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+++ b/test-data/peptide_shaker_modifications_result1.output_certificate	Fri Oct 12 08:56:06 2018 -0400
@@ -0,0 +1,79 @@
+
+Project Details
+
+1: PeptideShaker Version: 1.16.31
+2: Date: Thu Oct 11 10:41:54 CEST 2018
+3: Experiment: Galaxy_Experiment_2018101110411539247311
+4: Sample: Sample_2018101110411539247311
+5: Replicate Number: 1
+6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet
+
+Database Search Parameters
+
+1: Precursor Tolerance Unit: ppm
+2: Precursor Ion m/z Tolerance: 100.0
+3: Fragment Ion Tolerance Unit: Da
+4: Fragment Ion m/z Tolerance: 0.5
+5: Cleavage: Enzyme
+6: Enzyme: Trypsin
+7: Missed Cleavages: 2
+8: Specificity: Specific
+9: Database: input_database.fasta
+10: Forward Ion: b
+11: Rewind Ion: y
+12: Fixed Modifications: Carbamidomethylation of C
+13: Variable Modifications: Oxidation of M
+14: Refinement Variable Modifications: Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C
+15: 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: Yes
+
+Validation Summary
+
+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: Probabilistic Score: PhosphoRS
+2: Accounting for Neutral Losses: No
+3: Threshold: 95.0
+
+Spectrum Counting Parameters
+
+1: Method: NSAF
+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, CH4OS
+5: Neutral Losses Sequence Dependence: Yes
+6: Fragment Ion m/z Tolerance: 0.5