3.3 Maxquant: Group Specific Parameters Tab

Select “General” tab.

Set Type: select Standard for label-free quantitation (see Note 4).

Set Multiplicity: select 1 for label-free quantitation (see Note 5).

Set Variable modifications (e.g. methionine oxidation and protein N-terminal acetylation).

Specify Digestion mode and Enzyme used (e.g. “ Specific” and “Trypsin/P” for full-tryptic cleavage constraints).

Set max. # of missed cleavages: default = 2.

Set Match type: Match from and to.

Select “Instrument” tab.

Choose instrument used (e.g. Thermo Fisher Orbitrap, Bruker Q-TOf, AB Sciex Q-TOF). The default parameters will change accordingly based on the instrument selected.

Select “Label-free quantification” tab.

Set Label-free quantitation: select LFQ.

Set the LFQ min. ratio count to 1 (see Note 6).

Keep “Fast LFQ” enabled (see Note 7).

Select “Advanced” tab.

Set the max. number of modifications per peptide: default = 5.