Figure 2.

To assess the deviation in retention times for matched samples, we ran two identical nano-LC–MS/MS experiments 10 days apart on the same LC–MS system. (A) The relationship between apex retention times of the 7589 unique peptides common between experiments displays a high degree of linearity (R² = 0.9989) but a skewed slope and nonzero intercept (m = 1.033; b = −0.647). (B) Average deviation from unity was nearly a minute off (μ = −0.805 min), with a broad distribution over 2 min wide. (C) Peptides ranked by their relative elution order exhibit a normal distribution around zero (μ = −1.097).