Thermo Fisher Orbitrap Mass Spectrometry Instrumentation

The University of Alberta is providing an Advanced Contract Award Notice to contract with Thermo Fisher Scientific to acquire two refurbished Mass Spectrometry instruments that are not available from alternate manufacturers. This same instrumentation was acquired previously via an open bidding process resulting in only one Proposal, Ref # RFP 2022-0163. Two more of these instruments were acquired with no challenges to the Sole Source justification, Ref # ACAN 2023-0082. These processes have verified that this is indeed a sole source. Technical Justification of sole source The detailed structural information needed for this project will necessitate MS2, MS3, and MSN fragmentation datasets to be acquired at over 240,000 at 200m/z. ● The new instruments will need to be able to measure 16-plex TMT labeling samples to facilitate high sensitivity single cell proteomics. ● To conduct this research, the HRMS must be capable of resolving mass shifts from complex mixtures of co-eluting isotopomers of carbon, nitrogen, and hydrogen. Isotopomers must be identified by exact mass of the parent ion. ● It is our understanding that they are the only vendor that can supply systems that are compatible with our existing instrumentation and meet our mandatory requirements (e.g. both to perform singlecell proteomics as well as deep proteome-wide analysis using micrograms of material on the same instrument, which are vital to perform our specific research. Mandatory equipment specifications include, however, may not be limited to:● Resolving power up to 480,000 FWHM at m/z 200 and isotopic fidelity up to 240,000 FWHM. ● Able to scan up to 45 Hz in MS2 pAGC controlled data dependent experiment using a resolutionsetting of 7,500 at m/z 200. ● The infrastructure needs to support MS3 fragmentation capability● Both instruments need to be capable of performing TMT labeling experiments, such as 16plex TMT.Only Thermo instruments are currently capable of acquiring such data ● Mass accuracy must be better than 1 ppm with internal calibration. ● Ability to perform single cell proteomics as well as deep proteome-wide analysis using micrograms of material on a single instrument ● The mass spectrometer platform must be compatible with existing LC front ends and MS instruments through seamless software connectivity.T here is an absence of competition for technical reasons: Thermo Fisher is the only vendor that is able to supply a system capable of achieving all the technical requirements for the project on the same instrument. We have researched the market, and the only other company with the potential to meet the requirements is Bruker, and their instruments are not able to meet all requirements, even at a much higher price point ● Individual Bruker instruments can do either single cell proteomics OR full proteome analysis from picogram to microgram amount. They do not have an instrument that can do both on a single instrument. In order to obtain most (but not all) of the requirements through Bruker we would have t opurchase 2 separate instruments, each that would cost as much or more than the Thermo package. ● The Thermo Fisher instruments that we are requesting can each do single cell or full proteomeanalysis with inputs from 1 cell to 1 microgram. Bruker has 1 instrument that can accommodate input amounts ranging from 1 cell – 10 nanograms, but to go above 10 nanograms input would require a different instrument.● The Bruker instruments are not ideal for the project: because a) the Bruker instruments are unable to do MS3 fragmentation, and b) the Bruker instruments are unable to do multiplex TMT single celllabeling, both of which are project requirements To ensure compatibility with existing products: we recently purchased an Orbitrap Fusion Lumosinstrument, that makes use of accessories (such as FAIMS, ion generator, analysis software, and Proteome Discoverer software) that can be interchanged with the requested items.● By having instruments that are able to interchange input and processing attachments and software we reduce the potential for down time that would affect key projects, as well as increase the flexibility of the suite of instruments in the lab by enabling the attachment of different front-end inputs.