During the last few years quantitative multiplexed proteomics has undergone a drastic transformation from an error prone, insensitive method to a robust technique that routinely delivers data with unprecedented quality and throughput (see Wühr et al 2012, McAlister et al. 2014, Wühr et al. 2015, Peshkin et al. 2015). The major advantage of multiplexed proteomics is that more samples (currently up to 10) can be compared in a single experiment with very high accuracy (coefficient of variation is less than 5%, if experiments are performed optimally). The principles of multiplexed proteomics, its inherent interference problem, and the recently developed methods that can overcome this problem are explained in this slide-show: Quantitative Multiplexed Proteomics: Principle, Problems, and Solutions.
Despite multiplexed proteomics recent increase in speed and sensitivity many important proteins are still below the limit of detection and quantification.To overcome this limitation we aim to develop new methods so that we can reliably detect and quantify very low abundant signaling molecules like transcription factors or kinases. Most importantly, we will further develop the complement reporter ion method. In its published form this method currently delivers the most accurate proteomic quantification data (see Wühr et al 2015, or slide-show above) . However, in its published form it is only about as sensitive as the MS3 method. With improvements on isobaric tags, sample preparations and instrumentation we believe that it will be possible to fully exploit the potential of the complement reporter ion method to reliably quantify proteins below the 1nM scale - the level at which the lowest known active transcription factors are expressed.