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. Author manuscript; available in PMC: 2024 Mar 24.
Published in final edited form as: Curr Protoc Immunol. 2020 Sep;130(1):e105. doi: 10.1002/cpim.105

Table 2.

Data Processing Parameters

Platform MaxQuant Proteome Discoverer 2.4
Search algorithm Andromeda SequestHT/Mascot
Database Fasta File of full proteome of Arabidopsis thaliana (Mouse-ear cress) by UniProtKB; Taxon identifier 3702 Fasta File of full proteome of Arabidopsis thaliana (Mouse-ear cress) by UniProtKB; Taxon identifier 3702
Enzyme Trypsin (full) Trypsin (full)
Multiplicity/max. labeled 3 3
Missed cleavages 2 2
Min. peptide length 3 3
Peptides for quantification Unique + razor Unique + razor
Fragment mass tolerance 20 ppm (First search) 4.5 ppm (Main search) 0.02 Da
Neutral losses Water, ammonia Water, ammonia
Static modifications Carbamidomethyl (C) Carbamidomethyl (C)
Dynamic modifications Oxidation (M) Acetylation (N-term) Phosphorylation (S,T,Y) Oxidation (M) Acetylation (N-term) Phosphorylation (S,T,Y)
Target FDR <1% <1%