Table I. Main processing steps of the computational workflow. The table lists the most important and time consuming steps in the MaxQuant pipeline for LC-IMS-MS/MS data. In the second column, the number of plus signs signifies the extent of changes in the code in order to accommodate ion mobility information. For instance, “+++” for “feature detection” indicates fundamental changes. The right column contains the percentage of computation time that is spent on the step on the HeLa data set consisting of ten replicates, on 60 core machine running Windows Server 2016.

Workflow component	Changes for IMS	Percentage computation time
Feature detection	+++	31.2%
MS/MS preparation	+++	15.6%
Initial search	-	14.1%
Recalibration	++	1.8%
Main search	-	19.1%
PSM FDR	-	1.9%
Alignment	++	12.5%
Match between runs	++	0.4%
Protein groups/FDR	–	2.6%
Label-free quantification	–	0.3%
Writing of results	+	0.4%