High-resolution MALDI Fourier transform mass spectrometry of oligonucleotides

The Role of Mass Spectrometry in the "Omics" Era

Mass spectrometry (MS) is one of the key analytical technology on which the emerging ''-omics'' approaches are based. It may provide detection and quantization of thousands of proteins and biologically active metabolites from a tissue, body fluid or cell culture working in a ''global'' or ''targeted'' manner, down to ultra-trace levels. It can be expected that the high performance of MS technology, coupled to routine data handling, will soon bring fruit in the request for a better understanding of human diseases, leading to new molecular biomarkers, hence affecting drug targets and therapies. In this review, we focus on the main advances in the MS technologies, influencing genomics, transcriptomics, proteomics, lipidomics and metabolomics fields, up to the most recent MS applications to meta-omic studies.

Large Molecule Characterization Based upon Individual Ion Detection with Electrospray Ionization-FTICR Mass Spectrometry

We report a new method for mass spectrometric measurements of high-molecular-weight species based on the summation of sequential Fourier transform ion cyclotron resonance (FTICR) spectra of individual multiply charged ions. This approach produces statistically useful mass spectra for large multiply charged molecular species formed by electrospray ionization and circumvents conventional limitations upon achievable resolving power and precision for high-molecular-weight species which arise due to Coulombic constraints. For very large molecules with tens to thousands of charges each, the total number of charges required to define the charge-state distribution, and thus provide accurate mass information, greatly exceeds the useful charge capacity of the FTICR cell. As trapped ion populations approach or exceed this capacity, FTICR performance degrades due to large frequency shifts, peak coalescence phenomena, and rapid loss of ion packet coherence, which effectively precludes high-resolution and precision measurements for molecules above ∼80-kDa size for a 7-T magnetic field strength. The present approach is based on the summation of many spectra having moderate populations of individual ions and relies on sensitivity sufficient for individual ion detection. While the number of trapped ions contributing to each mass spectrum may generally be insufficient to define the isotopic or charge-state distributions (and thus produce accurate information on the molecular weight distribution in a conventional fashion), the present data processing and summation approach suppresses the noise component (as well as smaller signals) that would otherwise be problematic. Importantly, this approach circumvents natural limitations for very high molecular weight species due to Coulombic interactions and thus provides a basis for much greater resolution and mass measurement accuracy than otherwise possible. This paper presents the details of this approach and its demonstration for the 66-kDa protein bovine serum albumin (where the conventional approach is also feasible) and discusses important aspects of the data manipulation.

Mass spectrometry in systems biology: an overview

As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future.

Ion thermalization using pressure transients in a quadrupole ion trap coupled to a vacuum matrix-assisted laser desorption ionization source and a reflectron time-of-flight mass analyzer

Efficient trapping and detection of intact peptide ions is demonstrated in a quadrupole ion trap (QIT) coupled to an external vacuum matrix-assisted laser desorption ionization (MALDI) source. Deactivation of metastable ions generated by MALDI is achieved in a pressure transient environment inside the QIT established by pulsing gas to access the higher pressures required for fast thermalization, without affecting vacuum conditions in the ion source and time-of-flight (TOF) mass analyzer. Pressure transients are experimentally determined and a threshold of approximately 10 mTorr is identified where internally excited ions, which commonly observed to dissociate upon injection in a QIT, are stabilized. Fragment-free spectra are presented for a set of peptides by using 2,5-dihydroxybenzoic acid (DHB) as a matrix, and significantly reduced fragmentation is observed by using a-cyano-4-hydroxycinnamic acid (CHCA). Intact peptide spectra of a protein tryptic digest are also recorded with CHCA. The process of translational cooling for externally injected ions in a dynamic pressure environment is visualized by using ion trajectory simulations that employ hard sphere collisions. Statistical theory of dynamic equilibrium of ions stored in rf fields is applied to our QIT to characterize a translationally thermalized ion cloud, to explain observed ejection efficiency into the TOF mass analyzer, and to further discuss collisional deactivation of metastable ions.

Analysis of nucleic acids by FTICR MS

Fourier transform ion cyclotron resonance (FTICR) mass spectrometry represents a unique platform with which to study nucleic acids and non-covalent complexes containing nucleic acids moieties. In particular, systems in which very high mass measurement accuracy is required, very complex mixtures are to be analyzed, or very limited amounts of sample are available may be uniquely suited to interrogation by FTICR mass spectrometry. Although the FTICR platform is now broadly deployed as an integral component of many high-end proteomics-based research efforts, momentum is still building for the application of the platform towards nucleic acid-based analyses. In this work, we review fundamental aspects of nucleic acid analysis by FTICR, focusing primarily on the analysis of DNA oligonucleotides but also describing applications related to the characterization of RNA constructs. The goal of this review article is to give the reader a sense of the breadth and scope of the status quo of FTICR analysis of nucleic acids and to summarize a few recently published reports in which researchers have exploited the performance attributes of FTICR to characterize nucleic acids in support of basic and applied research disciplines including genotyping, drug discovery, and forensic analyses.

Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA

Atmospheric pressure (AP) MALDI has been combined with Fourier transform mass spectrometry (FTMS) to obtain the unambiguous characterization of RNA samples modified by solvent accessibility reagents used in structural studies of RNA and protein-RNA complexes. The formation of cation adducts typical of MS analysis of nucleic acids was effectively reduced by extensive washing of the anionic analytes retained onto the probe surface by strong interactions with a cationic layer of poly(diallyldimethylammonium chloride) (PADMAC). This rapid desalting procedure allowed for the detection of DNA and RNA samples in high femtomole quantities distributed over a 4 x 4 mm sample well. AP MALDI-FTMS was shown to provide high-resolution spectra for analytes as large as approximately 6.4 kDa with little or no evidence of metastable decomposition. The absence of significant metastable decay observed for precursor ions selected for tandem experiments offered a further measure of the low energy content typical of ions generated by AP MALDI. This feature proved to be very beneficial in the characterization of chemically modified RNA samples, which become particularly prone to base losses upon alkylation. The high resolution offered by FTMS enabled the application of a data-reduction algorithm capable of rejecting any signal devoid of plausible isotopic distribution, thus facilitating the analysis of complex analyte mixtures produced by nuclease treatment of RNA substrates. Proper selection of nucleases and digestion conditions can ensure the production of hydrolytic fragments of manageable size, which could extend the range of applicability of this bottom-up strategy to the structural investigation of very large RNA and protein-RNA complexes.

Production and fragmentation of multiply charged ions in 'electron-free' matrix-assisted laser desorption/ionization

An unusually large fraction of multiply charged ions is observed in 'electron-free' matrix-assisted laser desorption/ionization (MALDI). Here we investigate how the yield of multiply charged ions depends on experimental parameters in MALDI. It is found to increase if measures are taken to limit the number of electrons in the plume, for example, by using non-metallic MALDI targets or low laser pulse energies. The ionization energy of the matrix is another important parameter that affects the yield of multiply charged ions: matrices with high ionization energies lead to greater intensities of multiply charged ions. It is furthermore proposed that some of the fragment ions observed in MALDI are due to reactions of analyte with electrons in the plume. The possibility of electron capture dissociation of multiply charged ions produced by MALDI is shown.

Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.

Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved

Sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) of DNA is critical for obtaining high quality mass spectra. Sample impurity, solvent content, substrate surface and environmental conditions (temperature and humidity) all affect the rate of matrix-analyte co-crystallization. As a result, laser fluence threshold for desorption/ionization varies from spot to spot. When using 3-hydroxypicolinic acid (3-HPA) as the matrix, laser fluence higher than the threshold value reduces mass resolution in time-of-flight (TOF) MS as the excess energy transferred to DNA causes metastable decay. This can be overcome by either searching for 'hot' spots or adjusting the laser fluence. However, both solutions may require a significant amount of operator manipulation and are not ideal for automatic measurements. We have added various sugars for crystallization with the matrix to minimize the transfer of excess laser energy to DNA molecules. Fructose and fucose were found to be the most effective matrix additives. Using these additives, mass resolution for DNA molecules does not show noticeable deterioration as laser energy increases. Improved sample preparation is important for the detection of single nucleotide polymorphisms (SNPs) using primer extension with a single nucleotide. During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization.

A high pressure matrix-assisted laser desorption/ionization Fourier transform mass spectrometry ion source for thermal stabilization of labile biomolecules

A high pressure matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) ion source was designed and tested. With this design, pressure is pulsed to an estimated 1-10 mbar in the region of the MALDI sample during desorption with the result of significantly decreased fragmentation compared to similar systems operating with pressures of <0.1 mbar. The thermal stabilization of vibrationally excited ions under these conditions is shown with small peptides desorbed from the "hot" matrix alpha-cyano-4-hydroxycinnamic acid, and with the highly labile oxidized beta-chain of insulin. Fragile gangliosides with several sialic acid residues are desorbed under high pressure and remain intact without the typical losses of sialic acid, and a protein standard, ubiquitin (8565.64 Da), is desorbed with minimal dehydration. Under high pressure collisional cooling conditions, non-covalent matrix adduction to the molecular ions becomes prominent, but with the trapped ions in an FT mass spectrometer, the ions can be mildly activated to detach the matrix adducts. The new source, additionally, generates significant levels of the multiply charged ions which are commonly seen in MALDI-TOFMS, but are rarely observed in MALDI-FTMS. This effect is more likely due to the elimination of a mass filtering effect in the previous FTMS ion source than to collisional cooling of the ions.

Formulation of matrix solutions for use in matrix-assisted laser desorption/ionization of biomolecules

We report a simple method for converting solid matrices into useful matrix solutions for matrix-assisted laser desorption/ionization (MALDI). This method is based on the dissolution of the solid matrix in a liquid support of low volatility such as glycerol. An appropriate solubilizing reagent was added to promote the dissolution of the matrix materials into the liquid support. Selection of the solubilizing reagent is empirically related to an acid-base relationship, i.e., an acidic solid matrix requires a basic organic compound to form a stable matrix solution in the liquid support and vice versa. A tenfold increase in the solubility can be obtained for many solid matrices when appropriate solubilizing reagents are added into the glycerol support. This solubility enhancement is tentatively attributed to the ion-pair formation in a polar nonvolatile liquid support. In addition, the hydrophobicity of the solid matrix seems to play an important role in the efficiency of the resulting matrix solution. By using glycerol as liquid support, a hydrophilic matrix, such as 2,5-dihydroxybenzoic acid (DHB), showed a substantial "peripheral effect," in which good analyte ion signals could only be recorded at the peripheral region of the sample droplet. More hydrophobic matrices, such as alpha-cyano-4-hydroxycinnamic acid (alpha-CCA), exhibit better and more homogeneous responses at different regions of the droplets. The performance of these matrix solutions was evaluated in terms of the durability, reproducibility, sensitivity, high mass capability, and generality. A typical sample droplet can afford more than an hour of repeated sampling with excellent shot-to-shot reproducibility. A low picomole sensitivity was demonstrated using a luteinizing hormone releasing hormone (LHRH) in a Fourier transform ion cyclotron resonance mass spectrometer with a homemade external MALDI ion source. By using a commercial MALDI time-of-flight mass spectrometer, proteins with masses as high as 66,000 Da were successfully analyzed by using these matrix solutions.

Mass spectrometry at low and high mass

The introduction of novel methods as well as expanding applications to diverse areas highlight truly impressive progress in mass spectrometry. These developments are illustrated here by two seemingly different areas of research: new methods designed for the determination of isotopic enrichment and novel ionization methods; and mass analyzers which have enabled the precise determination of the molecular weight of proteins and large oligonucleotides.

Time, life ... and mass spectrometry. New techniques to address biological questions

Within the last ten years, startling new developments in two ionization methods--matrix-assisted laser desorption (MALDI) and electrospray (ESI)--have been described by Karas et al. [M. Karas, D. Bachmann, U. Bahr, F. Hillenkamp, Int. J. Mass Spectrom. Ion Proc., 78 (1987) 53.] and by Fenn et al. [J.B. Fenn, M. Mann, C.K. Meng, S.F. Wong, C.M. Whitehouse, Science, 246 (1989) 64.], respectively. Their work demonstrated that these techniques, under appropriate experimental conditions, have high sensitivity and wide mass range, extending to hundreds of thousands of daltons and beyond, and thus can be extremely effective for the study of biopolymers. The result has been a revolution in the way that mass spectrometry experiments are carried out, a widening of the range of investigators who employ mass spectrometry in their own laboratories and a penetration of mass spectrometry into the investigation of biological phenomena that exceeds any previous expectations. Progress in improving mass spectral ionization and mass analysis methods and in interpreting and understanding the spectra is actively being pursued and exploited in many laboratories, to capitalize even further upon these advances. The results should facilitate understanding of structure-activity relationships pertinent to biology and medicine. In our laboratory, the focus of research is on oligosaccharide and glycoconjugate structural determinations, and on the improvement of methods for these important classes of compounds that relate to development, immune response, signalling, lipid and protein transport and disease. Representative examples of applications of MALDI and ESI mass spectrometry to these and other biological questions are provided herein.

Fourier transform mass spectrometry-advancing years (1992-mid. 1996)

This article is one of a series of Fourier transform mass spectrometry (FTMS) reviews that has appeared in this journal at ca. 3-4 year intervals. A comprehensive review of the recent theoretical developments, instrumental developments, electrospray ionization (ESI), and MALDI is given. Ion dissociation techniques are also discussed because of their contributions to gaining insight into chemical structure. Special sections have been devoted to discussing the emerging fields of surface analysis, polymer analysis, Buckminsterfullerenes (buckyballs), and hydrogen/deuterium exchange studies. This review, although not all-inclusive, is intended to be a starting point for those wishing to learn more about the current status of FTMS, and also as a representative cross-section of the literature for those familiar with the technique. © 1997 John Wiley & Sons, Inc.