i2MassChroQ_VERSION	1.2.0
i2MassChroQ_project_name	proteobench_sage_fdr_prot_001
AnalysisSoftware_name	Sage
AnalysisSoftware_version	0.15.0-alpha
sage_chimera	F
sage_database_bucket_size	8192
sage_database_decoy_tag	rev_
sage_database_enzyme_c_terminal	T
sage_database_enzyme_cleave_at	KR
sage_database_enzyme_max_len	50
sage_database_enzyme_min_len	5
sage_database_enzyme_missed_cleavages	2
sage_database_enzyme_restrict	P
sage_database_fasta	/gorgone/pappso/moulon/users/Olivier/20240131_proteobench/database/ProteoBenchFASTA_DDAQuantification.fasta
sage_database_generate_decoys	T
sage_database_ion_kinds	b y
sage_database_max_variable_mods	2
sage_database_min_ion_index	2
sage_database_peptide_max_mass	5000
sage_database_peptide_min_mass	500
sage_database_static_mods	C:57.021465
sage_database_variable_mods	M:15.994915 [:42.0106 ^E:-18.010565 ^Q:-17.026548
sage_deisotope	T
sage_fragment_tol	-0.02 0.02 da
sage_isotope_errors	-1 3
sage_max_fragment_charge	1
sage_max_peaks	150
sage_min_matched_peaks	6
sage_min_peaks	15
sage_mzml_paths	/gorgone/pappso/moulon/raw/20240131_proteobench/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.mzML /gorgone/pappso/moulon/raw/20240131_proteobench/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.mzML /gorgone/pappso/moulon/raw/20240131_proteobench/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.mzML /gorgone/pappso/moulon/raw/20240131_proteobench/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.mzML /gorgone/pappso/moulon/raw/20240131_proteobench/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.mzML /gorgone/pappso/moulon/raw/20240131_proteobench/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.mzML
sage_output_paths	/gorgone/pappso/moulon/users/Olivier/20240131_proteobench/sage/all_samples_acetyl/results.sage.tsv /gorgone/pappso/moulon/users/Olivier/20240131_proteobench/sage/all_samples_acetyl/results.json
sage_override_precursor_charge	F
sage_precursor_charge	2 4
sage_precursor_tol	-10 10 ppm
sage_predict_rt	T
sage_report_psms	1
sage_score_type	SageHyperScore
sage_version	0.15.0-alpha
sage_wide_window	F
i2m_count_peptides_per_protein_accross_msruns	T
i2m_minimum_peptides_per_protein	1
i2m_minimum_protein_log10_evalue	-2
i2m_pep_repro	1
i2m_protein_qvalue_threshold	0.007
i2m_psm_fdr_threshold_target	0.01
peptide_fdr	0.0141726898633
protein_fdr	0.00948714423209
psm_fdr	0.0099991764759
mcq_alignment_ms1_smoothing_window	15
mcq_alignment_ms2_smoothing_window	5
mcq_alignment_ms2_tendency_window	10
mcq_detection_zivy	1 7 6 200000 150000
mcq_isotope_minimum_ratio	0.8
mcq_mbr	F
mcq_version	3.0.0
mcq_xic_extraction_type	max
mcq_xic_ppm_range_max	10
mcq_xic_ppm_range_min	10
mcq_xic_pre_filter	antiSpike|5 antiSpike|5
mcqr_normalization_method	median.RT
mcqr_version	1.0.1
