i2MassChroQ_VERSION	1.0.16
AnalysisSoftware_name	X! Tandem
AnalysisSoftware_version	X! Tandem Alanine (2017.2.1.4)
decoy_accession_regexp	.*:reversed$
list path, default parameters	/gorgone/pappso/tmp/i2masschroq.TsbTbV/QExactive_analysis_FDR.xml
list path, sequence source #1	/gorgone/pappso/moulon/users/Olivier/20240131_proteobench/database/ProteoBenchFASTA_DDAQuantification.fasta
list path, sequence source description #1	no description
list path, taxonomy information	/gorgone/pappso/tmp/i2masschroq.TsbTbV/database.xml
modelling, duplicate peptide ids	4052
modelling, duplicate proteins	712
modelling, total peptides used	1764817672
modelling, total proteins used	63778
modelling, total spectra used	116593
output, histogram column width	30
output, histograms	yes
output, maximum valid expectation value	0.1
output, maximum valid protein expectation value	0.01
output, mzid	yes
output, one sequence copy	yes
output, parameters	yes
output, path	/gorgone/pappso/moulon/users/Olivier/20240131_proteobench/tandem/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.xml
output, path hashing	no
output, performance	yes
output, proteins	yes
output, results	all
output, sequences	yes
output, sort results by	spectrum
output, spectra	yes
output, spectrum index	true
output, xsl path	tandem-style.xsl
process, start time	2024-05-15T14:21:33
process, tandemng	tandemng 2017 0.3.7
process, version	X! Tandem Alanine (2017.2.1.4)
protein, C-terminal residue modification mass	0
protein, N-terminal residue modification mass	0
protein, cleavage C-terminal mass change	17.00305
protein, cleavage N-terminal mass change	1.00794
protein, cleavage semi	no
protein, cleavage site	[RK]|{P}
protein, modified residue mass file	
protein, quick acetyl	yes
protein, quick pyrolidone	yes
protein, stP bias	yes
protein, taxon	usedefined
protein, use minimal annotations	yes
quality values	3998 7084 5746 4805 4479 4066 3625 3447 3179 2830 2618 2405 2210 1913 1826 1638 1470 1378 1287 1182
refine	yes
refine, cleavage semi	yes
refine, maximum missed cleavage sites	3
refine, maximum valid expectation value	0.01
refine, modification mass	57.02146@C
refine, modification mass 1	
refine, modification mass 2	
refine, point mutations	no
refine, potential C-terminus modifications	
refine, potential N-terminus modifications	+42.01056@[
refine, potential modification mass	15.99491@M
refine, potential modification mass 1	
refine, potential modification mass 2	
refine, potential modification motif	
refine, potential modification motif 1	
refine, potential modification motif 2	
refine, spectrum synthesis	yes
refine, unanticipated cleavage	no
refine, use potential modifications for full refinement	yes
refining, # input models	6220
refining, # input spectra	73169
refining, # partial cleavage	45516
refining, # point mutations	0
refining, # potential C-terminii	0
refining, # potential N-terminii	585
refining, # unanticipated cleavage	0
residue, modification mass	57.02146@C
residue, modification mass 1	
residue, modification mass 2	
residue, potential modification mass	15.99491@M
residue, potential modification mass 1	
residue, potential modification mass 2	
residue, potential modification motif	
residue, potential modification motif 1	
residue, potential modification motif 2	
scoring, a ions	no
scoring, b ions	yes
scoring, c ions	no
scoring, cyclic permutation	yes
scoring, include reverse	yes
scoring, maximum missed cleavage sites	1
scoring, minimum ion count	4
scoring, pluggable scoring	no
scoring, x ions	no
scoring, y ions	yes
scoring, z ions	no
spectrum, dynamic range	100
spectrum, fragment mass type	monoisotopic
spectrum, fragment monoisotopic mass error	0.02
spectrum, fragment monoisotopic mass error units	Daltons
spectrum, maximum parent charge	4
spectrum, minimum fragment mz	150
spectrum, minimum parent m+h	500
spectrum, minimum peaks	15
spectrum, mzFormat	1
spectrum, neutral loss mass	18.01057
spectrum, neutral loss window	0.02
spectrum, parent monoisotopic mass error minus	10
spectrum, parent monoisotopic mass error plus	10
spectrum, parent monoisotopic mass error units	ppm
spectrum, parent monoisotopic mass isotope error	yes
spectrum, path	/gorgone/pappso/moulon/raw/20240131_proteobench/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
spectrum, sequence batch size	1000
spectrum, threads	4
spectrum, total peaks	100
spectrum, use contrast angle	no
spectrum, use neutral loss window	yes
spectrum, use noise suppression	yes
timing, initial modelling total (sec)	736.03
timing, initial modelling/spectrum (sec)	0.0063
timing, load sequence models (sec)	0.19
timing, refinement/spectrum (sec)	0.0358
xtandem_preset_file	/gorgone/pappso/tmp/i2masschroq.TsbTbV/QExactive_analysis_FDR.xml
i2m_count_peptides_per_protein_accross_msruns	false
i2m_minimum_peptides_per_protein	2
i2m_minimum_protein_log10_evalue	-3.099999035
i2m_pep_repro	1
i2m_psm_fdr_threshold_target	0.009
peptide_fdr	0.01196294798
protein_fdr	0.009873268494
psm_fdr	0.008998493465
mcq_alignment_ms1_smoothing_halfwindow	0
mcq_alignment_ms2_smoothing_halfwindow	15
mcq_alignment_ms2_tendency_halfwindow	10
mcq_alignment_msrun_reference_for_rt_alignment	LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML
mcq_detection_detection_threshold_on_max	200000
mcq_detection_detection_threshold_on_min	150000
mcq_detection_maxmin_half_edge	6
mcq_detection_mean_filter_half_edge	1
mcq_detection_minmax_half_edge	7
mcq_filter_anti_spike_half	5
mcq_mbr	F
mcq_xic_extraction_type	max
mcq_xic_ppm_range_max	10
mcq_xic_ppm_range_min	10
mcqr_normalization_method	median.RT
mcqr_version	0.6.15
