the example repo:

git clone https://github.com/PNNL-HubMAP-Proteoform-Suite/IsoMatchMS_Trelliscope_Examples.git

Test function coverage

85.6%