@article{111971,
  author = {Matthew Sonnett and Eyan Yeung and Martin W{\"u}hr},
  title = {Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster},
  abstract = { Quantitative analysis of proteomes across multiple time points, organelles, and<br>perturbations is essential for understanding both fundamental biology and disease<br>states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous<br>measurement of peptide abundances across several different conditions. These<br>multiplexed approaches are promising in principle because of advantages in throughput<br>and measurement quality. However, in practice existing multiplexing approaches suffer<br>from key limitations. In its simple implementation (TMT-MS2), measurements are<br>distorted by chemical noise leading to poor measurement accuracy. The current state-ofthe-<br>art (TMT-MS3) addresses this, but requires specialized quadrupole-iontrap-Orbitrap<br>instrumentation. The complement reporter ion approach (TMTc) produces high accuracy<br>measurements and is compatible with many more instruments, like quadrupole-<br>Orbitraps. However, the required deconvolution of the TMTc cluster leads to poor<br>measurement precision. Here, we introduce TMTc+, which adds the modeling of the MS2-<br>isolation step into the deconvolution algorithm. The resulting measurements are<br>comparable in precision to TMT-MS3/MS2. The improved duty cycle, and lower filtering<br>requirements make TMTc+ more sensitive than TMT-MS3 and comparable with TMT-MS2.<br>At the same time, unlike TMT-MS2, TMTc+ is exquisitely able to distinguish signal from<br>chemical noise even outperforming TMT-MS3. Lastly, we compare TMTc+ to quantitative<br>label-free proteomics of total HeLa lysate and find that TMTc+ quantifies 7.8k versus 3.9k<br>proteins in a 5-plex sample. At the same time the median coefficient of variation<br>improves from 13\% to 4\%. Thus, TMTc+ advances quantitative proteomics by enabling<br>accurate, sensitive, and precise multiplexed experiments on more commonly used<br>instruments. },
  year = {2018},
  journal = {Analytical Chemistry},
  url = {https://pubs.acs.org/doi/abs/10.1021/acs.analchem.7b04713},
  language = {eng},
}