LC-MS/MS system with high-resolution mass spectrometer and nano-UHPLC - 2/2

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The demand for high-end proteome analysis on the university campus Tübingen has increased significantly over the past few years. This is mainly due to the fact that the technology of mass spectrometry-based proteome analysis has dramatically advanced and now offers a great variety of analytical options for many areas of bio-medical research. The current instrumentation has been in operation for more than 8 years and has been heavily used, the downtime due to maintenance has significantly increased over the last two years. This has resulted in a waiting queue of more than two months for samples to be analysed in our core facility, and unfortunately, we had to reject sample measurements due to increasing demand and rising projects for the medical campus of Tübingen. Moreover, the technology is outdated, not satisfying current needs for in-depth proteomic analysis of small and complex samples and therefore needs to be replaced with a state-of-the-art instrument. Therefore, we request to replace this mass spectrometer, with a new instrument. As we approach an increasing number of projects with very limited sample sizes derived of for example endogenous protein complexes, primary tissue as well as of induced pluripotent stem cell-based origin, where a highly sensitive device with high scan rates and ultra-high resolution is needed. Furthermore, to increase both the throughput and reproducibility, the new instrument has to allow data-independent acquisition and, for validation purposes and to detect specific proteins in complex samples, targeted analysis of specific peptides. In particular, targeted analysis is essential for translational research as well as for validation in large sample numbers. Additionally, for separation of the complex mixtures, an ultra-high performance liquid chromatography system needs to be connected to the mass spectrometer which allows a reproducible separation of complex peptide mixtures at high resolution and nano flow rates. The set-up we are requesting is a combination of a nano ultra-high performance liquid chromatography system, coupled with a ion-mobility unit connected to an ultra-high resolution mass spectrometry machine. This combination is a perfect setup to achieve a precise retention time, limit sample dispersion and system carryover, reduce spectral noise background and deliver sensitive and accurate identification and quantification of peptides at a high resolution.