Table 24.

Processing Workflow Nodes and Basic Parameters

Spectrum Files RC
Search Settings
Protein Database	Contaminants.fasta; Homo Sapiens (Swiss Prot TaxID=9606)
Enzyme Name	Trypsin (Full)
1. Static Modification	Carbamidomethyl/ +57.021 Da (C)
Spectrum Selector
General Settings
Precursor Selection	Use MS1 Precursor
Provide Profile Spectra	TRUE
Spectrum Properties Filter
Min. Precursor Mass	350 Da
Max. Precursor Mass	5000 Da
Peak Filters
S/N Threshold (FT-only)	1.5
Sequest HT
Input Data
Protein Database	Contaminants.fasta; Homo Sapiens (Swiss Prot TaxID=9606)
Enzyme Name	Trypsin (Full)
Max. Missed Cleavage Sites	2
Min. Peptide Length	6
Max. Peptide Length	144
Tolerances
Precursor Mass Tolerance	5 ppm
Fragment Mass Tolerance	0.02 Da
Spectrum Matching
Weight of a Ions	0.2
Weight of b Ions	1
Weight of x ions	0.2
Weight of y ions	1
Dynamic Modifications
Max. Equal Modifications Per Peptide	2
Max. Dynamic Modifications Per Peptide	3
1. Dynamic Modification	Oxidation/ +15.995 Da (M)
2. Dynamic Modification	Deamidated/ +0.984 Da (N, Q)
Dynamic Modifications (protein terminus)
1. N-Terminal Modification	Acetyl/ +42.011 Da (N-terminus)
2. N-Terminal Modification	Met-loss + Acetyl/ −89.030 Da (M)
Static Modifications
1. Static Modification	Carbamidomethyl/ +57.021 Da (C)
Percolator
Target/Decoy Strategy
Target/Decoy Selection	Concatenated
Validation based on	q-Value
Input Data
Maximum Delta CN	0.05
FDR Targets
Target FDR (Strict)	0.01
Target FDR (Relaxed)	0.05