Table II Variation of metrics in replicate analyses of egg yolk protein digest

Avg., average; intra/inter, intraseries/interseries; med., median; pep(s)., peptide(s); IQ, interquartile; abund., abundance; IDs, identifications; ID'd, identified; fract., fraction.

MetricAvg. valueAvg. intraseries %dev%Dev of intraseries %devInterseries %devRatio avg. intra/inter
C-1A (bleed −4 min)0.008234.883.942.871.23
C-1B (bleed +4 min)0.14994.843.980.630.13
C-2A (IQ pep. RT period)11.562.431.40.30.12
C-2B (peptides/min)41.92.591.210.790.31
C-3A (med. peak width)11.340.351.920.140.41
C-3B (IQ for peak widths)
DS-1A (oversampling; once/twice)3.314.352.523.110.71
DS-1B (oversampling; twice/thrice)2.517.241.880.250.03
DS-2A (MS1 scans over C-2A)345.31.067.632.532.39
DS-2B (MS2 scans over C-2A)1,8992.391.450.660.27
DS-3A (med. MS1 max/MS1 sampled all IDs)2.482.442.492.010.82
DS-3B (med. MS1 max/MS1 sampled for bottom 50% by abund.)1.441.451.411.080.75
IS-1A (MS1 >10× jumps)00000
IS-1B (MS1 >10× falls)00000
IS-2 (med. precursor m/z)689.610.322.030.521.66
IS-3A (ratio IDs 1+/2+)0.2631.651.984.983.02
IS-3B (ratio IDs 3+/2+)0.3931.291.914.183.24
IS-3C (ratio IDs 4+/2+)0.1051.941.736.463.33
MS1-1 (ion injection (ms) for IDs)5.63.17013.864.36
MS1-2A (S/N)317.81.771.426.63.73
MS1-2B (med. TIC/1e3 over C-2A)5,470.61.7611.9815.318.68
MS1-3A (dynamic range 95th/5th for IDs)
MS1-3B (med. MS1 signal for IDs)66,26522.3713.336.66
MS2-1 (ion injection (ms) for IDs)1000000
MS2-2 (S/N for IDs)220.51.445.152.041.41
MS2-3 (med. no. peaks for IDs)314.61.841.612.461.34
MS2-4A (fract. ID'd Q1)0.7481.621.261.851.15
MS2-4B (fract. ID'd Q2)0.5851.
MS2-4C (fract. ID'd Q3)0.4531.481.283.522.37
MS2-4D (fract. ID'd Q4)0.3683.791.546.171.63
P-1 (med. f-value score for IDs)0.8910.243.910.381.54
P-2A (total IDs)2,767.
P-2B (unique ion IDs)1,260.50.591.71.62.71
P-2C (unique peptide IDs)859.50.551.850.871.59
P-3 (semi/fully tryptic peps.)0.133.331.423.280.99
Median values1.761.72.21.29