Dear LIMPA team,

Are there specific settings or any recommendations to perform PTM analysis using LIMPA?

Thank you.

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a protein differential expression analysis.

From limpa's point of view, the only difference between PTM analysis and protein expression analysis, is that differential abundance is evaluated for each row of the raw data, instead of summarizing peptides or low-level features into proteins. For a PTM analysis, limpa expects to get a matrix of log2 intensities values (with some NAs) with a row for each PTM and a column for each biological sample.