Table 25.

Consensus Workflow Nodes and Basic Parameters

MSF Files
Storage Settings
Spectra to Store	Identified or Quantified
Feature Traces to Store	All
PSM Grouper
Peptide Group Modifications
Site Probability Threshold	75
Peptide Validator
General Validation Settings
Validation Mode	Automatic (Control peptide level error rate if possible)
Target FDR (Strict) for PSMs	0.01
Target FDR (Strict) for Peptides	0.01
Peptide and Protein Filter
Peptide Filters
Peptide Confidence At Least	High
Keep Lower Confident PSMs	FALSE
Protein Filters
Minimum Number of Peptide Sequences	1
Protein Grouping
Protein Grouping
Apply strict parsimony principle	TRUE
Peptide in Protein Annotation
Flanking Residues
Annotate Flanking Residues of the Peptide	TRUE
Modifications in Peptide
Protein Modifications Reported	Only for Master Proteins
Modifications in Protein
Modification Sites Reported	All And Specific
Minimum PSM Confidence	High
Report Only PTMs	True
Positions in Protein
Protein Positions for Peptides	Only for Master Proteins
Feature Mapper
Chromatographic Alignment
Perform RT Alignment	TRUE
Maximum RT Shift [min]	2
Feature Linking and Mapping
Minimum S/N Threshold	3
Precursor Ions Quantifier
General Quantification Settings
Peptides to Use	All
Precursor Quantification
Precursor Abundance Based On	Area
Normalization and Scaling
Normalization Mode	Total Peptide Amount
Exclude Peptides from Protein Quantification
For Protein Roll-Up	Use All Peptides
Quan Rollup and Hypothesis Testing
Protein Abundance Calculation	Summed Abundances
N for Top N	5
Protein Annotation
Annotation Aspects
1. Aspect	Biological Process
2. Aspect	Cellular Component
3. Aspect	Molecular Function
Protein Marker
Contaminant Database
Protein Database	Contaminants.fasta
Protein FDR Validator
Confidence Thresholds
Target FDR (Strict)	0.01
Target FDR (Relaxed)	0.05