Matrix-assisted laser desorption ionization of oligonucleotides with various matrices

Matrix assisted ionization: new aromatic and nonaromatic matrix compounds producing multiply charged lipid, peptide, and protein ions in the positive and negative mode observed directly from surfaces

Matrix assisted inlet ionization (MAII) is a method in which a matrix:analyte mixture produces mass spectra nearly identical to electrospray ionization without the application of a voltage or the use of a laser as is required in laserspray ionization (LSI), a subset of MAII. In MAII, the sample is introduced by, for example, tapping particles of dried matrix:analyte into the inlet of the mass spectrometer and, therefore, permits the study of conditions pertinent to the formation of multiply charged ions without the need of absorption at a laser wavelength. Crucial for the production of highly charged ions are desolvation conditions to remove matrix molecules from charged matrix:analyte clusters. Important factors affecting desolvation include heat, vacuum, collisions with gases and surfaces, and even radio frequency fields. Other parameters affecting multiply charged ion production is sample preparation, including pH and solvent composition. Here, findings from over 100 compounds found to produce multiply charged analyte ions using MAII with the inlet tube set at 450 °C are presented. Of the compounds tested, many have -OH or -NH(2) functionality, but several have neither (e.g., anthracene), nor aromaticity or conjugation. Binary matrices are shown to be applicable for LSI and solvent-free sample preparation can be applied to solubility restricted compounds, and matrix compounds too volatile to allow drying from common solvents. Our findings suggest that the physical properties of the matrix such as its morphology after evaporation of the solvent, its propensity to evaporate/sublime, and its acidity are more important than its structure and functional groups.

Sodium controlled selective reactivity of protonated deoxy-oligonucleotides in the gas phase

Metastable fragmentation of the positively charged, hexameric oligonucleotides 5'-d(TTXYTT) (X and Y are dC, dG, or dA) and 5'-d(CTCGTT), 5'-d(TTCGTC) and 5'-d(CTCGTC) is studied after matrix assisted laser desorption/ionization (MALDI). The influence of the degree of sodiation, i.e., when the acidic protons are one by one exchanged against sodium ions, is systematically studied for the exchange of up to seven protons against sodium ions. Exchanging the acidic protons against sodium gradually quenches the backbone cleavage through the w and a-B channels, and quantitative quenching of these channels is generally achieved with the exchange of four protons against sodium ions. At the same time, the exchange of protons against sodium ions promotes the loss of a neutral, high proton affinity base. The formation of the w and a-B fragments is found to be highly dependent on the sequence of the central bases. A single mechanism consistent with these observations is proposed. In addition to the quenching of the classical w and a-B reaction channels, a drastic and abrupt on/off-switching of new reaction channels is observed as the degree of sodiation successively increases. These channels involve selective loss of the two central bases and the excision of a phosphodiester group and a sugar unit from the center of the oligonucleotides. Synchronously, the two terminal fragments recombine to form a tetramer containing the two terminal nucleosides from each end of the hexamer. Possible mechanism explaining these remarkable channels are discussed.

Characterization of the molecular mass distribution of pullulans by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using 2,5-dihydroxybenzoic acid butylamine (DHBB) as liquid matrix

The performances of several matrices were investigated for the accurate determination of the molecular mass distributions of pullulans by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The ionic liquid matrix (ILM) 2,5-dihydroxybenzoic acid butylamine (DHBB) gave better and more reliable results than the crystalline matrices 2,5-dihydroxybenzoic acid (DHB) and 2,4,6-trihydroxyacetophenone (THAP). With the ILM it was possible to obtain spectra of pullulans up to more than 100 kDa, the highest molar mass reported thus far. Owing to the known advantages of liquid matrices providing better spot-to-spot reproducibility, an almost noise-free spectrum and constant baselines were obtained when working under optimized conditions. In particular, the extent of in-source fragmentation occurring with this group of fragile polymers was considerably and decisively reduced. Thus, a more reliable representation of the true oligomer and polymer distributions is experimentally attainable, especially for distributions with small polydispersity values. The maximum error in the measured distribution associated with fragmentation was estimated by model calculations describing the changes in the polymer distribution upon different probabilities of fragmentation events. These simulation results indicated that the data obtained by MALDI-TOFMS using the liquid DHBB matrix were of high reliability. In particular, the average value of the distributions, M(w), and the polydispersity were obtained with predicted uncertainties of between 3 and 15% depending on the width of the distribution and the mass of the polymers.

Negative ion ultraviolet matrix-assisted laser desorption ionization mass spectrometry and post source decay of glycosyl esters of nucleoside pyrophosphates

Six different glycosyl esters of nucleoside pyrophosphates (monosaccharide nucleotides) were analyzed by means of matrix-assisted laser desorption/ionisation reflectron time-of-flight mass spectrometry (MALDI/RToF MS) in the negative ion mode. Several matrices were evaluated and 3-hydroxypicolinic acid as well as alpha-cyano-4- hydroxycinnamic acid (CHCA) turned out to be the matrices of choice applying the thin layer technique to obtain maximum sensitivity for deprotonated molecular ion detection and maximal fragmentation particular with CHCA. The determination of the molecular mass with a mass accuracy below 0.1% was feasible with sample amounts in the lower femtomole range applying a MALDI desk-top mass spectrometer. A further important refinement of this technique was the use of post source decay (PSD) fragment ion analysis with a curved field reflector (which means no stepping of the reflector voltage). Detailed structural information of the six selected monosaccharide nucleotides could be obtained with PSD and differences in the fragmentation pattern were used to distinguish them. This method (based on molecular mass and PSD fragment ion analysis) has been applied to verify the presence of a glycosyl ester of nucleoside pyrophosphate in samples from Saccharomyces cerevisiae.

Matrix-assisted laser desorption/ionization mass spectrometry of polysaccharides with 2',4',6'-trihydroxyacetophenone as matrix

So far, there have been only a few matrices reported for detection of polysaccharides with molecular weight higher than 3000 Daltons by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). In this work, we found that 2',4',6'-trihydroxyacetophenone (THAP) is a good matrix for MALDI time-of-flight MS analysis of polysaccharides with broad mass range. Large polysaccharides, dextrans, glycoproteins and polysialic acids have been successfully detected by MALDI-MS with THAP as matrix.

Effect of matrix crystal structure on ion abundance of carbohydrates by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry

Sample preparation techniques for carbohydrate analysis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are explored, with particular emphasis on analyte/matrix co-crystallization procedures. While carbohydrates are known to prefer 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix of choice, these analytes are quite specific about matrix crystal structure, which in turn is dependent on the rate of drying of analyte/matrix spots on the MALDI target. With N-acetylglucosamine (GlcNAc) and N-acetylneuraminic acid (sialic acid or NeuAc) as test monosaccharides, significant increases in ion abundances are demonstrated with 2,5-DHB/NeuAc spots (>10-fold improvement) and 2,5-DHB/GlcNAc spots ( approximately 5-fold improvement) with active drying. The fine structure of crystals generated in active and passive drying was investigated using powder diffraction. Passively dried samples were shown to consist of an ordered polymorph, crystallizing in the space group P2(1)/a, while the actively dried samples produced a disordered phase crystallizing in the space group Pa. These data provide the wherewithal to engineer a matrix best suited for carbohydrate analyses.

Mass spectrometry of RNA

A complex population of non-coding RNAs is present in higher organisms. These RNAs have a multitude of functions and execute control over gene expression through various, often poorly understood, mechanisms. At present, the identification and analysis of functional regulatory RNAs and disparate ribonucleoprotein complexes remain an experimental challenge for biologists. They require specially designed approaches and techniques in genomics and RNA biochemistry. Developments in technologies based on mass spectrometry could offer sensitive and efficient solutions to analysis of the sequence, structure, modification and composition of RNA.

[Determination of oligonucleotide molecular masses by MS-MALDI]

MALDI mass spectrometry (MS) of 14- to 42-mer homogeneous oligonucleotides and their mixtures was carried out using a Vision 2000 instrument (Thermo BioAnalysis, Finnigan, United States). Conditions for the determination of oligonucleotide molecular masses were optimized by applying various matrices and operation modes. The most reproducible results with minimal uncontrolled decomposition of the oligonucleotides including their apurinization during the MALDI MS registration were obtained using 2,4,6-trihydroxyacetophenone as a matrix instead of 3-hydroxypicolinic acid, usually employed in the mass spectrometry of oligonucleotides. Our approach allows the determination of molecular masses of oligonucleotides obtained by chemical synthesis and the evaluation of their component composition and purity. It was applied to the mass spectrometric analysis of oligonucleotides containing a 3'-(methyl-C-phosphonate) group or a modified 1,N6-ethenodeoxyadenosine unit.

A study of fast and metastable dissociations of adenine-thymine binary-base oligonucleotides by using positive-ion MALDI-TOF mass spectrometry

In the present study, fast and metastable dissociations of a number of adenine-thymine binary-base oligonucleotides under the conditions of UV matrix-assisted laser desorption/ionization mass spectrometry were investigated. 2-Aminobenzoic acid/ammonium fluoride (ABA/NH4F) matrix system was used. The spectra obtained under metastable and fast dissociation conditions exhibit distinctive dissociation products. From the post-source-decay analysis, all oligonucleotides underwent predominantly metastable dissociations at the 3' C-O linkages to form [a(n)-B]+ and w(n)+ complimentary ion series. Based on the present results, the so-called "[wn+80]+" ions were postulated to be the complimentary [Z(8-n)AH]+ ions rather than the expected phosphate rearrangement products. In addition, these oligonucleotides were found to generate fast dissociation products of b(n)+, d(N)+, w(N)+ and y(N)+ ions through backbone cleavages at 5' C-O, 5' O-P, 3' C-O and 3' P-O linkages, respectively. Product ion series formed under PSD conditions were not observed. The implications of this mutually exclusive occurrence of the two sets of fragment ions under fast and metastable conditions using ABA/NH4F matrix would be discussed. A model of ion activation under UV-MALDI conditions was also proposed.

Nonresonant MALDI of oligonucleotides: mechanism of ion desorption

Oligonucleotide ions have been detected using matrix-assisted laser desorption/ionization (MALDI) under nonresonant laser irradiation of the sample. When mass resolution was not limited by adduct attachment to the analyte ions, the nonresonant MALDI spectra demonstrated better resolution than the spectra acquired with resonant ultraviolet irradiation. We found that preparation of thin-film samples on absorbing substrate surfaces was critical for the success of NR-MALDI. The possible acoustic mechanisms of ion formation and desorption are discussed.

Ionization mechanism of oligonucleotides in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The ionization of nucleosides in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was systematically investigated using adenine (A), thymine (T), guanine (G) and cytosine (C) with several common matrices. Experimental results of the protonation and deprotonation of the bases of A, T, G and C in the matrices 2,5-dihydroxybenzoic acid (2,5-DHB), alpha-cyano-4-hydroxycinnamic acid (alpha-CHCA) and 3-hydroxypicolinic acid (3-HPA) provide an insight into the ionization mechanism of oligonucleotides in MALDI. It was found that the low ion signal from DNA in poly-G in MALDI as reported in earlier work could be attributed to the fact that the base of G is difficult to ionize. Our results suggest that the ionization of DNA in MALDI is dominated by the protonation and deprotonation of bases and it is basically independent of the backbone of DNA. Both the protonation and deprotonation are strongly structure dependent. The protonation is dominated by pre-protonation before laser ablation, while the deprotonation is controlled by the thermal reaction.

Polyamine co-matrices for matrix-assisted laser desorption/ionization mass spectrometry of oligonucleotides

The analysis of oligonucleotides using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has led to the investigation of the use of matrix additives (i.e., co-matrices) to help improve the poor spectral quality commonly observed during the analysis of this class of compounds. The use of certain matrix additives in MALDI-MS has been investigated previously, and these additives have been shown to enhance the desorption/ionization efficiency of oligonucleotides during the MALDI experiment. Specifically, amine bases, such as piperidine, imidazole, and triethylamine, have been shown to improve mass spectral quality as assessed by improved molecular ion resolution and increased molecular ion abundance. These improvements occur due to competition between the oligonucleotide and the co-matrix for protons generated during the MALDI event. Co-matrices with proton affinities near or above the proton affinities of the nucleotide residues serve as proton sinks during the desorption/ionization process. In this work, we have investigated the use of polyamines as co-matrices for MALDI mass spectrometric analysis of oligonucleotides. Spermine tetrahydrochloride, spermine, spermidine trihydrochloride, and spermidine were evaluated for their effectiveness at enhancing the mass spectral quality of oligonucleotides analyzed using MALDI-MS. The solution-phase pK( b) values and the gas-phase proton affinities of these polyamines were determined, and it was found that the polyamines appear to be more basic than the monofunctional amines investigated previously. The mass spectral data shows that spermidine and spermine are extremely effective co-matrices, yielding improved molecular ion resolution and molecular ion abundances. The spermine co-matrices are more effective than the spermidine co-matrices, but adduction problems with the spermine co-matrices limits their overall utility. In general, polyamine co-matrices are found to be more effective than monofunctional amine co-matrices at improving the mass spectral data obtained during MALDI-MS of oligonucleotides.

Mass spectrometry of nucleotides and oligonucleotides

Recent advances in the use of mass spectrometry for the determination of the molecular weight and sequencing of oligonucleotides are discussed. Matrix-assisted laser desorption (MALDI) and electrospray ionization (ESI) mass spectrometry have been shown to be especially important techniques for both molecular weight assignment and sequencing of oligonucleotides, and are the focus of this article which covers the literature through early 1996.

Laser desorption mass spectrometry for point mutation detection

A point mutation can be associated with the pathogenesis of inherited or acquired diseases. Laser desorption mass spectrometry coupled with allele specific polymerase chain reaction (PCR) was first used for point mutation detection. G551D is one of several mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene present in 1-3% of the mutant CFTR alleles in most European populations. In this work, two different approaches were pursued to detect G551D point mutation in the cystic fibrosis gene. The strategy is to amplify the desired region of DNA template by PCR using two primers that overlap one base at the site of the point mutation and which vary in size. If the two primers based on the normal sequence match the target DNA sequence, a normal PCR product will be produced. However, if the alternately sized primers that match the mutant sequence recognize the target DNA, an abnormal PCR product will be produced. Thus, the mass spectrometer can be used to identify patients that are homozygous normal, heterozygous for a mutation or homozygous abnormal at a mutation site. Another approach to identify similar mutations is the use of sequence specific restriction enzymes which respond to changes in the DNA sequence. Mass spectrometry is used to detect the length of the restriction fragments generated by digestion of a PCR generated target fragment.

Mass spectrometry of nucleic acids

The present article is a survey of ESI and MALDI mass spectrometric analysis of nucleic acid oligomers and polymers. In order to limit the extent of the review, mass spectrometry of mononucleotides is generally not considered, except where such data are important for an understanding of the analysis of larger nucleic acids. The first part of the review is a condensed description of the structure and the acid-base properties of nucleic acids. The remaining part is divided into three main sections, dealing with the practical aspects of the two ionization techniques, fragmentation, and applications, respectively. The first section includes an extensive discussion of experimental parameters and problems, which are important for the analysis of different types of nucleic acid samples, including noncovalent complexes and mixtures. At the end of this section, as well as the following one, a comparison between MALDI and ESI as ionization techniques for nucleic acid is given. In addition to a detailed discussion of ion fragmentation, the fragmentation section includes an overview of the direct mass spectrometric sequencing of nucleic acids performed with either technique. The fragmentation reactions occurring upon MALDI and ESI are compared. The last section describes the life science applications of ESI-MS and MALDI-MS of nucleic acids; an account of experiments demonstrating the potential of a method, and of the bona fide solving of problems by ESI and MALDI is given. © 1997 John Wiley & Sons, Inc.

Quadrupole ion trap mass spectrometry

A number of other features of ITMS systems that will enhance their ability to analyze biological macromolecules are worth mentioning. As has already been demonstrated for ESI/quadrupole, ESI/magnetic sector, and ESI/FTICR systems, the capability of inducing fragmentation of the ESI-generated multiply charged ions of biological macromolecules in the capillary/skimmer region of the ESI source and subsequently selectively analyzing fragments can also be carried out with the QITMS, as we have demonstrated using bovine serum albumin (data not shown). The ability to carry out chemical reactions on biological macromolecules inside the QITMS has been demonstrated by McCluckey et al. by showing that the introduction of a pulse of volatile base, such as diethylamine, can result in proton removal from multiply charged protein ions, resulting in species with lower charge states. The application of the technique of deuterium exchange of active hydrogens on peptides to simplify the interpretation of MS/MS sequencing experiments can be implemented for ESI/QITMS. Carrying out such exchange inside the ITMS may also be possible, with resulting analytical advantages. Reports of a hybrid QITMS-TOF system, which was operated with either ESI or MALDI methodology, and which demonstrated low femtomolar sensitivity with higher resolution of the TOF analyzer because of ion injection of essentially monoenergetic ions from the QITMS into the TOF, illustrate additional uses of the QITMS. The reverse combination (e.g., ESI/TOF/QITMS or MALDI/TOF/QITMS) could afford preselection of ions for even higher performance in the QITMS, because space charging (loss of performance such as resolution because of too much charge in close proximity in the ion trap) would be minimized. Opportunities for the application of QITMS technology for the analysis of biological macromolecules abound, including ultrahigh-sensitivity protein sequencing using specifically derivatized amino acids released by Edman chemistry; rapid sequencing of MHC-associated antigenic peptides of variable length (approximately nonamers for the MHC I complexes to > dodecamers for the MHC II complexes), which are available in only very low amounts (femtomole/attomole) and in very complex mixtures (5000-10,000 species) of closely related peptide structures; ultrahigh-sensitivity analysis of peptides and proteins directly in vivo using microelectrospray; direct analysis of metal ion binding to peptides and proteins and analysis of noncovalent interactions, including conformation; and possible analysis of plasmid DNA, as has been suggested by ESI ionization of a 2-MDa DNA species. In summary, the ability of the QITMS to interface to key separations systems such as HPLC and HPCE through the critical ionization techniques of ESI and MALDI, coupled with the high mass range, high mass resolution, high sensitivity, high-efficiency CID, and MS capabilities of this device, will provide an astonishing array of cost-effective capabilities for the qualitative and quantitative analysis of biological macromolecules.

The detection of intact double-stranded DNA by MALDI

DNA fragments have been analyzed by matrix-assisted laser desorption ionization (MALDI) and electrospray mass spectrometry. In many cases, only the single-stranded oligonucleotides have been detected. Recently, spectra of intact double-stranded DNA have been obtained in both electrospray and massive cluster impact ionization. We show here the first MALDI spectra of intact double-stranded DNA (EcoR1 adaptor 12/16) that is clearly not due to nonspecific dimer formation. 6-Aza-2-thiothymine was used as the matrix in the presence of ammonium citrate. Via the same procedure but with other matrices commonly employed for oligonucleotide analysis, the intact DNA duplex was not detected. No sign of the homodimer of either of the single strands is observed. Although the spectrum also shows peaks attributable to each of the single strands, these are demonstrated to arise from the DNA solution and not the sample preparation or desorption process.

Increased stability of nucleic acids containing 7-deaza-guanosine and 7-deaza-adenosine may enable rapid DNA sequencing by matrix-assisted laser desorption mass spectrometry

The use of matrix-assisted laser desorption mass spectrometry (MALDI-MS) has been suggested as an ultrafast readout of Sanger DNA sequencing ladders in a manner analogous to that used with sequencing gels. Currently, a serious limitation of MALDI-MS for the analysis of DNA results from the tendency for oligonucleotides to undergo facile fragmentation in the gas phase. The present study was undertaken to gain an understanding of the influence of various chemical structural features of purine bases on the stability of oligodeoxynucleotide ions produced by MALDI. The study focused on the stability of model compounds of the type d(TTTTTTTTTTXTTTTTTTTT TTTT), where T designates deoxythymidine and X a purine-containing 2'-deoxynucleotide. A variety of different purine derivatives were chosen as the base in the nucleotide X. The mass spectra of the model compounds containing 7-deaza analogues of guanine and adenine reveal a significantly increased stability compared to the 7-aza analogues under the conditions of MALDI-MS. The previously reported incorporation of the 7-deaza-2'-deoxy-adenosine triphosphate and the 7-deaza-2'-deoxy-guanosine triphosphate into DNA by polymerases suggests their use in a Sanger dideoxy sequencing experiment. The dideoxy termination products with the 7-deaza-purines instead of the 7-aza-purines might be sufficiently stable to allow separation and detection of the sequencing ladder by MALDI-MS. Thus, an ultrafast (seconds) read-out of DNA sequence may become feasible.

Characterization of oligonucleotides and nucleic acids by mass spectrometry

The continued refinement of two recent methods for producing gas-phase ions, electrospray ionization and matrix-assisted laser desorption ionization, has resulted in new techniques for the rapid characterization of oligonucleotides by mass spectrometry. Using commercially available instruments, molecular mass measurements at the 20-mer level, with errors less than 2 Da, can now be made routinely in less than 15 min. Progress has also been achieved in the development of mass spectrometry for rapid sequencing of oligonucleotides smaller than 25 residues.

High resolution matrix-assisted laser desorption/ionization time-of-flight analysis of single-stranded DNA of 27 to 68 nucleotides in length

Mass spectra of single-stranded DNA oligonucleotides were acquired using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Resolution enhancement using space-velocity correlation focusing allows for facile observation of different oligomers, the direct observation of individual DNA-metal adducts, and investigation of counter ion structure.

7-Deaza purine bases offer a higher ion stability in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry

Oligodeoxynucleotides which contain 7-deaza analogues of the normal purine nucleotides have been synthesized both enzymatically and chemically. When subjected to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis, the modified samples offer both higher stability and increased sensitivity compared to otherwise identical unmodified oligodeoxynucleotides. In view of these observations, models for the fragmentation of oligodeoxynucleotides in MALDI-MS with positive ion detection mode are presented. Additionally, the potential use of 7-deaza purine nucleotides in the MALDI-MS analysis of DNA sequencing reactions is discussed.

Matrix-assisted laser desorption/ionization mass spectrometry: improved matrix for oligosaccharides

The aim of this article was to study the influence of different matrix molecules on the quality of matrix-assisted laser desorption/ionization mass spectra of oligosaccharides. An important criterion was the sample preparation, i.e. the crystallization process leading to the matrix from which the analytes were desorbed and investigated. Quality criteria were, among others, the resulting molecular peak intensity, the mass resolution, and the suppression of unwanted matrix peak. It was found that a mixture of 2,5-dihydroxy benzoic acid (DHB) and 1-hydroxy isoquinoline (HIC) in a weight ratio of 3:1 was best suited for the analytical investigation of oligosaccharides. In addition, this matrix mixture was found to be quite tolerant against all kinds of buffers, salts, and even additives such as sodium dodecyl sulfate (SDS). Furthermore, we determined the different affinities of the alkaline metals to the carbohydrates and found that cesium and potassium ions ionize oligosaccharides about three times better than sodium ions and therefore have an important influence on the quantum yield.

3-Aminopicolinic acid as a matrix for laser desorption mass spectrometry of biopolymers

3-Aminopicolinic acid (3-APA) was tested and found to be a useful matrix for matrix-assisted laser desorption/ionization of DNA and protein. Single-stranded DNA segments of 150-mer and double-stranded DNA of 246 base pairs were successfully detected by using 3-APA as an ultraviolet-absorbing matrix in a linear time-of-flight mass spectrometer. In the case of the double-stranded DNA, only parent ions corresponding to single-stranded DNA were observed. The comparison with 3-hydroxypicolinic acid and picolinic acid matrices is discussed.

Matrix assisted laser desorption/ionization mass spectrometry of enzymatically synthesized RNA up to 150 kDa

Enzymatically synthesized RNA samples (in vitro transcripts) were analysed by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Spectra of RNA up to 150 kDA (461 nucleotides) are shown. Polymerase generated sample heterogeneity and its contribution to mass resolution are discussed. A time course exonuclease digest of a 55 nt in vitro transcript was analyzed to investigate the performance of MALDI-MS on complex mixtures. Based on these data, the analysis by MALDI-MS of DNA sequencing reactions, produced by the action of an RNA polymerase, is discussed.

Picolinic acid as a matrix for laser mass spectrometry of nucleic acids and proteins

We found that picolinic acid is a very good matrix for matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry of oligonucleotides, proteins and tRNA. Among the oligonucleotides, picolinic acid was shown to be effective for homo-oligonucleotides, d(G)40 and d(C)60, and for mixed-base oligonucleotides up to 190 bases. In the case of the single-stranded oligonucleotides, and of double-stranded ones as well, only parent ions corresponding to single-stranded DNA were observed. The efficiency for MALDI of oligonucleotides using the picolinic acid matrix was superior to that using 3-hydroxypicolinic acid. MALDI of transfer RNA phenylalanine-specific (tRNA(Phe)), a 76-base ribonucleic acid, was detected with a signal-to-noise ratio of > 10. By comparison with 3-hydroxypicolinic acid the results with picolinic acid are notably superior for all oligonucleotides.

Detection of 500-nucleotide DNA by laser desorption mass spectrometry

We report the first detection of DNA segments as large as 500 nucleotides by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, using picolinic acid and 3-hydroxypicolinic acid mixtures as desorption matrices. The successful detection of 500-nucleotide DNA indicates that laser mass spectrometry is now emerging as a new biotechnology tool for DNA-related research. It should be possible to utilize fast detection of large DNA segments by laser mass spectrometry for rapid human genome sequencing.

Matrix-assisted laser desorption/ionization mass spectrometry of restriction enzyme-digested plasmid DNA using an active Nafion substrate

Matrix-assisted laser desorption/ionization using a 3-hydroxypicolinic acid matrix from an active Nafion substrate has been used for detection of restriction enzyme-digested double-stranded plasmid DNA using time-of-flight mass spectrometry. DNA strands of up to 267 base pairs were detected with minimal sample purification, although only as species corresponding to single-stranded DNA.

Comparison of IR- and UV-matrix-assisted laser desorption/ionization mass spectrometry of oligodeoxynucleotides

UV-matrix assisted laser desorption/ionization mass spectrometry (UV-MALDI-MS) with 3-hydroxypicolinic acid as matrix and IR-MALDI-MS with succinic acid as matrix have proved their feasibility for highly accurate and sensitive mass determination of nucleic acids (DNA and RNA). In this work, a detailed comparison of these two MALDI-methods and between positive- and negative ion mass spectra for the analysis of oligodeoxynucleotides is undertaken. Mass spectra of DNA sequences with up to 40 nucleotides are shown. Both linear and reflectron time-of-flight mass analyzers were used within this study and are compared for their potential in the MALDI analysis of oligodeoxynucleotides. The role of molecule-ion fragmentation is also discussed.

Matrix-assisted laser desorption/ionization of restriction enzyme-digested DNA

Matrix-assisted laser desorption/ionization, by a time-of-flight mass spectrometer, has been successfully used for detection of restriction enzyme-digested DNA. However, the oligonucleotide segments detected correspond to the molecular weights of single strands.