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 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.