Mascor Deamon search	Parameters	Notes
Database	depends on the organism (i.e. for HeLa cells: human database, version 3.68; 87,061 entries)
Enzyme	Arg-C	Arg-C cleave at the C-terminal of all arginine residues
Variable modifications	acetyl (K), oxidation (M), D3-acetylation (K), methyl-D3-acetyl (K), dimethyl (k), trimethyl (K)	acetyl [42.010 Da], oxidation [15.995 Da], D3-acetylation [+45.0294 Da], methyl-D3-acetyl  [sum of +14.016 Da and +45.0294 Da], dimethyl [28.031], trimethyl [42.046 Da]
Missed cleavages	up to 2
Mass accuracy of the parent ions in the search	10 ppm
Mass-accuracy for CID MSMS	0.5 Da
MaxQuant search	Parameters	Notes
Database	depends on the organism
Enzyme	trypsin/P	Trypsin cleaves at the C-terminal of all lysine and arginine residues. The search is performed taking in account the fact that the efficiency of trypsin to cleave lysine and arginine is reduced when the next amino acid is the proline (/P).
Fixed modification	carbamidomethylation
Variable modifications	N-acetyl (Protein), oxidation (M)
Missed cleavages	up to 3
Label parameters	lys8 and arg10
Maximum label amminoacid	3 for Trypsin
Mass-accuracy of the parent ions in the initial “Andromeda” search	20 ppm
Mass accuracy of the parent ions in the main “Andromeda” search	6 ppm
Mass-accuracy for CID MSMS	0.5 Da (six top peaks per100 Da)
Peptide false discovery rates (FDR)	0.01
Protein  false discovery rates (FDR)	0.01	Setting the FDR for peptide and protein to 0.01 means that both peptides and proteins identified are expected to contain 1% of false positives. This value is estimated using a target-decoy database
Maximum posterior error probability (PEP)	1	PEP is the probability that an individual peptide is a false positive match. PEP equal to 1 in your setting means that all peptides will be taken irrespective of the PEP thus filtering is based exclusively on FDR.
Minimum peptide length	6
Minimum number of peptides	2
Minimum number of unique peptides	1
Using only unmodified peptides and oxidation (M)/acetyl (Protein N-Term)	activate the option	Peptides with modifications should generally not be counted for protein quantification since their abundance may not reflect the ratio of the corresponding protein.
Minimum ratio count	1
“Match between runs”	activate the option	This option matches precursor masses in a 2-min retention time window (after realignment of the runs) based on the accurate mass measurement and allows transferring the MS/MS identification between the different LC MS/MS runs.