Cutting edge proteomics technology facilitated timsTOF Pro 

PTM Bio is a precision medicine company that owns a leading MS-based integrated proteomics and epigenetics platform with industry leading sensitivity and accuracy. The China-based company provides a variety of services, including of protein profiles for biomedical research and biopharmaceutical communities, and delivers high quality data and insights to industry, academia, and government organizations. PTM Bio was the first research lab in China to install Bruker’s timsTOF Pro and currently has five systems in operation. Its customers seek to acquire deeper coverage of the proteome with higher accuracy and sensitivity.

Over the last few years, trapped ion mobility spectrometry (TIMS) combined with quadrupole time of flight MS (QTOF-MS) has become an increasingly popular MS method to identify proteins, quantify protein expression, discover new biomarkers, and characterize therapeutic antibodies. Compared with previous MS technologies used by PTM Bio, Bruker’s timsTOF Pro can identify more proteins in exactly the same conditions, and is also a powerful technique for quantification.

Bruker’s timsTOF Pro is powered by parallel accumulation–serial fragmentation (PASEF^®) technology, which boosts research capabilities due to a combination of speed, sensitivity, selectivity, and robustness. TIMS (a gas phase separation technique) combined with PASEF^® greatly enhances peak capacity and speeds up MS/MS data acquisition. Together, these features enable analytical results from 20-minute gradients that previously took more than an hour.

This high data acquisition speed increases proteomic analysis throughput without sacrificing sensitivity or robustness. 

Dr. Cheng summarizes: “The timsTOF Pro can quantify more using a smaller sample and improves the likelihood of finding important proteins for different aims. I admire the ability of the Bruker timsTOF Pro to do this – it is extremely advantageous for the proteomics community.”

Post-translational modifications (PTMs) are involved in most cellular processes and increase the functional diversity of the proteome. These modifications impact almost all aspects of normal cell biology and pathogenesis and the analysis of protein PTMs is challenging. Using TIMS, PTMs can be better separated from each other resulting in a higher identification rate.

The dynamic nature of the proteome is further exacerbated by the effects of PTMs, leading to a variety of proteoforms being expressed from one protein, each with dedicated biological activity. Understanding the role of proteoforms in health and disease using TIMS TOF-MS is making considerable contributions to personalized medicine. The speed and robustness of TIMS TOF-MS is key in analyzing large sample cohorts for clinical research. Analysis of clinical samples using the timsTOF Pro followed by bioinformatic data mining allows researchers to gather information about individual biological responses to diseases with the aim of developing personalized treatment options.