Table II Metrics for differential diagnosis of LC-MS performance issues

ID'd, identified; peps, peptides; dev, deviation; ID, identification; S/N, signal to noise ratio.

Metric codeaDescription of metricaStudy 6 (unspiked yeast, 120 ng)Study 8 (120 ng)Study 8 (600 ng)
MeanMean intralab %devInterlab %devMeanMean intralab %devInterlab %devMeanMean intralab %devInterlab %dev
A. LTQs
    Chromatography
        C-2ARetention period over which 50% of peps were ID'd (min)28.43.04.827.23.46.133.71.48.3
        C-2BPeptide ID rate during C-2A46.44.45.551.53.130.061.71.826.3
        C-3AMedian peak width for unique peps (s)22.20.68.019.51.458.318.90.854.6
    Dynamic sampling
        DS-1Median ratio of peps identified once/twice8.37.216.17.44.335.06.92.841.6
        DS-1BMedian ratio of peps identified twice/thrice5.112.216.66.610.224.65.57.022.4
        DS-2ANo. MS1 scans taken over C-2A541.02.22.6715.73.821.8959.61.622.0
        DS-2BNo. of MS2 spectra produced over C-2A4,195.73.20.93,998.23.32.75,192.21.74.5
    Ion source
        IS-1ACount where MS1 signal jumped >10× in adjacent full scans0.00.00.00.00.00.03.766.70.0
        IS-1BCount where MS1 signal fell >10× in adjacent full scans0.00.00.00.00.00.04.066.70.0
        IS-2Median precursor m/z for IDs637.20.60.4612.50.84.2670.10.35.2
        IS-3BRatio of 3+/2+ for all IDs0.37.026.90.33.127.00.45.716.8
    MS1
        MS1-1MS1 ion injection time (ms)3.613.632.95.21.944.81.30.043.3
        MS1-2AMedian MS1 S/N value for spectra up to and including C-2A127.215.039.5104.19.143.9159.26.236.5
    MS2
        MS2-2Median S/N for ID'd MS2 spectra62.02.813.882.13.273.2142.81.251.8
    Peptide identification
    P-2CNo. of unique tryptic peps2,566.22.23.92,717.94.827.63,988.41.920.4
Median3.05.53.227.01.822.0
B. Orbitraps
    Chromatography
        C-2ARetention period over which 50% of peps were ID'd (min)27.13.312.630.11.915.336.31.112.1
        C-2BPeptide ID rate during C-2A65.63.713.273.22.417.672.61.926.3
        C-3AMedian peak width for unique peps (s)18.41.611.214.90.720.015.40.523.2
    Dynamic sampling
        DS-1Median ratio of peps identified once/twice17.83.620.521.15.528.719.15.318.7
        DS-1BMedian ratio of peps identified twice/thrice7.511.226.66.27.75.75.47.77.5
        DS-2ANo. of MS1 scans taken over C-2A529.03.311.3656.92.211.0902.20.714.0
        DS-2BNo. of MS2 spectra produced over C-2A3,988.04.013.74,400.81.220.75,705.61.320.0
    Ion source
        IS-1ACount where MS1 signal jumped >10× in adjacent full scans32.3133.30.00.00.00.00.00.00.0
        IS-1BCount where MS1 signal fell >10× in adjacent full scans24.7133.30.00.00.00.00.00.00.0
        IS-2Median precursor m/z for IDs608.60.93.9593.10.62.1639.60.33.3
        IS-3BRatio of 3+/2+ for all IDs0.36.356.40.24.821.20.32.75.0
    MS1
        MS1-1MS1 ion injection time (ms)85.75.039.3109.36.028.029.84.433.7
        MS1-2AMedian MS1 S/N value for spectra up to and including C-2A481.97.537.7574.43.427.6652.02.416.0
    MS2
        MS2-2Median MS2 S/N for IDs66.65.034.176.45.033.4143.62.425.3
    Peptide identification
        P-2CNo. of unique tryptic peps3,463.84.222.84,329.31.826.85,069.10.822.4
Median4.213.72.220.01.316.0
  • a A series of metrics (see supplemental Section G and the accompanying study by Rudnick et al. (32)) was computed (from the historical benchmarking data sets described herein) to demonstrate average values obtained for both the LTQ instruments (part A) and the Orbitrap instruments (part B). Intra- and interlaboratory variation is also shown.