September 1, 2011 (Vol. 31, No. 15)

Latest Enhancements Have Allowed Technique to Become a Rising Star in Proteomics Studies

Mass spectrometry has emerged as the leading technology for protein characterization. New instrumentation is more versatile and user friendly, expanding the application of mass spec technology to areas that were previously beyond its scope.

A range of new offerings in mass spec instrumentation and their application to protein profiling were discussed at Waters’ recent “Mass Spectrometry” conference.

“In the field of proteomics today, the current methods of choice for molecular characterization are liquid chromatography combined with mass spectrometry, tandem mass spec, and nuclear magnetic resonance mass spectrometry,” said James Langridge, Ph.D., director of proteomics at Waters.

“However, none of these approaches provides an unambiguous profile of target molecules. Therefore our team has investigated ion-mobility spectrometry combined with mass spec to distinguish isobaric—those having the same molecular weight—metabolites.”

As Dr. Langridge pointed out, a particular atomic group may be positioned on a ring structure in one of several positions that are indistinguishable by mass spectrometry. However, with ion-mobility separation, the shape of the molecule enters into the equation and the two isobars can be separated into two distinct peaks.

The T-wave ion-mobility separation is performed by the Waters Synapt high-definition MS system, which combines ion-mobility-based measurements and separations with quadrupole time of flight MS.

The Waters system is built around the concept of a tri-partite device, the Triwave, in which the gaseous ions are accumulated in a trap. They are then moved to the ion-mobility separation segment of the Triwave and finally transferred to the TOF segment of the machine where they are subjected to mass analysis.

The Synapt system can perform a number of operations that are important in proteomics studies, according to Dr. Langridge. These include analysis of intact proteins and protein complexes, enhanced protein sequencing, and improved protein identification.

“I believe that the Triwave technology provides a number of key benefits, including the formation of first- and second-generation product ions from a precursor in a single experiments and the ability to perform a wide spectrum of tasks, such as characterization of post-translational modifications, maximization of sample information content, and a high-resolution analysis of small molecules,” Dr. Langridge concluded.

Waters is investigating alternative methodologies for molecular characterization including ion-mobility spectrometry combined with mass spec to distinguish isobaric metabolites.

Interrogating the Membrane Proteome

As quantitative investigations flesh out the texture of the proteome, it has become evident that around one-third is composed of membrane proteins. However, membrane proteins tend be to be large and unwieldy, difficult to purify while still retaining functionality, and hard to crystallize.

For these reasons they are underrepresented in proteomics studies, and investigators have often ignored them despite their pivotal importance in cell function.

This has changed in recent years, explained Kathryn Lilley, Ph.D., assistant director of research at the Cambridge Centre for Proteomics and the department of biochemistry at the University of Cambridge. She noted that membrane proteins are of special interest to the pharma industry, given the importance of receptors as targets of specific drugs.

There are still challenges to be considered, however. “Questions raised when targeting membrane proteins include abundance, solubility, and suitability for standard proteomics workflow operations,” stated Dr. Lilley.

She and her co-workers addressed these issues through the development of proteomics tools to define the expression of resistance nodulation division efflux pumps—which are low abundance, membrane-bound proteins—in Pseudomonas aeruginosa. Mutations in these proteins are a frequent cause of multiple drug resistance.

Absolute quantification of the amount of protein requires the use of a marker peptide as a standard. Dr. Lilley chose enolase and calibrated the absolute abundance based on the performance of its top three scoring peptides. This approach is extremely flexible, she said, and applies over several orders of magnitude.

Dr. Lilley discussed a second example of her approach to membrane protein characterization known as selected reaction monitoring, a complementary proteomic procedure based on the targeted analysis of a set of predetermined proteins and peptides.

Selected peptides, based on their mass to charge ratio, are fragmented in the collision cell of a triple quadrupole mass spectrometer. The detected fragment ions, referred to as transitions, are used to construct a specific and highly sensitive assay for the detection of a particular peptide in a sample.

This approach was also combined with global mass spectrometry-based protein localization studies in experiments aimed at localizing particular membrane proteins to the plant Golgi apparatus.

“We found that a global membrane proteome analysis is more achievable by a combination of a variety of different mass spectrometry approaches,” Dr. Lilley said. “We have employed quantification of the membrane protein targets, identification of their binding partners, and a focus on the subcellular location of possible candidates for development of workable hypotheses.”

Global Proteome Quantification

Rob Beynon, Ph.D., chair of proteomics at the University of Liverpool, put forth what he refers to as “a rather modest ‘grand challenge’. For a simple proteome, first quantify, in copies per cell, the abundances of all proteins. Secondly, determine the rate at which those proteins are turned over in the cell. Finally, determine both sets of parameters with high confidence and quantify the inherent biological variance in the data.”

Dr. Beynon described his experiences with the Waters ExpressionE system, which employs a high bandwidth UPLC/MSE data-acquisition strategy to consistently oversample complex protein digests, thereby delivering datasets containing evidence for all peptides above the limits of detection.

He discussed his research group’s experience with label-free proteomics as a solution to quantification problems. This approach has some difficult issues; isoform resolution and quantification remain significant problems, as do post-translational variants. However, label-free methods, particularly those based on summed peptide intensities, are remarkably valuable for many proteomics studies.

“Identification is not the same as quantification,” Dr. Beynon cautioned. “Label-free approaches start to struggle for peptides or ions at about 0.1–1 fmol on column on the better instruments—at 1 fmol, this equates to about 3,000 copies per cell in yeast.” The situation is more pronounced in mammalian cells, as a typical load of a digest of HeLa cells, for example, equates to only 4,000 cells, or 150,000 copies per cell.

To get a handle on the problem, Dr. Beynon noted that the sensitivity required to meet the “grand challenge” would be a detection limit in yeast of around 10 copies of a given protein molecule per cell.

“On current instruments, we can routinely apply a digest derived from 200,000 cells, and in principle we can therefore reach between 30 and 300 copies per cell,” Dr. Beynon stated. “We anticipate instrument and informatics developments that should bring such methods to the required depth.”

He described his invention of the artificial QconCAT proteins, concatamers of tryptic peptides for several proteins, which when expressed heterologously in bacteria create stoichiometric equivalent sets of standard peptides. “The QconCAT approach is robust and the limiting factors are quantotypic peptide nomination and the development of appropriate selected reaction monitoring assays.”

Tissue Imaging

“Ion-mobility spectrometry is capable of separating molecules on the basis of their size or shape, whereas imaging mass spectrometry is an effective tool to measure the molecular weight and spatial distribution of molecules,” said Ron Heeren, Ph.D., research scientist at the Institute AMOLF, a section of the Foundation for Fundamental Research on Matter of the Dutch National Science Foundation. He discussed his lab’s investigations combining these approaches in biomedical tissue imaging.

“Histological imaging with mass spectrometry has a number of advantages. No labeling is required, thus biomolecules are unaltered; it is possible to image biomolecular modification including post-translational modifications and distribution of metabolites; detailed structural information can be provided; and mass spectrometry imaging can generate a molecular picture of the pathology of the case.”

Dr. Heeren discussed the application of ion-mobility mass spectrometry imaging. The technology is based on the use of generated ions that travel through a drift tube that has an applied electric field and a carrier buffer gas that opposes the ion motion. The larger the ion size, the more area is available for the buffer gas to collide and impede the ion’s drift—the ion then requires a longer time to migrate through the drift tube. This added separation provided increased resolution and structural information.

Dr. Heeren and his colleagues have applied ion-mobility mass spectrometry to histological analysis. One series of experiments demonstrated how application of this technology can produce a clearer image of cartilage development in normal and diseased states. The protocol used joints in animal models and in humans to map tissues, combining conventional histological staining with mass spectrometry analysis.

One of the markers the team followed was fibronectin, which undergoes dramatic changes in conditions involving joint deterioration. Other markers that change in response to inflammatory conditions include p53 and Il-17, putative breast cancer, cell adhesion, and angiogenesis markers.

Dr. Heeren strongly supports imaging mass spectrometry technology as a game changer in the field of molecular histology. With its ability to visualize the location and quantitative levels of critical proteins, it is a far more specific technology than classic staining used traditionally in the pathology laboratory. “The ‘new glasses’ help us visualize and understand more molecular details of different diseases,” he concluded.

There are numerous mass spectrometry options available for characterization of biological molecules, and the list continues to expand. Mass spectrometry companies are understandably reticent about the nature of their forthcoming offerings, but consumers can anticipate that the mantra of “faster, better, easier, cheaper” will continue to drive the industry forward.

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