Table I. Protein identification in replicate runs. The number of proteins is given for each single 480 min run analyzed alone and with transfer of identifications using the “match between runs” feature in MaxQuant. Matching was performed for two samples, three samples, and for each of the experiments with the three others.

	Protein in a single run	Proteins in two runs	Proteins in three runs	Matched runs
Experiment 1	4529	5120	5348	5272
Experiment 2	4622			5292
Experiment 3	4542			5328
Matched experiment	4654			5286