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QC_bsa_config.yml
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---
# This section holds the alert settings for this QC case.
:autorun: true
:alert: true
:alert_email: "ryanmt@byu.net"
# This should probably be around 2-3... 2 will encompass 95% confidence of a normal distribution
:default_allowed_variance: 2
# Here you'll find all the parameters sorted by their categories and subcategories, so you can set any filters you want to be active on these, custom to each parameter.
:peptide_ids:
:AveragesVsRtForIdedPeptides:
:charge_q4: false
:charge_q1: false
:length_q4: false
:length_q1: false
:PrecursorMZForIds:
:med_charge_4: false
:med_charge_3: false
:med_charge_2: false
:med_charge_1: false
:med_q4_rt: false
:med_q1_rt: false
:med_q4_tic: false
:med_q1_tic: false
:precursor_max: false
:precursor_min: false
:quart_ratio: false
:half_width: false
:median: false
:TotalIonCurrentForIdsAtPeakMaxima:
:mid_interq_tic: false
:interq_tic: false
:med_tic_id_1000: false
:PeptideCounts:
:ions_peptide: false
:net_oversample: false
:miss_tryp_abund: false
:miss_tryp_cnts: false
:miss_tryp_peps: false
:semi_tryp_abund: false
:semi_tryp_cnts: false
:semi_tryp_peps: false
:ions: true
:peptides: true
:TrypticPeptideCounts:
:ions_peptide: true
:abundance_1000: false
:abundance_pct: false
:ions: true
:peptides: true
:ms2:
:Ms2IdAbundReported:
:_95_5_pctile: false
:_75_25_pctile: false
:half_width: false
:median: true
:Ms2IdSpectra:
:s_n_interq: false
:s_n_median: true
:npeaks_interq: false
:npeaks_median: false
:Ms1IdAbundAtMs2Acquisition:
:_95_5_pctile: false
:_75_25_pctile: false
:half_width: false
:median: true
:PrecursorMZPeptideIonMZ2ChargeOnlyReject045MZ:
:ppm_interq: false
:ppm_median: true
:mean_absolute: false
:median: true
:spectra: false
:ms1:
:Ms1TotalIonCurrentForDifferentRtPeriods:
:to_end_of_run: true
:last_id_quart: true
:middle_id: true
:_1st_quart_id: true
:Ms1IdMax:
:_95_5_pctile: false
:_75_25_pctile: false
:_95_5_midrt: false
:_75_25_midrt: false
:median_midrt: false
:quart_ratio: false
:half_width: false
:median: true
:Ms1DuringMiddleAndEarlyPeptideRetentionPeriod:
:ms1_falls_10x: true
:ms1_jumps_10x: true
:max_ms1_fall: true
:max_ms1_jump: true
:esi_off_early: false
:esi_off_middle: false
:s2s_4qrt_med: false
:s2s_3qrt_med: false
:s2s_2qrt_med: false
:s2s_1qrt_med: false
:s2s_3q_med: false
:scan_to_scan: false
:npeaks_median: false
:tic_median_1000: true
:s_n_median: true
:ion_treatment:
:PrecursorMZMonoisotopeExactMZ:
:next_half_8: false
:next_half_7: false
:next_half_6: false
:next_half_5: false
:next_half_4: false
:next_half_3: false
:next_half_2: false
:top_half: false
:betw_1_6_0_8: true
:betw_3_1_1_6: true
:betw_6_3_3_1: false
:betw_12_5_6_3: false
:betw_25_0_12_5: false
:betw_50_0_25_0: false
:betw_100_0_50_0: false
:more_than_100: false
:ion_source:
:TopIonAbundanceMeasures:
:fractab_top_100: false
:fractab_top_10: false
:fractab_top: false
:top_50_abund: true
:top_25_abund: false
:top_10_abund: false
:IonInjectionTimesForIdsMs:
:ms2_fract_max: false
:ms2_maximun: false
:ms2_median: false
:ms1_maximum: false
:ms1_median: true
:PercentOfIdsAtDifferentChargesAndMobileProtonsRelativeToIdsWith1MobileProton:
:ch_3_mp_1: false
:ch_3_mp_0: false
:ch_3_mp_1: false
:ch_2_mp_1: false
:ch_2_mp_0: false
:ch_2_mp_1: false
:ch_1_mp_1: false
:ch_1_mp_0: false
:ch_1_mp_1: false
:NumbersOfIonIdsAtDifferentChargesWith1MobileProton:
:ch_4_mp_1: false
:ch_3_mp_1: false
:ch_2_mp_1: false
:ch_1_mp_1: false
:AveragePeptideLengthsForCharge2ForDifferentNumbersOfMobileProtons:
:naa_ch_2_mp_2: false
:naa_ch_2_mp_1: false
:naa_ch_2_mp_0: false
:naa_ch_2_mp_1: false
:AveragePeptideLengthsForDifferentChargeStates:
:charge_4: false
:charge_3: false
:charge_2: false
:charge_1: false
:IonIdsByChargeStateRelativeTo2:
:charge_4: false
:charge_3: false
:charge_2: false
:charge_1: false
:_2_ion_count: false
:NumberOfIonsVsCharge:
:charge_5: false
:charge_4: false
:charge_3: false
:charge_2: false
:charge_1: false
:SpectrumCounts:
:ms1_scans_other: false
:ms1_scans_full: true
:ms2_scans: true
:dynamic_sampling:
:Ms1maxMs1sampledAbundanceRatioIdsInefficientSampling:
:med_bottom_1_2: false
:med_top_quart: false
:med_top_dec: false
:med_top_100: false
:_9dec_all_ids: false
:_3q_all_ids: false
:median_all_ids: true
:SingleSpectrumPeptideIonIdentificationsOversamplingMeasure:
:_1_vs_1_spec: false
:_1_vs_1_pepion: false
:fract_1_ions: false
:peptide_ions: true
:RatiosOfPeptideIonsIdedByDifferentNumbersOfSpectraOversamplingMeasure:
:twice_thrice: true
:once_twice: true
:PeptideIonIdsBy3SpectraHiVs13SpectraLoExtremeOversampling:
:spec_cnt_excess: false
:spec_pep_hi: false
:ratio_hi_lo: false
:spec_cnts_hi: false
:ratio_hi_lo: false
:pep_ions_hi: false
:EarlyAndLateRtOversamplingSpectrumIdsUniquePeptideIdsChromatographicFlowThroughBleed:
:last_decile: false
:first_decile: false
:NearbyResamplingOfIdsOversamplingDetails:
:quart_dm_z: false
:median_dm_z: false
:_1dec_rt_diff_s: false
:_1q_rt_diff_s: false
:med_rt_diff_s: false
:repeated_ids: false
:chromatography:
:RtMs1maxRtMs2ForIdsSec:
:third_quart: false
:first_quart: false
:median_diff: false
:med_diff_abs: false
:WideRtDifferencesForIds4Min:
:spectra: true
:peptides: true
:PeakWidthsAtHalfMaxOverRtDecilesForIds:
:last_decile: false
:median_value: false
:first_decile: false
:PeakWidthAtHalfHeightForIds:
:ms1_scan_fwhm: true
:ms1_interscan_s: false
:_9dec_value: false
:_3quart_value: false
:med_100_disp: false
:med_16th_disp: false
:med_quart_disp: false
:median_disper: false
:med_top_100: false
:med_top_16th: false
:med_top_quart: false
:median_value: true
:MaxPeakWidthForIdsSec:
:last_decile: false
:third_quart: false
:median_value: false
:MiddlePeptideRetentionTimePeriodMin:
:pep_id_rate: false
:ms1_scans: false
:ms2_scans: false
:qratio_time: false
:mid_time: false
:start_time: false
:half_period: false
# These are pretty useless, so I would recommend leaving them out of any alerts.
:run_comparison:
:MagnitudeOfRtCorrectionOfIntensitiesOfMatchingPeptidesInOtherRuns:
:comp_to_last: false
:comp_to_first: false
:UncorrectedAndRtCorrectedRelativeIntensitiesOfMatchingPeptidesInOtherRuns:
:corr_rel_last: false
:corr_rel_first: false
:uncor_rel_last: false
:uncor_rel_first: false
:MedianRatiosOfMs1IntensitiesOfMatchingPeptidesInOtherRuns:
:comp_to_last_2: false
:comp_to_first_2: false
:comp_to_last: false
:comp_to_first: false
:median_2_diff: false
:median_diff: false
:DifferencesInElutionRankPercentOfMatchingPeptidesInOtherRuns:
:comp_to_last: false
:comp_to_first: false
:median_diff: false
:average_diff: false
:RelativeUniquenessOfPeptidesInDecileFoundAnywhereInOtherRuns:
:last_decile: false
:first_decile: false
:RelativeFractionOfPeptidesInRetentionDecileMatchingAPeptideInOtherRuns:
:comp_to_last: false
:comp_to_first: false
:last_decile: false
:first_decile: false
:all_deciles: false