2023011-RES-ACAN - Orbitrap Astral LC/MS System ACAN

BACKGROUND:
Notice is hereby given by the University of Ottawa of the intent to enter into a contract with Thermo Fisher Scientific  to purchase a Orbitrap Astral mass spectrometer (MS) for the purpose of identification and quantification of peptides and modified peptides at high mass accuracy and precision for metaproteomics and proteomics analysis.

PROCESS:
Suppliers who consider their equipment functional, successfully tested, readily available and fully compliant may submit in writing a statement of specifications to the contact person identified in this Notice, on or before the closing date of this Notice. In the statement of specifications, the supplier must unequivocally demonstrate how their equipment, at minimum, equals, or exceeds the stated requirements.

If no other supplier submits a statement of specifications, on or before the closing date of this Notice, the competitive requirements of the University Of Ottawa will be considered having been met.

Following notification to any suppliers not successful in unequivocally demonstrating that their statement of specifications equals or exceeds the requirements set out in this Notice, the contract may then be awarded to the pre-identified supplier.

Date of issue: November 17, 2023
Closing Date:    December 12, 2023, at 3:00:00 P.M. EST

INTENDED USE:
A goal of the research program is the development and application of metaproteomics, proteomics and post-translation analysis from clinical samples, animals, and cultures. The mass spectrometer system will allow the study of peptides and proteins from complex metaproteomic, proteomics, and peptidomic samples.
The instrument will be used as follows:

• Identification and quantitation of peptides and proteins derived from complex microbiome, human and animal samples.
• Data independent acquisition from metaproteomics and proteomics samples.
• High-throughput operations working 24 hours a day, 7 days a week.

1. 1. The mass spectrometer must provide high-resolution in MS and MSMS.
   2. The mass spectrometer must be capable of on-the-fly data acquisition and processing.
   3. The mass spectrometer must be able to perform Higher Energy Collisional Dissociation (HCD) of peptides.
   4. During the transition between MS and MSMS, the mass spectrometer must be able to isolate the parent down to 0.4Da
   5. CSA certification to meet Ontario standards must be included (CE is not an accepted equivalent).
   6. Supplier must supply, install and act as single point of contact for all warranty and service relating to the instrument.

1. 1. MS/MS: Orbitrap analyzer MS/MS sensitivity: 50 fg Reserpine on column yields S/N 100:1 RMS or better.
   2. tSIM: 50 fg Reserpine on column yields S/N 150:1 RMS or better

1. 1. 480,000 FWHM at m/z 200 at an acquisition rate of 1 Hz.

6. M/z range
   1. 40 to 6,000 m/z (Astral and Orbitrap analyzer detection)
   2. 500 to 8,000 m/z (Orbitrap analyzer detection with optional Biopharma Mode)

7. Scan Functions
   1. The Astral analyzer must acquire and display Selected Ion Monitoring (SIM) scan data for monitoring selected ions for target compound analysis at a maximum rate of 140 Hz.
   2. The Astral analyzer must acquire and display Full Scan MS/MS spectra to produce Full Scan product ion spectra at a maximum rate of 200 Hz in data independent acquisition mode

8. Advanced Functions
   1. The mass spectrometer must have Automatic Gain ControlTM (AGC) to automatically control ion injection times for optimized ion populations across the entire chromatographic peak.

1. 2. The mass spectrometer must have an Advanced Precursor Determination (APD) algorithm to improve charge state determination, increasing the number of precursors available for data-dependent analysis.

1. 3. The mass spectrometer must have precursor prioritization logic allowing sorting of MS2 precursors based on their m/z and/or charge and/or abundance.

1. 4. The mass spectrometer must have Dynamic ExclusionTM capabilities to temporarily exclude an ion while allowing acquisition of MS/MS spectra for lower abundant co-eluting ions.

1. 5. The mass spectrometer must have Normalized Collision EnergyTM capabilities to automatically compensate for the mass and charge dependent energy deposition and provide instrument-to-instrument reproducibility.

1. 6. The mass spectrometer must be able to perform data dependent MS/MS acquisitions based on the information obtained from an earlier MS spectrum (Master Scan).

9. Compatibility
   1. The MS must be compatible with the Tandem mass tags (TMT) chemistry.

• Thermo Fisher Scientific mass spectrometers are the only mass spectrometers on the market that are compatible with the University’s existing MetalAb and iMetaLab software for metaproteomic analysis. This software was developed in-house by the University over the years based on data files generated using Thermo Fisher MS systems. A change in vendor would necessitate substantial recoding of the existing software and modifications to its algorithms depending on the type and quality of the MS results.  Moreover, we have amassed a substantial inventory of spare parts that are fully compatible with our prospective acquisition.
• Additionally, the University’s proteomic procedures (RapidAIM) were also designed using Thermo Fisher mass spectrometers. Proteomic operations run 24 hours a day, 7 days a week. Incorporating an alternative vendor’s system into the lab set up would require substantial modifications to sample handling and analysis procedures, as well as disruption of continuous operations. To facilitate transfer of already established procedures and to reduce the time required for training and optimization, the mass spectrometer must be compatible with existing procedures and hardware. This is particularly important as the instrument will be incorporated in our ongoing clinical intervention trials that require rapid data generation from patient samples to guide nutritional interventions.
• Thermo Fisher’s Orbitrap Astral mass spectrometer is controlled using XCalibur software and can work seamlessly with the current proteomic software and procedures. Importantly, the MS data acquired from our previous in-house instruments will remain directly comparable to the data generated by our latest acquisition, maintaining continuity and consistency in our research efforts.