Quantification

The platform provides label-free and isobaric TMT quantifications.

Label-free quantification (LFQ)

To run LFQ, select 'Enable LFQ' option. Assign ms1 tolerance and normalized spectral contrast angle values.

For a detailed explanation of the LFQ algorithm, including peak scoring strategies, configuration options, and best practices, see the LFQ Algorithm Reference.

TMT quantification

To enable TMT, click the TMT plex dropdown menu, and select a TMT types. "MSn level to use for reporter ion extraction" option provides MS2 or MS3 options for measuring reporter ions.