--- a/test-data/01/combined/txt/parameters.txt	Tue Jun 15 07:55:59 2021 +0000
+++ b/test-data/01/combined/txt/parameters.txt	Sun Jun 20 16:37:41 2021 +0000
@@ -1,105 +1,105 @@
-Parameter	Value
-Version	1.6.10.43
-User name	dglaetzer
-Machine name	FPROT-BEAST
-Date of writing	02/25/2020 15:36:33
-Include contaminants	True
-PSM FDR	0.01
-PSM FDR Crosslink	0.01
-Protein FDR	0.01
-Site FDR	0.01
-Use Normalized Ratios For Occupancy	True
-Min. peptide Length	7
-Min. score for unmodified peptides	0
-Min. score for modified peptides	40
-Min. delta score for unmodified peptides	0
-Min. delta score for modified peptides	6
-Min. unique peptides	0
-Min. razor peptides	1
-Min. peptides	1
-Use only unmodified peptides and	True
-Modifications included in protein quantification
-Peptides used for protein quantification	Razor
-Discard unmodified counterpart peptides	False
-Label min. ratio count	2
-Use delta score	False
-iBAQ	False
-iBAQ log fit	False
-Match between runs	False
-Find dependent peptides	False
-Fasta file	D:\shared\dglaetzer\maxquant_tool\test1\bsa.fasta
-Decoy mode	revert
-Include contaminants	True
-Advanced ratios	True
-Fixed andromeda index folder	
-Temporary folder	
-Combined folder location	
-Second peptides	True
-Stabilize large LFQ ratios	True
-Separate LFQ in parameter groups	False
-Require MS/MS for LFQ comparisons	True
-Calculate peak properties	False
-Main search max. combinations	200
-Advanced site intensities	True
-Write msScans table	False
-Write msmsScans table	True
-Write ms3Scans table	True
-Write allPeptides table	True
-Write mzRange table	True
-Write pasefMsmsScans table	True
-Write accumulatedPasefMsmsScans table	True
-Max. peptide mass [Da]	4600
-Min. peptide length for unspecific search	8
-Max. peptide length for unspecific search	25
-Razor protein FDR	True
-Disable MD5	False
-Max mods in site table	3
-Match unidentified features	False
-Epsilon score for mutations	
-Evaluate variant peptides separately	True
-Variation mode	None
-MS/MS tol. (FTMS)	20 ppm
-Top MS/MS peaks per Da interval. (FTMS)	12
-Da interval. (FTMS)	100
-MS/MS deisotoping (FTMS)	True
-MS/MS deisotoping tolerance (FTMS)	7
-MS/MS deisotoping tolerance unit (FTMS)	ppm
-MS/MS higher charges (FTMS)	True
-MS/MS water loss (FTMS)	True
-MS/MS ammonia loss (FTMS)	True
-MS/MS dependent losses (FTMS)	True
-MS/MS recalibration (FTMS)	False
-MS/MS tol. (ITMS)	0.5 Da
-Top MS/MS peaks per Da interval. (ITMS)	8
-Da interval. (ITMS)	100
-MS/MS deisotoping (ITMS)	False
-MS/MS deisotoping tolerance (ITMS)	0.15
-MS/MS deisotoping tolerance unit (ITMS)	Da
-MS/MS higher charges (ITMS)	True
-MS/MS water loss (ITMS)	True
-MS/MS ammonia loss (ITMS)	True
-MS/MS dependent losses (ITMS)	True
-MS/MS recalibration (ITMS)	False
-MS/MS tol. (TOF)	40 ppm
-Top MS/MS peaks per Da interval. (TOF)	10
-Da interval. (TOF)	100
-MS/MS deisotoping (TOF)	True
-MS/MS deisotoping tolerance (TOF)	0.01
-MS/MS deisotoping tolerance unit (TOF)	Da
-MS/MS higher charges (TOF)	True
-MS/MS water loss (TOF)	True
-MS/MS ammonia loss (TOF)	True
-MS/MS dependent losses (TOF)	True
-MS/MS recalibration (TOF)	False
-MS/MS tol. (Unknown)	20 ppm
-Top MS/MS peaks per Da interval. (Unknown)	12
-Da interval. (Unknown)	100
-MS/MS deisotoping (Unknown)	True
-MS/MS deisotoping tolerance (Unknown)	7
-MS/MS deisotoping tolerance unit (Unknown)	ppm
-MS/MS higher charges (Unknown)	True
-MS/MS water loss (Unknown)	True
-MS/MS ammonia loss (Unknown)	True
-MS/MS dependent losses (Unknown)	True
-MS/MS recalibration (Unknown)	False
-Site tables	Oxidation (M)Sites.txt
+Parameter	Value
+Version	1.6.17.0
+User name	niko
+Machine name	DESKTOP-I3UDKML
+Date of writing	06/16/2021 16:28:26
+Include contaminants	True
+PSM FDR	0.01
+PSM FDR Crosslink	0.01
+Protein FDR	0.01
+Site FDR	0.01
+Use Normalized Ratios For Occupancy	True
+Min. peptide Length	7
+Min. score for unmodified peptides	0
+Min. score for modified peptides	40
+Min. delta score for unmodified peptides	0
+Min. delta score for modified peptides	6
+Min. unique peptides	0
+Min. razor peptides	1
+Min. peptides	1
+Use only unmodified peptides and	True
+Modifications included in protein quantification	Oxidation (M);Acetyl (Protein N-term)
+Peptides used for protein quantification	Razor
+Discard unmodified counterpart peptides	False
+Label min. ratio count	2
+Use delta score	False
+iBAQ	False
+iBAQ log fit	False
+Match between runs	False
+Find dependent peptides	False
+Fasta file	/tmp/tmpyzym30dx/files/3/c/e/dataset_3cea3228-eaab-4e71-aba7-9ffa9900b54a.dat
+Decoy mode	revert
+Include contaminants	True
+Advanced ratios	True
+Fixed andromeda index folder	
+Combined folder location	
+Second peptides	True
+Stabilize large LFQ ratios	True
+Separate LFQ in parameter groups	False
+Require MS/MS for LFQ comparisons	True
+Calculate peak properties	False
+Main search max. combinations	200
+Advanced site intensities	True
+Write msScans table	False
+Write msmsScans table	True
+Write ms3Scans table	True
+Write allPeptides table	True
+Write mzRange table	True
+Write DIA fragments table	False
+Write pasefMsmsScans table	True
+Write accumulatedPasefMsmsScans table	False
+Max. peptide mass [Da]	4600
+Min. peptide length for unspecific search	8
+Max. peptide length for unspecific search	25
+Razor protein FDR	True
+Disable MD5	False
+Max mods in site table	3
+Match unidentified features	False
+Epsilon score for mutations	
+Evaluate variant peptides separately	True
+Variation mode	None
+MS/MS tol. (FTMS)	20 ppm
+Top MS/MS peaks per Da interval. (FTMS)	12
+Da interval. (FTMS)	100
+MS/MS deisotoping (FTMS)	True
+MS/MS deisotoping tolerance (FTMS)	7
+MS/MS deisotoping tolerance unit (FTMS)	ppm
+MS/MS higher charges (FTMS)	True
+MS/MS water loss (FTMS)	True
+MS/MS ammonia loss (FTMS)	True
+MS/MS dependent losses (FTMS)	True
+MS/MS recalibration (FTMS)	False
+MS/MS tol. (ITMS)	0.5 Da
+Top MS/MS peaks per Da interval. (ITMS)	8
+Da interval. (ITMS)	100
+MS/MS deisotoping (ITMS)	False
+MS/MS deisotoping tolerance (ITMS)	0.15
+MS/MS deisotoping tolerance unit (ITMS)	Da
+MS/MS higher charges (ITMS)	True
+MS/MS water loss (ITMS)	True
+MS/MS ammonia loss (ITMS)	True
+MS/MS dependent losses (ITMS)	True
+MS/MS recalibration (ITMS)	False
+MS/MS tol. (TOF)	40 ppm
+Top MS/MS peaks per Da interval. (TOF)	10
+Da interval. (TOF)	100
+MS/MS deisotoping (TOF)	True
+MS/MS deisotoping tolerance (TOF)	0.01
+MS/MS deisotoping tolerance unit (TOF)	Da
+MS/MS higher charges (TOF)	True
+MS/MS water loss (TOF)	True
+MS/MS ammonia loss (TOF)	True
+MS/MS dependent losses (TOF)	True
+MS/MS recalibration (TOF)	False
+MS/MS tol. (Unknown)	20 ppm
+Top MS/MS peaks per Da interval. (Unknown)	12
+Da interval. (Unknown)	100
+MS/MS deisotoping (Unknown)	True
+MS/MS deisotoping tolerance (Unknown)	7
+MS/MS deisotoping tolerance unit (Unknown)	ppm
+MS/MS higher charges (Unknown)	True
+MS/MS water loss (Unknown)	True
+MS/MS ammonia loss (Unknown)	True
+MS/MS dependent losses (Unknown)	True
+MS/MS recalibration (Unknown)	False
+Site tables	Oxidation (M)Sites.txt