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This documentation is intended to explain how to use the MultiplexMS - Companion tool.

In short, the tool performs three tasks:

(1) Creation of preparation tables and grids, based on a given list of sample names.

(2) Deconvolution of a pooled samples feature table, using the beforehand created grids.

(3) Removing absent and highly abundant features from the deconvoluted feature table.

Windows and MacOS versions can be downloaded from our GitHub repository.

We also provide demo data and a step-by-step instruction that shall help you understand how to use the Companion tool - download the demo data here.

The MultiplexMS study

All code and data that was used to produce plots in the MultiplexMS study are made available on Zenodo. Link to the Zenodo repository ( Mass spectrometric data produced for the study was published on MassIVE. Link to MS dataset (dataset MSV000090912)


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