September 1, 2006 (Vol. 26, No. 15)

Making MS Faster and More Efficient, Software To Handle it, and the Future of Personalization

In the past year, various new products designed to make mass spectrometry (MS) faster, as well as more efficient, user-friendly, and practical in a clinical setting have been introduced. While the technology has long been in industrial labs, constituting a $2-billion per year market, it is now an essential component of the diagnostic laboratory. Companies marketing such new and reconfigured instruments showcased their products at the recent the American Society of Mass Spectrometry (ASMS) meeting in Seattle.

New Mass Spectrometry Technology

Thermo Electron ( introduced the Accela High Speed Chromatography System, which meets the analytical needs of liquid chromatography and MS users working in drug development and discovery, quality control, academic research facilities, and the food and beverage industries. It is designed as both a conventional and an ultrahigh-pressure liquid chromatography system to optimize a wide range of procedures. Accela, devised for shorter run times and improved peak symmetry, can perform chromatographic separations in seconds to minutes.

Thermo also introduced new hardware and software products intended specifically for drug metabolism researchers, including MetWorks™ software for structural elucidation of complex metabolic samples. MetWorks uses an extensive Fragmentation Library™ to provide comparisons of sample and control files and detailed structural elucidation of compounds. The technology uses tandem MS to identify characteristic ions by isolation and fragmentation to create a set of product ions. This process can be continued through multiple stages (multistage MS; MSn), the output of which can be referred to and viewed as a fragmentation tree.

Spectral trees provide a logical way to view and interrogate structures from a mass spectrometer. This concept is put to work in MetWorks to find and identify multiple analytes in complex samples. Such experiments provide more confident identification of compounds than that available from simple single-stage MS. They also, in the case of complex mixtures, can improve detection limits while improving the specificity of detection.

The LTQ XL™ mass spectrometer is an enhanced version of the company’s LTQ linear ion trap, offering access to Pulsed Q dissociation, Multistage Activation, and optional electron-transfer dissociation. The electron-transfer option allows improved peptide/protein characterization by providing a different set of fragment ions from that realized in a conventional MS/MS experiment, performed using collision-induced dissociation.

The device employs chromatography as a means of separation but is, in fact, an ion trap spectrophotometer. These combined technologies enable better characterization of peptides and also provide for quantitative applications.

“Thermo’s optional vMALDI ion source and Orbitrap or FT detectors make the LTQ XL the universal proteomics platform of choice” stated Ken Miller, proteomics marketing manager for Thermo. Further extending the proteomics suite, the new LTQ FT Ultra™ includes an ICR cell. This delivers five times more sensitivity, going down to the attomole scale, and ultrahigh resolution. It also allows for a dynamic range in excess of 4,000, while achieving sub-ppm mass accuracy all on a liquid chromatography timescale.

Thermo also introduced High-Field Asymmetric Ion Mobility Technology to its family of TSQ Quantum™ triple quadrupole instruments for biomarker quantification and validation. Coupled with its high-resolution monitoring capability, chemical noise is eliminated allowing lower level biomarker detection. Finally, Thermo announced new proteomics software for proteomics applications, including BioWorks™ 3.3 for protein identification, SIEVE™ for label-free biomarker discovery, ProSightPC™ for protein analysis, and a tissue imaging analysis package.

Waters ( introduced a system that can analyze samples differentiated by size, shape, and charge, as well as mass, referred to as Synapt High Definition MS system (HDMS). The instrument employs high-efficiency ion mobility to introduce an additional dimension of sample separation, thereby improving specificity and sample definition. Such a strategy allows a more nuanced characterization of the sample.

The enabling technology of the system is the Waters Triwave™, combining high efficiency ion mobility-based measurements and separations with accurate, highly sensitive time-of-flight (TOF) MS. The Synapt HDMS™ system allows for elegant studies on the structure of protein molecules in various states of hydration. By determining collision cross sections of assemblies of the trp RNA binding protein TRAP, Carol Robinson, Ph.D., and her colleagues at the University of Cambridge were able to demonstrate that proteins can maintain their quaternary structure in the absence of bulk water in the gas phase. These findings open the door to a variety of investigations under wide-ranging conditions and have the potential to contribute to a characterization of the elusive changes that occur in transient and reversible macromolecular associations.

Other studies presented at “ASMS” discussed the use of the Synapt HDMS system in metabolite profiling and protein characterization reporting the ability of the system to maximize protein sequence coverage, and removing common background contamination through ion mobility-based separation prior to mass measurement.

Q-TOF Mass Spectrometers

The growing range of qualitative applications in biomarker discovery, protein characterization, metabolomics, metabolite ID, and structural studies has prompted a great demand for a new generation of Q-TOF mass spectrometers. Agilent’s first Q-TOF instrument has 1- to 2-ppm mass accuracy, higher sensitivity, speed, and dynamic range, according to Rick Carberry, senior director of LC/MS marketing. The new 6510 Q-TOF has a 10-fold sensitivity improvement over earlier instruments in its class.

Because the device shares its collision cell with the new Agilent triple quadrupole LC/MS, target ions from the first stage of a biomarker profiling experiment can be run in the second MS/MS stage without introducing variability. The instrument displays attomolar level sensitivity and wide dynamic range, over four orders of magnitude. This allows for the identification of peptides and other molecules present as traces in a biological sample.

Proteomic Sampling Devices

MALDI-MS figures importantly in proteomics research, but complex protein samples require specialized handling, particularly in the low abundance range. Conventional prep techniques can require many individual steps and transfer of materials, with losses at every step and concomitant poor yields and reproducibility. To address these problems, Qiagen ( has designed two different disposable MS chips to facilitate sample preparation.

Mass•Spec•Focus Chips are designed to facilitate low-throughput analysis of 2-D gels, perform sample processing, or purify steps directly on the chip. The samples are applied to the chip in concentric circular zones of differing hydrophobicity, which causes the fluid to form a drop and prevents it from spreading. Moreover, particular surface chemistries in the affinity capture zone allow peptides or, in case of the IMAC chip, solely phosphopeptides to be specifically retained and enriched. Very small quantities, in the range of 100s of attomoles, are sufficient for analysis.

After reaction of the analytes with the surface phase, unbound molecules or detergents are washed off and the matrix solution is added to the well. The resolubilized analyte and matrix are co-focused in the analysis zone, and the chip is read on the MS instrument. The Focus Chips were introduced only recently and as yet, peer-reviewed literature utilizing them has not appeared. However, the Chips have received a resounding endorsement from Mark Baker, Ph.D., CEO of the Australian Proteome Analysis facility, who praised the Focus Chips’ “dramatically better limits of detection.”

The second product in the Qiagen sample prep line is the Mass•Spec•Turbo Chip, designed for high-throughput analysis and high-sensitivity LC-MALDI, it offers distinct advantages over conventional stainless steel targets. The chips also possess a proprietary hydrophobic surface in combination with prespotted matrix spots, onto which the samples are directly applied, either manually or using a robotic applicator. The chips are manufactured under highly controlled cleanroom conditions and the matrix is deposited by vacuum sublimation to ensure an extremely high level of homogeneity.

The disposable chips is that they can be archived. The fact that they can be stored, retrieved, and used for large-scale projects involving thousands and thousands of samples adds to the versatility of the system. The MS chips can be combined with Qiagen’s Qproteome series of protein fractionation and depletion kits for standardized and reproducible sample preparation.

User-friendly Software

With such new tools into the MS arena has companies scrambling to rewrite software to match the expanded performance of the hardware for purposes ranging from drug discovery to food testing. Applied Biosystems ( and MDS Sciex ( announced two new software applications, one for food contaminant testing and the other, discussed below, for metabolite identification.

The new LightSight™ Software for Metabolite Identification is a drug discovery product significant for investigators, because the metabolites formed could be potentially toxic or more efficacious than the drug itself. Other available programs are quite tedious and time consuming, according to Diane Grotz, Ph.D., of Schering-Plough (, who discussed her findings. The metabolite ID solution enables pharmacologists to move quickly through thousands of drug candidates, triaging those that fail to meet the requirements for further development.

More than 100 pharmaceutical scientists from 35 companies provided input and feedback for the development of the LightSight™ Software, resulting in a metabolite ID package attuned to the way these highly specialized laboratories operate, according to the company.

This new pharmaceutical application can be employed with the 4000 Q TRAP® mass spectrometer, as well as other triple quadrupole and hybrid linear ion trap mass spectrometers from Applied Biosystems/MDS Sciex. It allows users to streamline and simplify their work, allowing for a larger number of experiments to be performed without an increase in resources or training.

MS, built around highly sophisticated instrumentation, is changing at breakneck speed. R. Graham Cooks, Ph.D., of Purdue University, addressed the potential for the personal mass spectrometer in his plenary lecture. Desorption electrospray ionization (DESI) allows MS to be used in the ambient environment. The technique involves ion formation without volatilization of solid samples from virtually any source. It requires no sample preparation so it lends itself to high-throughput measurements on small and large molecules. The material to be analyzed is ionized gently and then introduced into the mass spectrometer.

The DESI technology will allow the development of mobile analytical platforms, which will be applied to applications including forensic studies, screening for drugs of abuse, and metabolomic investigations. These innovations will greatly expand the versatility and range of applications of mass spectrometry, as it moves to smaller and more agile applications.

K. John Morrow, Jr., Ph.D., is president of Newport Biotech. Phone: (513) 237-3303. E-mail: [email protected].

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