Single-shot, high resolution and in-depth quantification platform for mammalian cell proteomes enables rapid systems analysis of ER stress

Mass spectrometry (MS) based shotgun proteomics is widely applied to characterize changes in the proteome between different cellular states, providing a basis for systems biology. So far, in-depth proteomics analysis has required elaborate fractionation and thus extensive MS analysis time or alternatively restriction to specific proteins of interest. This is undesirable for unbiased (discovery type) biological studies that involve multiple samples and multiple time points. Recently we showed that the near complete yeast proteome can be mapped in single-shot fashion by combining the quadrupole Orbitrap (Q Exactive) with high performance and high resolution chromatography with long columns (Nagaraj et al. MCP 2012). Here we develop our single-shot platform towards systems biology studies in human cell lines. We use this platform to study the dose dependent proteome changes in HeLa cells upon ER stress induced by treatment with tunicamycin.