--- a/test-data/peptide_shaker_certificate_result2.txt	Fri Jun 10 09:58:03 2016 -0400
+++ b/test-data/peptide_shaker_certificate_result2.txt	Fri Jan 13 14:15:42 2017 -0500
@@ -1,67 +1,68 @@
-Project Details1: PeptideShaker Version: 0.39.1
-2: Date: Thu Jun 04 20:07:16 CEST 2015
-3: Experiment: Galaxy_Experiment_2015060420071433441234
-4: Sample: Sample_2015060420071433441234
+Project Details1: PeptideShaker Version: 1.13.6
+2: Date: Fri Jan 13 11:06:50 CST 2017
+3: Experiment: Galaxy_Experiment_2017011311051484327131
+4: Sample: Sample_2017011311051484327131
 5: Replicate Number: 1
-6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet
+6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+, Comet and MyriMatch
 Database Search Parameters
 
-1: Precursor Accuracy Unit: ppm
+1: Precursor Tolerance Unit: ppm
 2: Precursor Ion m/z Tolerance: 100.0
-3: Fragment Ion m/z Tolerance: 0.5
-4: Enzyme: Trypsin
-5: Number of Missed Cleavages: Not implemented
-6: Database: input_database.fasta
-7: Forward Ion: b
-8: Rewind Ion: y
-9: Fixed Modifications: carbamidomethyl c
-10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q
-11: Refinement Variable Modifications: 
-12: Refinement Fixed Modifications: 
+3: Fragment Ion Tolerance Unit: Da
+4: Fragment Ion m/z Tolerance: 0.5
+5: Enzyme: Trypsin
+6: Maximum Missed Cleavages: 2
+7: Database: input_database.fasta
+8: Forward Ion: b
+9: Rewind Ion: y
+10: Fixed Modifications: Carbamidomethylation of C
+11: Variable Modifications: Oxidation of M, Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C
+12: Refinement Variable Modifications: 
+13: Refinement Fixed Modifications: 
 Input Filters
 
 1: Minimal Peptide Length: 1
 2: Maximal Peptide Length: 30
 3: Precursor m/z Tolerance: 10.0
 4: Precursor m/z Tolerance Unit: Yes
-5: Unrecognized Modifications Discarded: No
+5: Unrecognized Modifications Discarded: Yes
 Validation Summary
 
-1: #Validated Proteins: 0.0
-2: Protein Total: 0.0
-3Protein FDR Limit: 1.0 %
-4: Protein FNR Limit: 0.0 %
-5: Protein Confidence Limit: -1.0 %
-6: Protein PEP Limit: 101.0 %
-7: Protein Confidence Accuracy: 0.0 %
-8: #Validated Peptides: 0.0
-9: Peptide Total: 0.0
-10: Peptide FDR Limit: 1.0 %
-11: Peptide FNR Limit: 0.0 %
-12: Peptide Confidence Limit: -1.0 %
-13: Peptide PEP Limit: 101.0 %
-14: Peptide Confidence Accuracy: 0.0 %
-15: #Validated PSM: 0.0
-16: PSM Total: 0.0
-17: PSM FDR Limit: 1.0 %
-18: PSM FNR Limit: 0.0 %
-19: PSM Confidence Limit: -1.0 %
-20: PSM PEP Limit: 101.0 %
-21: PSM Confidence Accuracy: 0.0 %
-Postranslational Modification Scoring Settings
+1: Proteins: #Validated: 2.0
+2: Proteins: Total Possible TP: 2.0
+3: Proteins: FDR Limit [%]: 0.0
+4: Proteins: FNR Limit [%]: 0.0
+5: Proteins: Confidence Limit [%]: 100.0
+6: Proteins: PEP Limit [%]: 0.0
+7: Proteins: Confidence Accuracy [%]: 0.0
+8: Peptides: #Validated: 16.0
+9: Peptides: Total Possible TP: 16.0
+10: Peptides: FDR Limit [%]: 0.0
+11: Peptides: FNR Limit [%]: 0.0
+12: Peptides: Confidence Limit [%]: 100.0
+13: Peptides: PEP Limit [%]: 0.0
+14: Peptides: Confidence Accuracy [%]: 0.0
+15: PSMs: #Validated PSM: 42.0
+16: PSMs: Total Possible TP: 42.0
+17: PSMs: FDR Limit [%]: 0.0
+18: PSMs: FNR Limit [%]: 0.0
+19: PSMs: Confidence Limit [%]: 100.0
+20: PSMs: PEP Limit [%]: 0.0
+21: PSMs: Confidence Accuracy [%]: 0.0
+PTM Scoring Settings
 
-1: A-score: No
+1: Probabilistic Score: PhosphoRS
 2: Accounting for Neutral Losses: No
-3: False Location Rate: 1.0
+3: Threshold: 95.0
 Spectrum Counting Parameters
 
 1: Method: NSAF
-2: Validated Matches Only: Yes
+2: Validated Matches Only: No
 Annotation Settings
 
 1: Intensity Limit: 0.75
 2: Automatic Annotation: Yes
-3: Selected Ions: b, y
-4: Neutral Losses: H2O, NH3
+3: Selected Ions: y, b
+4: Neutral Losses: H2O, NH3, CH4OS
 5: Neutral Losses Sequence Dependence: Yes
 6: Fragment Ion m/z Tolerance: 0.5