Smart Targets

Want to perform a targeted protein assay in human tissue but are unsure your target is abundant enough or supported by good commercial antibodies? We do too, so we sought to make this planning step easier. By combining publicly accessible data on proteins in tissue, we hope you can make smart target decisions.

Data Sources

Protein Abundance from Bottom-up Proteomics

We derive protein abundance in human tissue from two bottom-up proteomics (BUP) studies. The Human Protein Atlas Consortium performed label-free BUP on 29 tissue samples.¹ Tryptic peptides were analyzed by a Q-Exactive Plus mass spectrometer coupled to nanoflow liquid chromatography. Label-free quantitation was performed with MaxQuant using the iBAQ approach. In a separate study, the Genotype-Tissue Expression (GTEx) Consortium performed quantitative bottom-up proteomics of 201 samples from 32 different tissue types from 14 healthy donors using tandem-mass-tag (TMT) 10plex/MS3 quantitation.² In each TMT10plex run, eight tissue samples and two pooled reference samples were included. Since direct comparison of protein abundances across BUP studies is difficult, we instead chose to use the more transferable normalized rank to compare abundances. Normalized abundances range 0 to 1 where 1 corresponds to the most abundance protein and proteins not detected have a normalize rank of 0.

References

1. Wang, D.; Eraslan, B.; Wieland, T.; Hallström, B.; Hopf, T.; Zolg, D. P.; Zecha, J.; Asplund, A.; Li, L.; Meng, C.; Frejno, M.; Schmidt, T.; Schnatbaum, K.; Wilhelm, M.; Ponten, F.; Uhlen, M.; Gagneur, J.; Hahne, H.; Kuster, B. A Deep Proteome and Transcriptome Abundance Atlas of 29 Healthy Human Tissues. Mol Syst Biol 2019, 15 (2), e8503. https://doi.org/10.15252/msb.20188503.

2. Jiang, L.; Snyder, M. P. A Quantitative Proteome Map of the Human Body. Cell 2020, 183 (1), 269-283.e19. https://doi.org/10.1016/j.cell.2020.08.036.