Configuring 
Assemble run info 
Finish run info 
Testing fasta files 
Testing raw files 
Feature detection 
Deisotoping 
MS/MS preparation 
Calculating peak properties 
Combining apl files for first search 
Preparing searches 
MS/MS first search 
Read search results for recalibration 
Mass recalibration 
Calculating masses 
MS/MS preparation for main search 
Combining apl files for main search 
MS/MS main search 
Preparing combined folder  
Correcting errors 
Reading search engine results 
Preparing reverse hits 
Finish search engine results 
Filter identifications (MS/MS) 
Calculating PEP 
Copying identifications 
Applying FDR 
Assembling second peptide MS/MS 
Combining second peptide files 
Second peptide search 
Reading search engine results (SP) 
Finish search engine results (SP) 
Filtering identifications (SP) 
Applying FDR (SP) 
Re-quantification 
Reporter quantification 
Retention time alignment 
Matching between runs 1 
Matching between runs 2 
Matching between runs 3 
Matching between runs 4 
Prepare protein assembly 
Assembling proteins 
Assembling unidentified peptides 
Finish protein assembly 
Updating identifications 
Estimating complexity 
Prepare writing tables  
Writing tables 
Finish writing tables