High performance mass spectrometry: applications for the Cambridge biological sciences community

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The Cambridge Centre for Proteomics (CCP) is a well-established mass spectrometry core facility in the Department of Biochemistry, University of Cambridge. CCP primarily offers proteomics services. Proteomics is the study of all proteins in a sample which could be proteins extracted from plant leaves, human parasites, bacteria, fungi and clinical samples such as plasma and urine. Researchers generally wish to know what proteins are present in their samples, but importantly the abundance of the proteins and how this changes in response to stress, drug treatment or disease state. Also, researchers may want information on the post translational modifications in the proteome and how this changes upon perturbation, with phosphorylation being the most popular modification studied.CCP uses mass spectrometry as its major tool to interrogate the proteome. This instrument measures the mass of ions introduced typically via a liquid chromatography device, together referred to as LC-MS. From these mass measurements, both the identity of proteins present and their amount can be calculated. Mass spectrometry can also be used to characterise other biomolecules such as sugars, lipids and nucleic acids. CCP is a very popular and busy facility. It currently has access to two mass spectrometers. Its Thermo QExactive is 9 years old and is very unreliable. It is covered by a contract to fix it if it breaks, but its manufacturer will discontinue the contract for this instrument in the next 2 years. This instrument is insensitive compared with more modern instruments. CCP also has access to 55% of the time of a 5-year-old Thermo Fusion Lumos Tribrid, which is more sensitive and a very good instrument to carry out a form of quantitative proteomics known as isobaric tagging. This instrument lacks sensitivity compared with newer instruments and is able to separate ions introduced into the instrument based on their mobility in the gas phase. Together, these instruments do not provide CCP with the capacity to process samples submitted by its users.The need for a more up to data mass spectrometer has become critical. CCP supports its staff and equipment through fee for service and grant funding. CCP simply cannot sustain its services and will be faced with significant cuts. Moreover, it has increasing demands from it users including those with limited sample amounts or who need more elaborate characterisation of post translational modification.Other facilities in Cambridge are reserved for the institutes in which they sit and have no spare capacity to assist CCP.The requested LC-MS, Bruker TimsTOF Pro 2 is much more sensitive than CCP's current instruments. It processes samples more quickly and hence will increase the capacity of CCP and reduce sample turnround significantly. It also is equipped with an ion mobility functionality which assists in both sensitivity and distinguishing very similar molecules based on their cross sectional area as gaseous ions. This instrument excels at quantitative label free proteomics approaches that do not require the use of isobaric tagging, and is highly complementary to what is currently available here. Its ion mobility function also helps distinguish other classes of biomolecules with similar masses but subtly different behaviours within ion mobility. There is no similar LC-MS instrument in CCP or indeed in Cambridge.This LC-MS system will support all CCP users from across the University of Cambridge, outside research institutes, users form other academic institutions and users from industry. The proposed equipment, will not only allow them to carry out their planned work, but enable new avenues of research which have been hitherto impossible with existing instrumentation. The support from the University of Cambridge means that this proposal requests less than half of the cost of the TimsTOF Pro 2, and thus represents value for money.