Table I Descriptions of metrics

Th, thomsons; ID, identification; IDed, identified; max, maximum; Betw/in, between/within; Med, median; pctile, percentile; tryp, tryptic; Pep, peptide; interQ, interquartile; fract, fraction.

CodeCategoryMetric groupMetricUnitsOptimalPurpose/useDescription
C-1AChromatographyFraction of repeat peptide IDs with divergent RT−4 minFractionEstimates very early peak broadeningFraction of all peptides identified at least 4 min earlier than max MS1 for ID
C-1BChromatographyFraction of repeat peptide IDs with divergent RT+4 minFractionEstimates very late peak broadeningFraction of all peptides identified at least 4 min later than max MS1 for ID
C-2AChromatographyInterquartile retention time periodPeriod (min)minLonger times indicate better chromatographic separationTime period over which 50% of peptides were identified
C-2BChromatographyInterquartile retention time periodPep ID ratePeps/minHigher rates indicate efficient sampling and identificationRate of peptide identification during C-2A
C-3AChromatographyPeak width at half-height for IDsMedian valuesSharper peak widths indicate better chromatographic resolutionMedian peak widths for all identified unique peptides (s)
C-3BChromatographyPeak width at half-height for IDsInterquartile distancesTighter distributions indicate more peak width uniformityMeasure of the distribution of the peak widths; small values indicate consistency
C-4AChromatographyPeak widths at half-max over RT deciles for IDsFirst decilesEstimates peak widths at the beginning of the gradientMedian peak width for identified peptides in last RT decile (late)
C-4BChromatographyPeak widths at half-max over RT deciles for IDsLast decilesEstimates peak widths at the end of the gradientMedian peak width for identified peptides in first RT decile (early)
C-4CChromatographyPeak widths at half-max over RT deciles for IDsMedian valuesEstimates peak widths in the middle of the gradientMedian peak width for identified peptides in median RT decile (middle)
C-5AChromatographyAverage elution order differencesaBetweenPercentEstimates peptide elution similarity run to runAverage elution rank order difference for identified peptides between series
C-5BChromatographyAverage elution order differencesaBetw/inRatioEstimates peptide elution similarity between seriesRatio of average rank order difference between series to average rank order difference within a series (low values indicate similarity between series)
C-6AChromatographyFraction of extra early eluting peptides in row series (− = fewer)aBetweenFractionUsed to detect differences in the numbers of early peptidesEstimates relative frequency of early eluting peptides
C-6BChromatographyFraction of extra late eluting peptides in row series (− = fewer)aBetweenFractionUsed to detect differences in the numbers of late peptidesEstimates relative frequency of late eluting peptides
DS-1ADynamic samplingRatios of peptide ions IDed by different numbers of spectraOnce/twiceRatioEstimates oversamplingRatio of peptides identified by 1 spectrum divided by number identified by 2 spectra
DS1-BDynamic samplingRatios of peptide ions IDed by different numbers of spectraTwice/thriceRatioEstimates oversamplingRatio of peptides identified by 2 spectra divided by number identified by 3 spectra
DS-2ADynamic samplingSpectrum countsMS1 scans/fullCountFewer MS1 scans indicates more samplingNumber of MS1 scans taken over C-2A
DS-2BDynamic samplingSpectrum countsMS2 scansCountMore MS2 scans indicates more samplingNumber of MS2 scans taken over C-2A
DS-3ADynamic samplingMS1 max/MS1 sampled abundance ratio IDsMedian all IDsRatioEstimates position on peak where sampled for peptides of all abundancesRatio of MS1 maximum to MS1 value at sampling for median decile of peptides by MS1 maximum intensity (1 = sampled at peak maxima)
DS-3BDynamic samplingMS1 max/MS1 sampled abundance ratio IDsMed bottom 1/2RatioEstimates position on peak where sampled for least abundant 50% of peptidesRatio of MS1 maximum to MS1 value at sampling for bottom 50% of peptides by MS1 maximum intensity (1 = sampled at peak maxima)
IS-1AIon sourceMS1 during middle (and early) peptide retention periodMS1 jumps >10×CountFlags ESI instabilityNumber of times where MS1 signal greatly decreased between adjacent scans more than 10-fold (electrospray instability)
IS-1BIon sourceMS1 during middle (and early) peptide retention periodMS1 falls >10×CountFlags ESI instabilityNumber of times where MS1 signal greatly increased between adjacent scans more than 10-fold (electrospray instability)
IS-2Ion sourcePrecursor m/z for IDsMedianThHigher median m/z can correlate with inefficient or partial ionizationMedian m/z value for all identified peptides (unique ions)
IS-3AIon sourceIDs by charge state (relative to 2+)Charge 1+RatioHigh ratios of 1+/2+ peptides may indicate inefficient ionizationNumber of 1+ peptides over 2+ peptides
IS-3BIon sourceIDs by charge state (relative to 2+)Charge 3+RatioHigher ratios of 3+/2+ peptides may preferentially favor longer peptidesNumber of 3+ peptides over 2+ peptides
IS-3CIon sourceIDs by charge state (relative to 2+)Charge 4+RatioHigher ratios of 4+/2+ peptides may preferentially favor longer peptidesNumber of 4+ peptides over 2+ peptides
MS1-1MS1 signalIon injection times for IDsMS1 medianmsLower times indicate an abundance of ionsMS1 ion injection time
MS1-2AMS1 signalMS1 during middle (and early) peptide retention periodS/N medianNoneHigher MS1 S/N may correlate with higher signal discriminationMedian signal-to-noise value (ratio of maximum to median peak height) for MS1 spectra up to and including C-2A
MS1-2BMS1 signalMS1 during middle (and early) peptide retention periodTIC medianCounts/1,000Estimates the total absolute signal for peptides (may vary significantly between instruments)Median TIC value for identified peptides over same time period as used for MS1-2A
MS1-3AMS1 signalMS1 ID max95/5 pctileRatioEstimates the dynamic range of the peptide signalsRatio of 95th over 5th percentile MS1 maximum intensity values for identified peptides (approximates dynamic range of signal)
MS1-3BMS1 signalMS1 ID maxMedianCountsEstimates the median MS1 signal for peptidesMedian maximum MS1 value for identified peptides
MS1-4AMS1 signalMS1 intensity variation for peptidesaWithin seriesPercentUsed to monitor relative intensity differences with a seriesAverage of between series intensity variations for identified peptides
MS1-4BMS1 signalMS1 intensity variation for peptidesaBetw/inRatioUsed to monitor relative intensity differences with a series compared with between seriesRatio of average intensity variation between series to average intensity variation within a series (low values indicate similarity between series)
MS1-5AMS1 signalPrecursor m/z − Peptide ion m/zMedianThMeasures the accuracy of the identificationsMedian real value of precursor errors
MS1-5BMS1 signalPrecursor m/z − Peptide ion m/zMean absoluteThMeasures the accuracy of the identificationsMean of the absolute precursor errors
MS1-5CMS1 signalPrecursor m/z − Peptide ion m/zppm medianppmMeasures the accuracy of the identificationsMedian real value of precursor errors in ppm
MS1-5DMS1 signalPrecursor m/z − Peptide ion m/zppm interQppmMeasures the distribution of the real accuracy measurementsInterquartile distance in ppm of the precursor errors
MS2-1MS2 signalIon injection times for IDsMS2 medianmsMS2 ion injection time
MS2-2MS2 signalMS2 ID S/NMedianRatioHigher S/N correlates with increased frequency of peptide identificationMedian S/N (ratio of maximum to median peak height) for identified MS2 spectra
MS2-3MS2 signalMS2 ID peaksMedianCountHigher peak counts can correlate with more signalMedian number of peaks in an MS2 scan
MS2-4AMS2 signalFraction of MS2 identified at different MS1 max quartilesID fract Q1FractionHigher fractions of identified MS2 spectra indicate efficiency of detection and samplingFraction of total MS2 scans identified in the first quartile of peptides sorted by MS1 maximum intensity
MS2-4BMS2 signalFraction of MS2 identified at different MS1 max quartilesID fract Q2FractionHigher fractions of identified MS2 spectra indicate efficiency of detection and samplingFraction of total MS2 scans identified in the second quartile of peptides sorted by MS1 maximum intensity
MS2-4CMS2 signalFraction of MS2 identified at different MS1 max quartilesID fract Q3FractionHigher fractions of identified MS2 spectra indicate efficiency of detection and samplingFraction of total MS2 scans identified in the third quartile of peptides sorted by MS1 maximum intensity
MS2-4DMS2 signalFraction of MS2 identified at different MS1 max quartilesID fract Q4FractionHigher fractions of identified MS2 spectra indicate efficiency of detection and samplingFraction of total MS2 scans identified in the last quartile of peptides sorted by MS1 maximum intensity
P-1Peptide identificationMS2 ID scoreMedianfvalHigher scores correlate with higher S/N and frequency of identificationMedian peptide identification score for all peptides; higher scores generally correlate with increased MS2 S/N
P-2APeptide identificationTryptic peptide countsIdentificationsCountTotal identifications correlate with high levels of peptide signals, performanceNumber of MS2 spectra identifying tryptic peptide ions (total “spectral counts”)
P-2BPeptide identificationTryptic peptide countsIonsCountA good overall performance measureNumber of tryptic peptide ions identified; ions differing by charge state and/or modification state are counted separately
P-2CPeptide identificationTryptic peptide countsPeptidesCountA good overall performance measureNumber of unique tryptic peptide sequences identified
P-3Peptide identificationPeptide countsSemi/tryp peptidesRatioIndicates prevalence of semitryptic peptides in sample; increasing ratios may indicate changes in sample or in sourceRatio of semi/fully tryptic peptide IDs
  • a Composite metrics that use values calculated over more than one series.