timsTOF HT LC-MS System for UR Proteomics Research

University Of Rochester, Rochester NY

Investigators

Abstract

Abstract We are requesting funds for the purchase of a timsTOF HT mass spectrometry (MS) and liquid chromatography system (Bruker) to be used for qualitative and quantitative proteomic analyses. This instrument will greatly expand the proteomic capabilities of the University of Rochester Mass Spectrometry Resource Laboratory (MSRL) and the services it offers to its user-base throughout the University of Rochester and Western New York. Currently, the existing MS instruments at the MSRL are being used at full capacity and there is a critical need for additional modernized instrumentation to alleviate project backlogs and take advantage of recent advances in label-free Data Independent Acquisition (DIA) proteomics. The acquisition of the timsTOF will augment our aging “3D” mass spectrometer (capable of detection of ions based LC retention time, mass to charge and MS/MS fingerprint) with a “4D” ion mobility platform capable of additional separation based on collision cross-section (CCS) properties of ions. Recent advances in mass spectrometry have provided powerful tools for high-throughput analysis of proteins that are widely employed in medical and biological research. Proteomic analyses are typically used for discovery applications and in clinical or analytical screens that require large-scale target detection and quantification of complex protein mixtures. Due to its potential for high impact on existing NIH-funded research programs and Centers, the University of Rochester Medical Center (URMC) has targeted proteomics as an area of critical development. The University's commitment to developing and supporting the MSRL has been essential for providing accessibility to modern mass spectrometry resources, services and expertise for the University of Rochester and Western New York research communities. The facility has experienced a dramatic increase in demand in recent years, spurred in part by an overall shortage of accessibility to high- end mass spectrometers in the region. The requested timsTOF HT mass spectrometer is a versatile instrument that excels at high-throughput quantitative proteomic applications, at a level beyond the capabilities of the current mass spectrometers in the core facility. Specifically, the timsTOF instrument offers high-capacity Trapped Ion Mobility (TIMS) analyzer, enables Parallel Accumulation and Serial Fragmentation (PASEF) and accurate, reproducible ion mobility separation and CCS determination. Importantly, the instrument can achieve sequencing speeds up to 150 Hz and 60,000 (FWHM) resolution at 1222 m/z. This rate of data acquisition far exceeds our current instrument and will enable significant enhancements in our project turnaround times. In this application, 9 major users and 4 minor users provide project descriptions that impact at least 20 NIH research grants. The diversity of users highlights the importance of this technology and the unmet level of need that will be addressed by the instrument. The need for sensitive high-throughput, high-resolution mass spectrometry is rapidly growing in the Medical Center and the College that encompass over 45 departments and research centers, and over 800 research laboratories. To ensure the highest level of access to proteomic technology and services, the requested instrument will be housed in the URMC Mass Spectrometry Resource Laboratory. Three dedicated core staff members will run the instrument, and the core staff and core director will manage projects, provide consulting, analyze data, and assist users with data interpretation and processing. Data storage, analysis, and processing will be performed at the University of Rochester's Center for Integrated Research Computing (CIRC), which manages a 144-core processor server for the facility. Institutional support and oversight will ensure that state- of-the-art mass spectrometry services are developed and accessible to the research community.