Set the order of the analyses: Raw data > Set Experiment for each row

Define search specific parameters: Group-specific parameters > Type, Digestion, Modifications, Label-free quantification

Define which peptides should be identifiable: Global parameters > Sequence

Define the statistical context of peptide identifications and activate "Match between runs": Global parameters > Identification        (FDR = False Discovery Rate, PSM = Peptide Sequence Modification)

Define the number of threads for the search - 2 GBytes memory/thread are required. 

Use the Menu Command File > Save Parameters... to save the parameters of the search

Start the search: Start

You can observe the database search using the Performance header. 

Comments: matthias.wilm@ucd.ie