Bruker timsTOF fleX: A Dual-Source Spatial and Molecular Omics Platform Uniquely
Solicitation number 2025012-RES-ACAN
Publication date
Closing date and time 2025/12/15 12:00 EST
Last amendment date
Description
BACKGROUND:
Notice is hereby given by the University of Ottawa of the intent to enter into a contract with Bruker Ltd to procure a Mass Spectrometer as specified below.
PROCESS:
Suppliers who consider their equipment functional, successfully tested, commercially available and fully compliant to the ACAN Mandatory Requirements 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 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 18th, 2025
Closing Date: December 15th, 2025, at 12:00:00 P.M. Eastern Standard Time
INTENDED USE:
The mass spectrometer will be used in the Metabolomics Core Facility to develop and apply spatial metabolomics, proteomics, post-translational analysis, and metaproteomics across clinical tumors, PDX/animal models, organoids, microbiome-associated cancers, and culture systems. There are planned studies on tumor microenvironment heterogeneity, drug distribution and biomarker validation using limited clinical and PDX tissue.
The mass spectrometer will be available to all members of the core facility, as well as other internal and/or external research teams interested in using the instrument for research purposes.
GENERAL DESCRIPTION AND PRIMARY CAPABILITIES:
The Bruker timsTOF fleX is a dual-source mass spectrometer offering comprehensive functionality through the integration of Trapped Ion Mobility Spectrometry (TIMS) and Time-of-Flight (TOF) technologies. The system supports both Electrospray Ionization (ESI) and Matrix-Assisted Laser Desorption Ionization (MALDI), enabling advanced workflows such as MALDI-guided SpatialOMx®. The timsTOF fleX is a dual-TIMS analyzer that delivers a near 100% duty cycle. Ions are accumulated in parallel in the first TIMS cell, then separated in the second cell based on their collisional cross section. This configuration supports Parallel Accumulation–Serial Fragmentation (PASEF®, US Patent US11047828B2), significantly improving MS/MS spectral quality by reducing chimeric spectra through ion mobility separation and enhancing signal-to-noise ratios via efficient ion accumulation.
The system also features an integrated smartbeam™ 3D MALDI laser, enabling true square-pixel imaging with high spatial resolution thanks to a focused 5 µm laser diameter. Switching between ESI and MALDI is seamless and controlled directly through the acquisition software, allowing flexible transitions between workflows.
To further streamline MALDI imaging, Bruker offers IntelliSlides™, single-use slides designed to automate and simplify sample setup. IntelliSlides™ are single-use consumables that incorporate permanent inscriptions indicating optimal placement of samples, registration marks (also known as teach marks or fiducials) that make automated sample registration possible, as well as provide a unique slide identifier for software tracking. They are compatible with standard histology and microscopy techniques. IntelliSlides™ increase both efficiency and reproducibility, making high-throughput MALDI imaging accessible to users at all experience levels.
With its high sensitivity, robust automation, and dual-source flexibility, the Bruker timsTOF fleX is ideally suited for a wide range of applications, from basic biological research to pre-clinical proteomics, metabolomics, and spatial omics imaging.
Mandatory Requirements - Mass Spectrometer:
1. General
1.1 The mass spectrometer must provide mass resolution of 60,000 at 1,222 m/z in Mass Spectrometry (MS) and Tandem Mass Spectrometry (MSMS).
4.1 Must be capable of 50 Hz or better for MS
4.2 Must be capable of 50 Hz or better for MS/MS (profile and peak detected spectra to disk)
4.3 Must be capable of up to 300 Hz MS/MS of mobility resolved precursors ions.
5. Mass Accuracy
5.1 Must be capable of < 0.8 ppm when calibrated internally, ESI mode
5.2 Must be capable of 2 ppm or better when calibrated externally, ESI mode
6. M/z range
6.1 20 – 20,000 m /z
7. Scan Functions
Justification of Pre-Selected Supplier:
Supplier: Bruker Ltd
Justification:
Bruker Ltd’s timsTOF fleX MALDI-2 uniquely integrates high-sensitivity MALDI-2 post-ionization, TIMS (ion mobility) separation, and iprm-PASEF multiplexed MS/MS imaging within a single platform. These combined capabilities enable near single-cell spatial metabolomics, isomer-aware lipid and small-molecule annotation, and multiplexed MS/MS validation in a single pass; capabilities that are required for the Metabolomics Core Facilities’ planned studies on tumor microenvironment heterogeneity, drug distribution, and biomarker validation using limited clinical and PDX tissue.
The specific capabilities that Bruker’s proprietary technologies offer are as follows:
MALDI2:
Allows for the visualization of subtle metabolic gradients across tumors and treatment zones that would otherwise remain undetected.
MALDI-2 substantially increases ion yields for many low-abundance small molecules and lipids versus conventional MALDI. That sensitivity boost is what enables detection of subtle spatial concentration gradients that fall below the detection limits of standard MALDI imaging. Without MALDI-2, many biologically relevant metabolites (low abundance, poor ionization efficiency) will not be detectable in single runs, preventing confident mapping of micro-gradients.
Specific research objectives this enables at uOttawa includes:
1. Single-cell / near single-cell spatial metabolomics: visualize metabolite distributions within micro-regions of tumors that reflect cellular heterogeneity and metabolic microenvironments.
2. Drug distribution & metabolism mapping: detect low-level parent drugs and metabolites in tissue micro-regions to study penetration, metabolism, and off-target accumulation.
3. Microenvironmental metabolic gradients: map nutrient, oncometabolite, or hypoxia-linked metabolite gradients that correlate with phenotype (proliferation, immune infiltration).
4. Biomarker discovery & validation: identify low-abundance metabolic biomarkers whose spatial localization informs biology and translational decisions.
Iprm-PASEF:
Provides targeted multiplexed MS/MS imaging for validating specific biomolecules directly in tissues essential for confirming candidate biomarkers and spatially mapping therapeutic targets. irpm-MALDI, proprietary to Bruker, allows for up to twenty-five (25) MS/MS per pixel. Without this increased capability, multiple MALDI imaging runs are required, which may not be possible as the sample might be completely consumed. Many of the planned sample types that will be studied at the University are limited/fragile: clinical biopsies, PDX sections, organoids, archived tissues, and small animal micro-dissections are all sample classes where tissue is limited and cannot sustain repeated imaging runs.
TIMS:
Adds an extra “mobility” dimension that helps distinguish isomeric or closely related compounds, increasing the accuracy of metabolite and lipid identifications critical for studying altered cancer metabolism.
Specific capabilities of TIMS are as follows:
Isomer-aware lipidomics/metabolomics: distinguish lipid and metabolite isomers that have identical m/z but different biological roles (e.g., positional/isomeric lipids implicated in signaling). This yields accurate pathway assignments and avoids mis-annotation.
Integration with PASEF workflows: TIMS + PASEF enables very high-speed MS/MS acquisition with reduced chimeras, critical for deep coverage from limited material.
Compatibility:
Integration with the existing Bruker environment.
Data format & analysis fragmentation: Bruker’s pipeline produces interoperable datasets (MALDI imaging + LC-MS) that are designed for seamless cross-comparison.
Method transfer & reproducibility: validated imaging workflows (calibration, fiducials, pixel registration, laser settings, ion mobility/ramp parameters, MALDI-2 settings) transfer seamlessly across Bruker workflows.
Research Community:
Procuring Bruker’s timsTOF fleX MALDI2 enables access to published data sets, method sharing and cross-study comparability as well as collaboration, data integration and joint publications with partner institutions.
Conclusion:
The Mass Spectrometer being acquired provides access to true single-cell-scale imaging, 4D metabolomics and high-confidence biomarker validation workflows; all of which are areas that are rapidly becoming central to cancer systems biology.
University Contact:
Owen Bouley
Conseiller principal, Approvisionnement, recherche | Senior Advisor, Procurement, Research
Groupe de gestion des projets stratégiques (GGPS) | Service des approvisionnements
Strategic Project Management Group (SPMG) | Procurement Services
Université d'Ottawa | University of Ottawa
550 Cumberland (L315), Ottawa, ON, K1N 6N8
Tél. | Tel.: 613-562-5800 Ext.: 3966
Courriel | eMail : obouley@uottawa.ca
Notice is hereby given by the University of Ottawa of the intent to enter into a contract with Bruker Ltd to procure a Mass Spectrometer as specified below.
PROCESS:
Suppliers who consider their equipment functional, successfully tested, commercially available and fully compliant to the ACAN Mandatory Requirements 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 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 18th, 2025
Closing Date: December 15th, 2025, at 12:00:00 P.M. Eastern Standard Time
INTENDED USE:
The mass spectrometer will be used in the Metabolomics Core Facility to develop and apply spatial metabolomics, proteomics, post-translational analysis, and metaproteomics across clinical tumors, PDX/animal models, organoids, microbiome-associated cancers, and culture systems. There are planned studies on tumor microenvironment heterogeneity, drug distribution and biomarker validation using limited clinical and PDX tissue.
The mass spectrometer will be available to all members of the core facility, as well as other internal and/or external research teams interested in using the instrument for research purposes.
GENERAL DESCRIPTION AND PRIMARY CAPABILITIES:
The Bruker timsTOF fleX is a dual-source mass spectrometer offering comprehensive functionality through the integration of Trapped Ion Mobility Spectrometry (TIMS) and Time-of-Flight (TOF) technologies. The system supports both Electrospray Ionization (ESI) and Matrix-Assisted Laser Desorption Ionization (MALDI), enabling advanced workflows such as MALDI-guided SpatialOMx®. The timsTOF fleX is a dual-TIMS analyzer that delivers a near 100% duty cycle. Ions are accumulated in parallel in the first TIMS cell, then separated in the second cell based on their collisional cross section. This configuration supports Parallel Accumulation–Serial Fragmentation (PASEF®, US Patent US11047828B2), significantly improving MS/MS spectral quality by reducing chimeric spectra through ion mobility separation and enhancing signal-to-noise ratios via efficient ion accumulation.
The system also features an integrated smartbeam™ 3D MALDI laser, enabling true square-pixel imaging with high spatial resolution thanks to a focused 5 µm laser diameter. Switching between ESI and MALDI is seamless and controlled directly through the acquisition software, allowing flexible transitions between workflows.
To further streamline MALDI imaging, Bruker offers IntelliSlides™, single-use slides designed to automate and simplify sample setup. IntelliSlides™ are single-use consumables that incorporate permanent inscriptions indicating optimal placement of samples, registration marks (also known as teach marks or fiducials) that make automated sample registration possible, as well as provide a unique slide identifier for software tracking. They are compatible with standard histology and microscopy techniques. IntelliSlides™ increase both efficiency and reproducibility, making high-throughput MALDI imaging accessible to users at all experience levels.
With its high sensitivity, robust automation, and dual-source flexibility, the Bruker timsTOF fleX is ideally suited for a wide range of applications, from basic biological research to pre-clinical proteomics, metabolomics, and spatial omics imaging.
Mandatory Requirements - Mass Spectrometer:
1. General
1.1 The mass spectrometer must provide mass resolution of 60,000 at 1,222 m/z in Mass Spectrometry (MS) and Tandem Mass Spectrometry (MSMS).
1.2 The mass spectrometer must provide spatial resolution down to 5 µm pixel size
1.3 The mass spectrometer must be capable of delivering ion mobility separation with mobility resolution greater than 200 and reproducible Collisional Cross Section (CCS) determination with ≤0.5% Relative Standard Deviation (RSD) between experiments.
1.4 The mass spectrometer must be capable of laser post-ionization at 266 nm for maximum sensitivity and increased accessible chemical class range.
1.5 The mass spectrometer must allow for parallel MS/MS imaging of up to 25 mobility-resolved precursors windows.
1.6 CSA certification to meet Ontario standards must be included (CE is not an accepted equivalent).
1.7 The mass spectrometer must be provided in a lease-to-own contract; with an initial eighteen (18) month loan, followed by an option, at the sole discretion of the University, to purchase the mass spectrometer at the end of the loan period.
1.8 Must include installation and a minimum of three (3) days of on-site training.
1.9 Must include delivery.
1.10 Must include a second site visit to relocate the mass spectrometer from Roger Guindon Hall (RGN) to the Advanced Medical Research Centre (AMRC) once the lab space is ready in late 2026, early 2027.
1.11 The solution must be integrated into a single platform and not rely on multiple independent instruments to achieve compliance with the Mandatory Requirements.
2. Sensitivity
2.1 Must include full scan sensitivity in MS with 50 fg S/N > 200:1
2.2 Must include full scan sensitivity in MALDI with GlubFib: S/N > 100:1 at m/z 1570.68 for 250 attomole (amol) on target S/N with 2,000 laser shots
3. Mass Resolution
3.1 Must be capable of 60,000 Full Sensitivity Resolution (FSR) at 1222 m/z independent of MS or MS/MS scan speed
4. Scan speed4.1 Must be capable of 50 Hz or better for MS
4.2 Must be capable of 50 Hz or better for MS/MS (profile and peak detected spectra to disk)
4.3 Must be capable of up to 300 Hz MS/MS of mobility resolved precursors ions.
5. Mass Accuracy
5.1 Must be capable of < 0.8 ppm when calibrated internally, ESI mode
5.2 Must be capable of 2 ppm or better when calibrated externally, ESI mode
6. M/z range
6.1 20 – 20,000 m /z
7. Scan Functions
7.1 Must include acquisition and display of full MS scan
7.2 Must include acquisition and display of MS/MS spectra
7.3 Must include acquisition and display of TIMS full MS scan in m /z and 1/k0 (ion mobility)
7.4 Must include acquisition and display of MS/MS spectra in m /z and 1/k0 (ion mobility), ESI mode
7.5 Must include acquisition and display of DIA MS/MS spectra in m /z and 1/k0 (ion mobility), ESI mode
7.6 Must include acquisition and display of PRM MS/MS spectra in m /z and 1/k0 (ion mobility), ESI mode
7.7 Must include acquisition of IPRM MS/MS spectra in m/z and 1/k0 (ion mobility), MALDI mode
8. Isolation and Fragmentation
8.1 The mass spectrometer must be capable of isolating ions values up to 3000 m /z. The quadrupole mass range must be up to 20,000 m /z in rf-only mode.
8.2 Collision-Induced Dissociation (CID) must run synchronously at a customized ion energy ramp with ion elution from the ion mobility device at up to 300 Hz MS/MS speed (ESI mode).
8.3 The quadrupole must run synchronously with TIMS for stepped and sliding isolation windows in Data-Independent Acquisition (DIA) modes (ESI mode).
9. MALDI Laser
9.1 Must include 355 nm wavelength solid state laser
9.2 Must be capable of a minimum of 10 billion laser shots
9.3 Must include a laser repetition rate of up to 10 kHz
9.4 Laser energy/pulse must be ≥ 100 μJ/pulse
10. Advanced post ionization Laser
10.1 Must include a 266 nm post ionization laser
10.2 Must be capable of a minimum of 1 billion laser shots
10.3 Post ionization laser repetition rate must be 1 kHz, or better
10.4 Laser energy/pulse must be ≥ 400 μJ/pulse
11. Imaging
11.1 Must be capable of both 5 μm pitch (Zoom mode: 5-15 μm pitch) and 5 μm pitch
11.2 Must be capable of speeds up to 15 pixel/sec
12. Advanced Functions
12.1 Must be capable of controlling the target value
12.2 Must be capable of controlling the ramp time for the ion mobility separation
12.3 Must be capable of controlling the dynamic exclusion
12.4 Must be capable of controlling the collision cell energy ramp
Justification of Pre-Selected Supplier:
Supplier: Bruker Ltd
Justification:
Bruker Ltd’s timsTOF fleX MALDI-2 uniquely integrates high-sensitivity MALDI-2 post-ionization, TIMS (ion mobility) separation, and iprm-PASEF multiplexed MS/MS imaging within a single platform. These combined capabilities enable near single-cell spatial metabolomics, isomer-aware lipid and small-molecule annotation, and multiplexed MS/MS validation in a single pass; capabilities that are required for the Metabolomics Core Facilities’ planned studies on tumor microenvironment heterogeneity, drug distribution, and biomarker validation using limited clinical and PDX tissue.
The specific capabilities that Bruker’s proprietary technologies offer are as follows:
MALDI2:
Allows for the visualization of subtle metabolic gradients across tumors and treatment zones that would otherwise remain undetected.
MALDI-2 substantially increases ion yields for many low-abundance small molecules and lipids versus conventional MALDI. That sensitivity boost is what enables detection of subtle spatial concentration gradients that fall below the detection limits of standard MALDI imaging. Without MALDI-2, many biologically relevant metabolites (low abundance, poor ionization efficiency) will not be detectable in single runs, preventing confident mapping of micro-gradients.
Specific research objectives this enables at uOttawa includes:
1. Single-cell / near single-cell spatial metabolomics: visualize metabolite distributions within micro-regions of tumors that reflect cellular heterogeneity and metabolic microenvironments.
2. Drug distribution & metabolism mapping: detect low-level parent drugs and metabolites in tissue micro-regions to study penetration, metabolism, and off-target accumulation.
3. Microenvironmental metabolic gradients: map nutrient, oncometabolite, or hypoxia-linked metabolite gradients that correlate with phenotype (proliferation, immune infiltration).
4. Biomarker discovery & validation: identify low-abundance metabolic biomarkers whose spatial localization informs biology and translational decisions.
Iprm-PASEF:
Provides targeted multiplexed MS/MS imaging for validating specific biomolecules directly in tissues essential for confirming candidate biomarkers and spatially mapping therapeutic targets. irpm-MALDI, proprietary to Bruker, allows for up to twenty-five (25) MS/MS per pixel. Without this increased capability, multiple MALDI imaging runs are required, which may not be possible as the sample might be completely consumed. Many of the planned sample types that will be studied at the University are limited/fragile: clinical biopsies, PDX sections, organoids, archived tissues, and small animal micro-dissections are all sample classes where tissue is limited and cannot sustain repeated imaging runs.
TIMS:
Adds an extra “mobility” dimension that helps distinguish isomeric or closely related compounds, increasing the accuracy of metabolite and lipid identifications critical for studying altered cancer metabolism.
Specific capabilities of TIMS are as follows:
Isomer-aware lipidomics/metabolomics: distinguish lipid and metabolite isomers that have identical m/z but different biological roles (e.g., positional/isomeric lipids implicated in signaling). This yields accurate pathway assignments and avoids mis-annotation.
Integration with PASEF workflows: TIMS + PASEF enables very high-speed MS/MS acquisition with reduced chimeras, critical for deep coverage from limited material.
Compatibility:
Integration with the existing Bruker environment.
Data format & analysis fragmentation: Bruker’s pipeline produces interoperable datasets (MALDI imaging + LC-MS) that are designed for seamless cross-comparison.
Method transfer & reproducibility: validated imaging workflows (calibration, fiducials, pixel registration, laser settings, ion mobility/ramp parameters, MALDI-2 settings) transfer seamlessly across Bruker workflows.
Research Community:
Procuring Bruker’s timsTOF fleX MALDI2 enables access to published data sets, method sharing and cross-study comparability as well as collaboration, data integration and joint publications with partner institutions.
Conclusion:
The Mass Spectrometer being acquired provides access to true single-cell-scale imaging, 4D metabolomics and high-confidence biomarker validation workflows; all of which are areas that are rapidly becoming central to cancer systems biology.
University Contact:
Owen Bouley
Conseiller principal, Approvisionnement, recherche | Senior Advisor, Procurement, Research
Groupe de gestion des projets stratégiques (GGPS) | Service des approvisionnements
Strategic Project Management Group (SPMG) | Procurement Services
Université d'Ottawa | University of Ottawa
550 Cumberland (L315), Ottawa, ON, K1N 6N8
Tél. | Tel.: 613-562-5800 Ext.: 3966
Courriel | eMail : obouley@uottawa.ca
Bidding and Documents are available on http://www.merx.com. Fees may apply; See https://www.merx.com/public/pricing for more information.
Contract duration
The estimated contract period will be 0 month(s), with a proposed start date of 2026/03/31.
Trade agreements
-
Canadian Free Trade Agreement (CFTA)
-
Canada-European Union Comprehensive Economic and Trade Agreement (CETA)
-
Please refer to tender description or tender documents
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Contact information
Contracting organization
- Organization
-
University of Ottawa
- Address
-
550 Cumberland StreetOttawa, Ontario, K1N 6N5Canada
- Contracting authority
- Owen Bouley
- Phone
- 613-562-5800 x3966
- Email
- obouley@uottawa.ca
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