Table I Summary of LC-MS results, average and CV (in percentages), for unspiked yeast reference proteome

pept., peptide(s); Avg, average.

Total no. of yeast spectraTotal no. of yeast pept. sequencesYeast proteins identified usingCN50aPerformance metricsb
1 pept.2 pept.>2 pept.C-3AC-2ADS-2BIS-3B
AvgCVAvgCVAvgCVAvgCVAvgCVAvgCVAvgCVAvgCVAvgCVAvgCV
A. Study 8 (600 ng loaded on column)
    Instrument@Lab
        LTQ@737,6002.05,4011.33431.11815.35741.918,0392.710.11.5321.05,3741.20.40.4
        LTQ2@954,5680.53,2570.63214.51659.94041.127,4162.630.20.9372.05,2722.00.50.6
        LTQ-XLx@654,5485.53,9015.33637.01690.34775.822,3935.616.30.8322.54,9303.70.321.4
        Orbitrap@866,9141.35,4881.83442.01664.86021.417,7381.914.00.2410.96,8532.10.35.4
        OrbitrapO@655,9980.95,0231.83634.01908.75723.617,9591.619.41.0321.94,5692.20.34.7
        OrbitrapW@568,3361.07,2111.03133.21825.47240.813,6563.012.70.7351.45,6951.00.40.8
    Interlaboratory variation
        All LTQs5,57231.54,18626.33436.11715.048517.622,61620.718.947.3347.45,1924.40.417.0
        All Orbitraps7,08316.65,90719.53407.41797.063312.716,45114.715.420.13610.55,70617.40.35.6
B. Study 8 (120 ng loaded on column)
    Instrument@Lab
        LTQ@734,5836.53,5634.92785.511812.54293.226,2824.910.11.5271.34,0381.30.35.5
        LTQ2@952,12412.11,66513.92294.6955.323011.958,65614.232.12.5299.04,0818.60.46.0
        LTQ-XLx@652,3672.32,1281.92755.91177.32914.544,1576.916.41.7263.43,8763.40.31.6
        Orbitrap@865,6542.15,0811.93311.317412.75730.818,1591.913.90.5342.05,0751.40.217.1
        OrbitrapO@654,3831.13,8681.13472.51781.14743.222,6151.218.21.4252.53,3650.50.21.7
        OrbitrapW@566,4911.75,9022.03442.41875.96490.815,3050.112.50.8322.84,7622.70.30.2
    Interlaboratory variation
        All LTQs3,02544.82,45240.426110.511011.831732.143,03237.619.550.5277.33,9985.30.323.8
        All Orbitraps5,50919.34,95120.73412.51803.556515.618,69319.714.917.33013.44,40118.00.219.6
C. Study 6 SOP (unspiked yeast; 120 ng loaded on column)
    Instrument@Lab
        LTQ@732,9413.82,4343.43262.31469.83200.835,4743.420.80.3294.14,2384.50.316.0
        LTQ2@952,6064.12,1406.12645.411310.52848.343,9692.721.60.0301.34,1812.10.45.5
        LTQ-XLx@652,5713.42,1654.92871.81276.42918.141,25611.624.22.1277.54,1687.30.37.0
        Orbitrap@862,79414.02,62313.93873.31885.736812.930,35316.718.34.9239.23,3239.70.026.5
        OrbitrapO@655,0223.74,6274.43914.92126.65654.018,2185.219.91.5295.84,3786.00.31.6
        OrbitrapW@563,8616.73,5506.63447.81626.14925.425,0615.119.80.2262.83,7623.00.33.6
        OrbitrapP@654,4537.94,1167.33414.31653.04395.321,7778.715.52.1301.44,4893.90.42.1
    Interlaboratory variation
        All LTQs2,7067.52,2477.329210.812913.12986.440,23310.822.27.0285.84,1964.50.324.6
        All Orbitraps4,03323.63,72923.03667.418212.746617.923,85221.618.410.42712.33,98813.40.351.1
  • a CN50 values denote the copy number corresponding to 50% probability of detection for a randomly selected yeast protein. CN50 values are derived from logistic regression coefficients obtained by regressing yeast protein detection (yes/no) against log10 TAP copy number (12). CN50 is then converted to the copy number scale by taking 10 to the CN50 power. All mean and CV calculations are performed on the copy number scale. (CN50 values for all runs of all instruments are provided in supplemental Section H.)

  • b Four performance metrics (described in supplemental Section G and in Table II), designed to diagnose LC-MS issues, are provided for individual instruments. C-3A is median peak widths for unique peptides; C-2A is retention period over which 50% of the identified peptides eluted; DS-2B is the number of MS2 spectra produced over C-2A; IS-3B is the ratio of the number of 3+/2+ charge states for all peptide identifications.