This case-study is a subset of the data of the 6th study of the Clinical Proteomic Technology Assessment for Cancer (CPTAC) (Paulovich et al. 2010). In this experiment, the authors spiked the Sigma Universal Protein Standard mixture 1 (UPS1) containing 48 different human proteins in a protein background of 60 micro g/micro L Saccharomyces cerevisiae strain BY4741.
Five different spike-in concentrations were used:
6A: 0.25 fmol UPS1 proteins/micro L
6B: 0.74 fmol UPS1 proteins/micro L
6C: 2.22 fmol UPS1 proteins/micro L
6D: 6.67 fmol UPS1 proteins/micro L
6E: 20 fmol UPS1 proteins/micro L
Three replicates are available for each concentration.
The data were searched with MaxQuant version 1.5.2.8 (Cox et al. 2008) including matching between runs. Detailed search settings were described in Goeminne et al. (2016).
Three files are readily available as tab-delimited spreadsheets:
cptac_a_b_peptides.txt: triplicates from lab 3 for groupes 6A and 6B.
cptac_a_b_c_peptides.txt: triplicates from labs 1, 2 and 3 for groupes 6A, 6B and 6C.
cptac_peptides.txt: triplicates from labs 1, 2, and 3 for all groups.
Paulovich, Amanda G, Dean Billheimer, Amy-Joan L Ham, Lorenzo Vega-Montoto, Paul A Rudnick, David L Tabb, Pei Wang, et al. 2010. Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance. Mol. Cell. Proteomics 9 (2): 242–54.
Cox, J, and M Mann. 2008. MaxQuant Enables High Peptide Identification Rates, Individualized p.p.b.-Range Mass Accuracies and Proteome-Wide Protein Quantification. Nat Biotechnol 26 (12): 1367–72. https://doi.org/10.1038/nbt.1511.
Goeminne, LJ, Gevaert K and Clement, L. 2016. Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics, Mol Cell Proteomics, 15:2 657-668.