Supporting material figure captions Supporting material Figure 1. CE-MS results of day 2 that have not been normalized. Shown is average t m (A), t m %RSD (B), average A (C) and A %RSD (D) for every laboratory and target peptide. For average A (C), a logarithmic scale was used. The number of test result and the color code is the same as in Figure 2. Supporting material Figure 2. Outlier identification. Graphical and numerical statistical tests for outlier identification were done with the data of day 2. Results for within a laboratory (A) and between laboratories (B) variation of t m ’ (laboratories 1-11), and within a laboratory (C) and between laboratories (D) variation of %A (laboratories 1-9) are shown. For all suspect data exceeding the outlier limits in Mandel’s k and h plots Cochran’s and Grubb’s tests were applied, respectively. Only data exceeding the 1 % critical value in these numerical tests were considered as outliers and are labeled by ‘*’ in Mandel’s k or h plots.

Supporting material Figure 1 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ AB

CD

Supporting material Figure 2 straggler outlier Cochran's test (p=11, n=6) 5 % critical value: % critical value: labpeptidevalue outlier (*)! * * * * * * t’ m A

Supporting material Figure 2 straggler outlier straggler outlier no outlier! B t’ m

Supporting material Figure 2 straggler outlier Cochran's test (p=9, n=6) 5 % critical value: % critical value: labpeptidevalue outlier (*)! * * * %A C

Supporting material Figure 2 straggler outlier straggler outlier Grubb’s test (p=9) 5 % critical value: % critical value: labpeptidevalue no outlier! %A D

Peptide no. Migration time (t m )Peak area (A) General mean (min) Repeatability (%RSD) Reproducibility (%RSD) Repeatability (%RSD) Supporting material Table 1. Precision results for data that have not been normalized. Day 2 data of laboratories 1-11 and 1-9 were used to calculate results for t m and A, respectively. For A, only repeatability results are shown.