timsTOF Pro2 mass spectrometer

Karolinska Institute (KI) department Microbiology, Tumor and Cell Biology is focused on high-throughput interaction proteomics using co-fractionation mass spectrometry approaches coupled to short-gradient data-independent acquisition (DIA) for protein-interaction profiling across various biological matrixes including bacteria, phages, viruses, human cells, clinical isolates, and tissue biopsies. The nature of our research requires …

CPV: 38433100 Mass spectrometer
Place of execution:
timsTOF Pro2 mass spectrometer
Awarding body:
Karolinska Institutet
Award number:
2-2671/2025

1. Buyer

1.1 Buyer

Official name : Karolinska Institutet

2. Procedure

2.1 Procedure

Title : timsTOF Pro2 mass spectrometer
Description : Karolinska Institute (KI) department Microbiology, Tumor and Cell Biology is focused on high-throughput interaction proteomics using co-fractionation mass spectrometry approaches coupled to short-gradient data-independent acquisition (DIA) for protein-interaction profiling across various biological matrixes including bacteria, phages, viruses, human cells, clinical isolates, and tissue biopsies. The nature of our research requires the ability to perform fast, high-sensitivity LC-MS/MS measurements using gradients shorter than 10 minutes, while maintaining deep proteome coverage, low limits of detection, and sub-one-second cycle times. These analytical requirements are essential to support our ongoing large-scale studies and the rapid processing of complex sample sets. The departments workflow imposes several technical constraints that few instruments can satisfy. We require the ability to perform deep proteome profiling using sub-10-minute gradients while retaining high quantitative accuracy and sensitivity. The mass spectrometer must also support CCS-aware analysis, ensure compatibility with existing and planned nano-LC chromatography systems, and deliver consistent performance across large sample batches. Acquisition software must support real-time processing, database searching, and integration with automation tools for quality control and high-throughput sample management. Moreover, the system must be able to run DIA strategies that leverage ion mobility separation to enhance specificity and identification confidence. These preconditions are driven by our need to handle growing sample numbers with fast acquisition time, without compromising analytical quality or reproducibility. The Bruker timsTOF Pro2 is the only instrument currently available that fulfills all technical and scientific requirements for our proteomics workflow. Its proprietary dual TIMS design allows simultaneous accumulation and mobility separation of ions, enabling the high-speed PASEF method, which dramatically improves sequencing speed and sensitivity. No other system supports this acquisition strategy or integrates ion mobility and mass spectrometry with such a high duty cycle. The system also supports CCS-calibrated DIA (dia-PASEF) and targeted quantitation (prm-PASEF), making it uniquely capable of handling both discovery and targeted proteomics applications in a high-throughput setting. These features are essential for our work with large sample cohorts analyzed under short LC gradients. Other vendors do not offer equivalent technologies or acquisition modes. In light of these technical constraints, and the lack of suitable alternatives despite thorough market research, the conditions for awarding the contract through a negotiated procedure without prior publication are met. KI will sign a contract with Bruker after a standstill period of 10 days after publishing this Voluntary ex ante transparency notice.
Procedure identifier : 9ea865e2-7b76-45d9-8792-a4d8ca361430
Internal identifier : 2-2671/2025
Type of procedure : Negotiated without prior call for competition

2.1.1 Purpose

Main nature of the contract : Supplies
Main classification ( cpv ): 38433100 Mass spectrometer

2.1.2 Place of performance

Country : Sweden
Anywhere in the given country

2.1.4 General information

Legal basis :
Directive 2014/24/EU

5. Lot

5.1 Lot technical ID : LOT-0000

Title : timsTOF Pro2 mass spectrometer
Description : Karolinska Institute (KI) department Microbiology, Tumor and Cell Biology is focused on high-throughput interaction proteomics using co-fractionation mass spectrometry approaches coupled to short-gradient data-independent acquisition (DIA) for protein-interaction profiling across various biological matrixes including bacteria, phages, viruses, human cells, clinical isolates, and tissue biopsies. The nature of our research requires the ability to perform fast, high-sensitivity LC-MS/MS measurements using gradients shorter than 10 minutes, while maintaining deep proteome coverage, low limits of detection, and sub-one-second cycle times. These analytical requirements are essential to support our ongoing large-scale studies and the rapid processing of complex sample sets. The departments workflow imposes several technical constraints that few instruments can satisfy. We require the ability to perform deep proteome profiling using sub-10-minute gradients while retaining high quantitative accuracy and sensitivity. The mass spectrometer must also support CCS-aware analysis, ensure compatibility with existing and planned nano-LC chromatography systems, and deliver consistent performance across large sample batches. Acquisition software must support real-time processing, database searching, and integration with automation tools for quality control and high-throughput sample management. Moreover, the system must be able to run DIA strategies that leverage ion mobility separation to enhance specificity and identification confidence. These preconditions are driven by our need to handle growing sample numbers with fast acquisition time, without compromising analytical quality or reproducibility. The Bruker timsTOF Pro2 is the only instrument currently available that fulfills all technical and scientific requirements for our proteomics workflow. Its proprietary dual TIMS design allows simultaneous accumulation and mobility separation of ions, enabling the high-speed PASEF method, which dramatically improves sequencing speed and sensitivity. No other system supports this acquisition strategy or integrates ion mobility and mass spectrometry with such a high duty cycle. The system also supports CCS-calibrated DIA (dia-PASEF) and targeted quantitation (prm-PASEF), making it uniquely capable of handling both discovery and targeted proteomics applications in a high-throughput setting. These features are essential for our work with large sample cohorts analyzed under short LC gradients. Other vendors do not offer equivalent technologies or acquisition modes. In light of these technical constraints, and the lack of suitable alternatives despite thorough market research, the conditions for awarding the contract through a negotiated procedure without prior publication are met. KI will sign a contract with Bruker after a standstill period of 10 days after publishing this Voluntary ex ante transparency notice.
Internal identifier : 2-2671/2025

5.1.1 Purpose

Main nature of the contract : Supplies
Main classification ( cpv ): 38433100 Mass spectrometer

5.1.2 Place of performance

Country : Sweden
Anywhere in the given country
Additional information :

5.1.6 General information

The procurement is covered by the Government Procurement Agreement (GPA) : yes

5.1.16 Further information, mediation and review

Review organisation : Förvaltningsrätten
Organisation signing the contract : Karolinska Institutet

6. Results

Value of all contracts awarded in this notice : 3 825 750 Swedish krona
Direct award :
Justification for direct award : The contract can be provided only by a particular economic operator because of an absence of competition for technical reasons
Other justification : The Bruker timsTOF Pro2 is the only instrument currently available that fulfills all technical and scientific requirements for our proteomics workflow. Its proprietary dual TIMS design allows simultaneous accumulation and mobility separation of ions, enabling the high-speed PASEF method, which dramatically improves sequencing speed and sensitivity. No other system supports this acquisition strategy or integrates ion mobility and mass spectrometry with such a high duty cycle. The system also supports CCS-calibrated DIA (dia-PASEF) and targeted quantitation (prm-PASEF), making it uniquely capable of handling both discovery and targeted proteomics applications in a high-throughput setting. These features are essential for our work with large sample cohorts analyzed under short LC gradients. Other vendors do not offer equivalent technologies or acquisition modes. In light of these technical constraints, and the lack of suitable alternatives despite thorough market research, the conditions for awarding the contract through a negotiated procedure without prior publication are met.

6.1 Result lot ldentifier : LOT-0000

6.1.2 Information about winners

Winner :
Official name : Bruker Nordic AB
Tender :
Tender identifier : 2-2671/2025
Identifier of lot or group of lots : LOT-0000
Contract information :
Identifier of the contract : 2-2671/2025
Date on which the winner was chosen : 24/06/2025
Organisation signing the contract : Karolinska Institutet

8. Organisations

8.1 ORG-0001

Official name : Karolinska Institutet
Registration number : 2021002973
Department : CIS
Postal address : Nobels väg 5
Town : STOCKHOLM
Postcode : 17177
Country subdivision (NUTS) : Stockholms län ( SE110 )
Country : Sweden
Contact point : Amanda Larsen
Telephone : +46 08-52480000
Internet address : http://www.ki.se
Roles of this organisation :
Buyer
Organisation signing the contract

8.1 ORG-0002

Official name : Förvaltningsrätten
Registration number : 202100-2742
Town : Stockholm
Postcode : 115 76
Country subdivision (NUTS) : Stockholms län ( SE110 )
Country : Sweden
Telephone : 08-561 680 00
Roles of this organisation :
Review organisation

8.1 ORG-0003

Official name : Bruker Nordic AB
Size of the economic operator : Medium
Town : Stockholm
Postcode : 14177
Country subdivision (NUTS) : Stockholms län ( SE110 )
Country : Sweden
Roles of this organisation :
Tenderer
Winner of these lots : LOT-0000

8.1 ORG-0004

Official name : Mercell Holding ASA
Registration number : 980921565
Postal address : Askekroken 11
Town : Oslo
Postcode : 0277
Country subdivision (NUTS) : Oslo ( NO081 )
Country : Norway
Contact point : eSender
Telephone : +47 21018800
Fax : +47 21018801
Internet address : http://mercell.com/
Roles of this organisation :
TED eSender

Notice information

Notice identifier/version : d8329bff-c864-476a-a3c6-b6809929d924 - 01
Form type : Direct award preannouncement
Notice type : Voluntary ex-ante transparency notice
Notice dispatch date : 25/06/2025 12:13 +00:00
Notice dispatch date (eSender) : 25/06/2025 12:13 +00:00
Languages in which this notice is officially available : English
Notice publication number : 00412251-2025
OJ S issue number : 120/2025
Publication date : 26/06/2025