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 Q Exactive HF-X mass spectrometer 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: January 29, 2018
Closing Date: February 23, 2018, 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.
FUNCTIONALITY:
The equipment must conform to the following specifications:
Mass Spectrometer: Minimum requirements
1. General
1.1 The mass spectrometer must provide high-resolution in MS and MSMS.
1.2 The mass spectrometer must be capable of on-the-fly data acquisition and processing.
1.3 The mass spectrometer must be able to perform Higher Energy Collisional Dissociation (HCD) of peptides.
1.4 During the transition between MS and MSMS, the mass spectrometer must be able to isolate the parent down to 0.4Da
1.5 CSA certification to meet Ontario standards must be included (CE is not an accepted equivalent).
1.6 Supplier must supply, install and act as single point of contact for all warranty and service relating to the instrument.
Performance Specifications
The instrument must meet the following performance specifications:
2. Sensitivity
2.1 MS/MS: 100 fg Reserpine on column yields S/N 150:1 or better.
3. Mass Resolution
3.1 Maximum resolution of 240,000 (FWHM) at m/z 200 for all scan modes and both polarities.
3.2 Capable of performing TMT with high resolution 45,000 (FWHM) resolution setting at m/z 200.
4. Scan speed
4.1 The mass spectrometer must be capable of 40 scans per second in Full MS Scan or SIM mode.
5. Mass Accuracy
5.1 < 3 ppm RMS – with external calibration over 24 h and without any kind of mass recalibration.
5.2 < 1 ppm RMS – with internal calibration.
6. M/z range
6.1 The mass spectrometer must be able to scan from m/z=50 – 6,000.
7. Scan Functions
7.1 The instrument must be programmable to set-up automated different MS based experiments using a graphical user interface.
7.2 Must acquire and display Full Scan mass spectra.
7.3 Must acquire and display Selected Ion Monitoring (SIM) scan data for target compound analysis.
7.4 Must acquire and display Full Scan MS/MS spectra.
7.5 Must acquire and display Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM) like data sets - Parallel Reaction Monitoring PRM.
7.6 Multiplexed SIM mass spectra of up to 10 precursor ions.
7.7 Multiplexed MS/MS mass spectra of up to 10 precursor ions.
7.8 Timed MS/MS for scheduled data acquisition of target compound fragment spectra.
7.9 “Data Independent Acquisition” capability.
8. Advanced Functions
8.1 Must be able to exclude ions dynamically, while allowing MS/MS spectra acquisition other precursors;
8.2 Must have ability to control the Collision Energy to automatically compensate for the mass and charge
8.3 Must be able to change the collision energy allowing multiple activation energies to be applied to the same precursor.
9. Compatibility
9.1 The MS must be compatible with the TMT chemistry.
9.2 The MS must be compatible with the MetaLAb and IMetaLab metaproteomic platform.
Justification of Pre-Selected Supplier:
Supplier:
Thermo Fisher Scientific (Mississauga) Inc., 2845 Argentia Road, Unit 4, Mississauga, ON L5N 8G6
Justification:
- 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.
- Additionally, the University’s proteomic procedures 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.
- Thermo Fisher’s Q-Exactive HF-X mass spectrometer is controlled using XCalibur software and can work seamlessly with the current proteomic software and procedures.
