Advances in mass spectrometry for proteome analysis

Proteomics. Making sense of genomic information for drug discovery

As an increasing number of available genomes triggers a gold rush in modern biology, the scientific challenge shifts towards understanding the total of the encoded information, most notably the proteins, their structures, functions and interactions. Currently this work is in its early stages but the near future will bring a merger of biology, engineering and informatics with a far broader impact on society than pure genomics has had so far. The challenge of characterizing the structures and functions of all proteins in a given cell demands technological advances beyond the classical methodologies of protein biochemistry. Mass spectrometry techniques for high-throughput protein identification, including peptide mass fingerprinting, sequence tagging and mass spectrometry on full-length proteins are providing the driving force behind proteomics endeavors. New technologies are needed to move high-resolution protein structure determination to an industrial scale. Nonetheless, improvements in techniques for the separation of intrinsic membrane proteins are enabling proteomics efforts towards identifying drug targets within this important class of biomolecules. Beyond the acquisition of data on sequences, structures and interactions, however, the major work in drug discovery remains: the screening of large candidate compound libraries combined with clever medicinal chemistry that guarantees selective action and defined delivery of the drug.

Growth signaling in breast cancer cells: outcomes and promises of proteomics

Methods in functional proteomics are now used to study the intracellular signaling pathways that underlie the development of breast cancer. As shown with fibroblast growth factor-2, the oncogenic/non-coding mRNA H19 and 14-3-3 proteins, proteomics is a powerful approach to identify signaling proteins and to decipher the complex signaling circuitry involved in growth of breast cancer cells. Together with genomics, proteomics is now providing a way to define molecular processes involved in breast cancerogenesis and to identify new therapeutic targets.

Assisted reproductive technologies: toward improving implantation rates and reducing high-order multiple gestations

Despite striking progress in reproductive medicine over the past quarter century, the number of high-order multiple gestations are unacceptably high, largely as a result of the drive to maintain pregnancy rates in a competitive range. Morphologic criteria are currently used to define the reproductive competence of individual embryos but are imperfect predictors of implantation potential. Current and potential strategies to improve the selection of embryos are described. By the use of several of these approaches, it is hoped that the overall number of embryos that are transferred will be reduced, thereby also reducing the multiple gestation rate.

The use of animal models in expression pharmacogenomic analyses

Expression pharmacogenomics applies genome/proteome scale differential expression technologies to both in vivo and in vitro models of drug response to identify candidate markers correlative with and predictive of drug toxicity and efficacy. It is anticipated to streamline drug development by triaging towards lead compounds and clinical candidates that maximize efficacy while minimizing safety risks. As the majority of expression pharmacogenomics will be performed on preclinical therapeutic candidates, compatibility with favored preclinical animal model systems will be essential. This review will address expression pharmacogenomics in the context of those animal model systems commonly used for pharmacokinetic, pharmacodynamic and toxicologic analyses. Specific discussions will cover: (A) relative robustness of genomic and proteomic technology platforms used to generate drug response data in critical model systems; (B) animal handling, treatment and other experimental design optimizations; (C) data analysis strategies for extracting and validating candidate pharmacogenomic markers; and (D) overarching limitations in applying expression pharmacogenomics to animal model systems.

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae

Using an integrated genomic and proteomic approach, we have investigated the effects of carbon source perturbation on steady-state gene expression in the yeast Saccharomyces cerevisiae growing on either galactose or ethanol. For many genes, significant differences between the abundance ratio of the messenger RNA transcript and the corresponding protein product were observed. Insights into the perturbative effects on genes involved in respiration, energy generation, and protein synthesis were obtained that would not have been apparent from measurements made at either the messenger RNA or protein level alone, illustrating the power of integrating different types of data obtained from the same sample for the comprehensive characterization of biological systems and processes.

Ion/ion chemistry as a top-down approach for protein analysis

Developing methodology for analyzing complex protein mixtures in a rapid fashion is one of the most challenging problems facing analytical biochemists today. Recent advances in mass spectrometry for the analysis of intact proteins (i.e. the top-down approach) show great promise for rapid protein identification. The ion/ion chemistry approach for the detection and identification of target proteins in complex matrices, determination of fragmentation channels as a function of precursor ion charge state, and post-translational modification characterization are discussed with particular emphasis on tandem mass spectrometry of intact proteins.

On the nature of the chemical noise in MALDI mass spectra

The so-called "chemical noise background" imposes a major limit on the practical sensitivity of MALDI mass spectrometry. Typically, as the amount of material of interest subjected to MALDI analysis is reduced, the signal decreases to the point where it can no longer be differentiated from the chemical noise. Using a newly designed MALDI-ion trap mass spectrometer, we describe experiments intended to throw light on the nature of the chemical noise background and to reduce its effects. Single-stage mass spectrometric signals from peptides were observed to disappear into the noise when the amount of sample applied to the MALDI sample stage was decreased to less than a femtomole. At these low levels, analysis of the collision-induced fragmentation spectra revealed the presence of ions originating from the peptide as well as cluster ions that originate from the chemical noise. The fragmentation pattern arising from dissociation of the cluster species suggests that they are composed largely of matrix molecules. A significant fraction of these cluster ions can be dissociated at activation energies lower than the threshold for peptide fragmentation. We used this finding to collisionally pre-activate MALDI ions to remove a significant portion of the chemical noise from the spectrum, allowing us to obtain readily discernible single stage MS signals from 100 attomols of peptide. The strategy also yielded high quality MS/MS spectra from 100 attomols of peptide. Different possibilities of collisional pre-activation for improving sensitivity are considered.

Manipulation of temperature to improve solubility of hydrophobic proteins and cocrystallization with matrix for analysis by MALDI-TOF mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) requires cocrystallization of analyte with a large excess of matrix, which must be mutually soluble in a solvent that encourages crystal growth upon evaporation. MALDI-MS of hydrophobic proteins can be difficult, because they tend to aggregate in polar solutions. High concentrations of denaturants and salts are often employed to combat protein aggregation, but this can result in signal suppression. By using various organic cosolvent systems and matrixes at different protein:matrix ratios, we were able to use MALDI-TOFMS to detect four bacterially expressed hydrophobic proteins comprising alanine-rich mutants of the basic region/leucine zipper protein (bZIP) GCN4. By manipulating sample temperature, we were able to maintain protein solubility. Protein aggregation was suppressed when mixing the protein and matrix solutions at 4 degrees C prior to warming to 37 degrees C, following the temperature-leap technique described by Xie and Wetlaufer (Protein Sci. 1996, 5, 517-523), who used this method to renature bovine carbonic anhydrase II. Manipulation of temperature encouraged our hydrophobic proteins to adopt conformations leading to the nonaggregating state, and solubility was maintained even when the concentration of denaturant was reduced from 4 M to 400 mM. The temperature-leap tactic was critical for maintaining protein solubility, preventing signal suppression normally seen with higher concentrations of salts, allowing for generation of superior spectra, and should prove applicable to other systems prone to aggregation.

Proteome, transcriptome and genome: top down or bottom up analysis?

Biological systems are comprised of protein components found at a wide variety of abundances from millions of molecules of a single species per cell to less than one copy per cell. Because of this wide range of concentrations, measurement or a full accounting of each system is presently unavailable. Conventional separation and analytical methods (two-dimensional gel electrophoresis and mass spectrometry) allow identification and quantitation of many of the most abundant gene products (top down methods); and the majority of gene products, which are found at low abundance, can be neither identified nor measured in complex mixtures at present. The gene products that are found at low levels can be characterized and their properties analyzed by preparing ordered gene libraries of limited complexity from mRNA. When such preparations are expressed in cell free systems and analyzed by two-dimensional gel electrophoresis, the features of the gene products are available for analysis. This 'bottom up' approach allows identification of gene product properties so that analytical procedures can be devised and applied to complex mixtures.

Unravelling cell wall formation in the woody dicot stem

Populus is presented as a model system for the study of wood formation (xylogenesis). The formation of wood (secondary xylem) is an ordered developmental process involving cell division, cell expansion, secondary wall deposition, lignification and programmed cell death. Because wood is formed in a variable environment and subject to developmental control, xylem cells are produced that differ in size, shape, cell wall structure, texture and composition. Hormones mediate some of the variability observed and control the process of xylogenesis. High-resolution analysis of auxin distribution across cambial region tissues, combined with the analysis of transgenic plants with modified auxin distribution, suggests that auxin provides positional information for the exit of cells from the meristem and probably also for the duration of cell expansion. Poplar sequencing projects have provided access to genes involved in cell wall formation. Genes involved in the biosynthesis of the carbohydrate skeleton of the cell wall are briefly reviewed. Most progress has been made in characterizing pectin methyl esterases that modify pectins in the cambial region. Specific expression patterns have also been found for expansins, xyloglucan endotransglycosylases and cellulose synthases, pointing to their role in wood cell wall formation and modification. Finally, by studying transgenic plants modified in various steps of the monolignol biosynthetic pathway and by localizing the expression of various enzymes, new insight into the lignin biosynthesis in planta has been gained.

Proteomic analysis of apoptosis initiation induced by all-trans retinoic acid in human acute promyelocytic leukemia cells

The irreversible destiny of apoptosis in its early stage might play a critical role in the apoptosis of human acute promyelocytic leukemia (APL) cell line induced by all-trans retinoic acid (ATRA). To characterize protein alterations during the apoptosis-initiation phase and to understand the metabolic status at that time, we investigated the protein profiles in the apoptosis-initiation phase of APL cell line HL-60 by proteomic analysis. ATRA-withdrawal was conducted to demonstrate that there was committed initiation phase of apoptosis triggered by 10(-6) M ATRA at day 3. Only after that time point, ATRA-treated cells irreversibly went to apoptosis. Also at that time point, the positive regulators of apoptosis such as STAT3 increased at protein level, whereas negative regulators (Bcl-2 and p-STAT3) decreased. In addition, caspase-3 also increased after that time. Furthermore, comparative proteomic analysis was utilized to examine the protein expression profiles during the initiation stage of apoptosis. Our results showed 12 upregulated and 7 downregulated proteins experiencing twofold alteration, including key regulators of signal transduction such as G-proteins and nucleic receptors, proteins related with metabolism, oxidation and reduction, proteins associated with the nucleus and cytoskeleton-related proteins. Some of them could be positive modulators to trigger apoptosis, whereas others could contribute to intracellular defense against apoptosis induced by exogenous triggers. The results above suggest that there is a subtle balance between apoptosis and the intracellular defense against apoptosis. Once the balance is disturbed, cells would irreversibly initiate to undergo the execution of apoptosis.

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching

MALDI-quadrupole time-of-flight mass spectrometry was applied to identify proteins from organisms whose genomes are still unknown. The identification was carried out by successively searching a sequence database-first with a peptide mass fingerprint, then with a packet of noninterpreted MS/MS spectra, and finally with peptide sequences obtained by automated interpretation of the MS/MS spectra. A "MS BLAST" homology searching protocol was developed to overcome specific limitations imposed by mass spectrometric data, such as the limited accuracy of de novo sequence predictions. This approach was tested in a small-scale proteomic project involving the identification of 15 bands of gel-separated proteins from the methylotrophic yeast Pichia pastoris, whose genome has not yet been sequenced and which is only distantly related to other fungi.

Spot the differences: proteomics in cancer research

Separation of thousands of cellular proteins by two-dimensional electrophoresis allows the detailed comparison of proteins from normal and diseased tissue. Mass spectrometry provides a fast and reliable way of characterising proteins of interest, particularly when the gene sequence of the source organism is known. The availability of the human genome sequence has opened up the possibility of identifying protein differences between normal and diseased tissue, thus providing the opportunity to search for tumour markers or for therapeutic targets. This new technology will give much-needed insight into the molecular mechanisms of tumour development and progression.

The human genome project: a historical perspective

Efforts in genomics over the last decade have created a stream of opportunities for drug discovery. High-throughput DNA sequencing has forced a re-definition of the paradigm for identification and validation of targets for drug development. One purpose of this review is to delineate the different approaches to sequence data generation and to establish their various uses for the definition of gene function. There still remain crucial dilemmas for the pharmaceutical industry. The multitude of potential targets can each absorb enormous validation costs and the vast majority are likely to prove academically interesting but useless for drug development. An additional dimension arises from the importance of sequence variation between different individuals. These differences can determine response to therapy and must inform both the drug development process and healthcare delivery. This presents great challenges and opportunities for drug companies, their customers and society as a whole. I will review the technological aspects in some detail and give my view of the legal and social aspects. The field of bioinformatics is at the core of functional and pharmacogenomics and advances will depend on the continuing evolution of tools to interpret data. For the most part this evolution is reviewed in the context of specific application areas rather than as a discrete field, in recognition of its all-pervasive effects.

Use of atmospheric pressure ionization mass spectrometry in enantioselective liquid chromatography

Recent advances in mass spectrometry have rendered it an attractive and versatile tool in industrial and academic research laboratories. As a part of this rapid growth, a considerable body of literature has been devoted to the application of mass spectrometry in studies involving enantioselectivity, molecular recognition, and supramolecular chemistry. In concert with separation techniques such as capillary electrophoresis and liquid chromatography, mass spectrometry allows rapid characterization of a large array of molecules in complex mixtures. A majority of these findings have been made possible by the introduction of 'soft-ionization' techniques such as electrospray ionization interface. Other techniques such as atmospheric pressure chemical ionization mass spectrometry have been widely used as a rugged interface for quantitative liquid chromatography-mass spectrometry. Herein, we present a brief overview of the above techniques accompanied with several examples of enantioselective capillary electrophoresis- and liquid chromatography-mass spectrometry in drug discovery and development. Although the emphasis of this article is on quantitative enantiomeric chromatography-mass spectrometry, we envisage that similar strategies are adaptable in qualitative studies.

The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics

Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed.