Therapeutic Discovery: Old Challenges and New MALDI-TOF Solutions

Biopharmaceutical research and development represents a rich treasure trove of diagnostic and therapeutic potential.

The field of metabolomics has grown considerably, as new MS technologies able to handle broader sample complexity have merged with advanced data analysis tools able to make sense of the breadth of data. Biomarker research has expanded as well, with the accuracy, speed, and throughput of advanced instruments increasingly able to handle challenging applications.

Both areas have been challenged in the past by sample matrix complexity and the inability to discern biologically relevant biomolecules from the high and varying abundance of background components. In clinical samples, a wide range of metabolomic or pathologic conditions affect the dynamic range of matrix components, for example immune serum proteins such as C-reactive protein, or dietary factors including lipids and carbohydrates.

Significant advancements in sample preparation, including matrix protein depletion and analyte enrichment technologies, have helped stratify the input material such that MS instruments can now scan a wider range of candidates with greater accuracy and precision -- and speed.

Speaking of speed, the area of high-performance MALDI-TOF mass spectrometry has grown significantly over the past few years, due in large part to leaps in technology making MALDI better able to produce actionable information from complex samples. In fact, MALDI-TOF instrumentation has garnered a large portion of the recent commercial market -- a trend that is expected to continue as advanced technology is integrated into simpler built-for-purpose instrument platforms for the testing and diagnostic markets.

Shimadzu has developed the MALDI-7090 instrument to handle high-performance MS/MS acquisition of discovery proteins and peptides from complex samples. Resolution is a parameter to keep in mind with MALDI and, although the resolution can theoretically be enhanced by extending the flight tube (towards infinity), the resolution of most lab scale MALDI's is dictated by the laser source, ion optics, and sample complexity -- considering path length held constant.

The MALDI-7090 includes a high-resolution dual wire-grad ion gate to allow the individual gating of parent compound species that are close in nominal mass. This allows optimal resolution of distinct MS/MS fragment ions. The Axial Spatial Distribution Focusing (ASDF) technology enables another level of enhancement by correction of the axial spatial distribution of the generated ions. The mass resolution becomes independent of the laser power used for sample ionization -- achieving 10,000 FHWM, unobtainable by pulsed extraction and ion optics alone.

Speed is brought to another level by integration of Multiplex system, which maximizes efficiency through the combination of the integrated 10 plate loader, the ultra fast 2kHz UV laser, and the MALDI Solutions multi-user software environment. MultiPlex streamlines analyses by assigning specific plate locations within the 10-plate loader, monitoring the progress of the submitted experiments. Designed for reliability the MultiPlex offers unmatched flexibility in both the high-throughput and multi-user environment.

Bruker is heavily invested in the MALDI space as well, celebrating 25 years of MALDI technology development this year. The FLEX series is Bruker's MALDI flagship, with a large variety of instrumentation to reach a wide range of applications in biopharmaceutical R&D and beyond.

Focusing on speed, the rapiflex MALDI PharmaPulse platform brings together high resolution MALDI-TOF with ultra-high throughput screening -- enabling the fully automatic handling of 384, 1536, 3072, and 6144 sample plates and analysis of over 1 M samples per week. This unprecedented speed is served by the HighRes suite of biosolutions including the ACell robot, PicoServe plate carousel, and LidValet -- along with a TTP Labtech mosquito HTS liquid handing robot. These components combine with Bruker's patented Smartbeam 3D 10 kHz laser, which offers adaptable profiles for highest performance in different workflows.

A key objective in discovery phase pharmaceutical research is the identification (and semiquantitation) of biologically and/or physiologically relevant compounds in a set of samples. In biomarker research, this may involve the identification of marker or panel of markers indicative of disease. In drug development, this may include the disappearance of a substrate or appearance of a product. While in biopharmaceutical research, this may involve the presence of a protein modulator of genetic or phenotypic activity.

With increases in resolution for complex samples and increases in speed, an attribute for which MALDI is well known, advanced instruments have the capabilities to screen a wide variety of samples with greater power than before. Furthermore, the power and speed of today's MALDI-TOF instruments may mean a boom for lead identification and the advancement of downstream verification and validation data streams.