A comparative study of in- and post-source decays of peptide and preformed ions in matrix-assisted laser desorption ionization time-of-flight mass spectrometry: Effective temperature and matrix effect

In-source decay (ISD) and post-source decay (PSD) of a peptide ion ([Y₆ + H]⁺) and a preformed ion (benzyltriphenylphosphonium, BTPP) generated by matrix-assisted laser desorption ionization (MALDI) were investigated with time-of-flight mass spectrometry. α-Cyano-4-hydroxycinammic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) were used as matrices. For both ions, ISD yield was unaffected by delay time, indicating rapid termination of ISD. This was taken as evidence for rapid expansion cooling of hot “early” plume formed in MALDI. CHCA was hotter than DHB for [Y₆ + H]⁺ while the matrix effect was insignificant for BTPP. The “early” plume temperature estimated utilizing previous kinetic results was 800–900 K, versus 400–500 K for “late” plume. The results support our previous finding that the temperature of peptide ions interrogated by tandem mass spectrometry was lower than most rough estimates of MALDI temperature.     

MALDI-TOF imaging mass spectrometry of artifacts in “dried droplet” polymer samples

Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) imaging of polystyrenes with various molecular masses was applied to study spatial molecular mass distribution of polymers in sample spots prepared by the “dried droplet” method. When different solvents and target surfaces were examined, a segregation of single homologous polymers was observed depending upon the evaporation rate of the solvent. For the observed patterns left by the evaporating droplet, a hypothesis is offered taking into account different hydrodynamic interactions and diffusion. The results illustrate that spot preparation using the conventionally “dried droplet” method is prone to artifacts and should be avoided for reliable and reproducible MALDI mass spectrometry experiments with regards to the determination of molecular masses and mass distributions.     

Features of laser desorption/ionization mass spectrometry fragmentation of vitamin B<Subscript>12</Subscript>

A comparative analysis of the laser desorption/ionization of vitamin B₁₂ by matrix-assisted laser desorption/ionization (MALDI) and desorption/ionization on porous silicon (DIOS) was carried out. The mass spectra obtained were interpreted and the pathways for ion formation and decomposition were established. The MALDI fragmentation of the positive vitamin B₁₂ ions is more extensive than the DIOS fragmentation. The most extensive fragmentation was found using the MALDI method for negative vitamin B₁₂ ions, which are lacking when using the DIOS method. __________ Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 43, No. 4, pp. 251–256, July–August, 2007.     

Introduction of a 20 kHz Nd:YVO4 laser into a hybrid quadrupole time-of-flight mass spectrometer for MALDI-MS imaging

A commercial hybrid quadrupole time–of–flight mass spectrometer has been modified for high-speed matrix-assisted laser desorption ionisation (MALDI) imaging using a short-pulse optical technology Nd:YVO₄ laser. The laser operating in frequency-tripled mode (λ = 355 nm) is capable of delivering 1.5-ns pulses of energy at up to 8 μJ at 5–10 kHz and 3 μJ at 20 kHz. Experiments to improve beam homogeneity and reduce laser speckle by mechanical vibration of the fibre-optic laser delivery system are reported along with data from trial and tissue imaging experiments using the modified instrument. The laser appeared to yield best results for MALDI-MS imaging experiments when operating at repetition rates 5–10 kHz. Combining this with raster imaging allowed images of rat brain sections to be recorded in 37 min. Similarly, images of the distribution of peptides in “on-tissue” digest experiments from tumour tissues were recorded in 1 h and 30 min rather than the 8-h acquisition time previously used. A brief investigation of targeted protein analysis/imaging by multiple reaction monitoring experiments “on-tissue” is reported. A total of 26 transitions were recorded over a 3-s cycle time and images of abundant proteins were successfully recorded.     

Enhanced in-source fragmentation in MALDI-TOF-MS of oligonucleotides using 1,5-diaminonapthalene

The capability to rapidly and confidently determine or confirm the sequences of short oligonucleotides, including native and chemically-modified DNA and RNA, is important for a number of fields. While matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been used previously to sequence short oligonucleotides, the typically low fragmentation efficiency of in-source or post-source decay processes necessitates the accumulation of a large number of spectra, thus limiting the throughput of these methods. Here we introduce a novel matrix, 1,5-diaminonapthalene (DAN), for facile in-source decay (ISD) of DNA and RNA molecular anions, which allows for rapid sequence confirmation. d-, w-, and y-series ions are prominent in the spectra, complementary to the (a-B)- and w- ions that are typically produced by MALDI post-source decay (PSD). Results are shown for several model DNA and RNA oligonucleotides, including combinations of DAN-induced fragmentation with true tandem TOF MS (MS/MS) for pseudo-MS³ and “activated-ion PSD.”     

An activated carbon substrate surface for laser desorption mass spectrometry

A method to obtain laser desorption/ionization mass spectra of organic compounds by depositing sample solutions onto a carbon substrate surface is demonstrated. The substrate consists of a thin layer of activated carbon particles immobilized on an aluminum support. In common with the porous carbon suspension samples used in previous “surface-assisted laser desorption/ionization” (SALDI) work, the mass spectra contain only a few “matrix” background ion peaks, minimizing interference with analyte ion peaks. The presence of glycerol ensured that the ion signals were stable over hundreds of laser shots. In addition, the carbon substrate surface has several advantages over the suspension samples. The use of a very thin layer of carbon significantly improves the sensitivity. Detection limits range from attomoles for crystal violet to femtomoles for bradykinin. Very little sample preparation is required as the analyte solution is simply pipetted onto the substrate surface and glycerol added. When using an alternate sample deposition method, a mass resolution for bradykinin of 1800 is achieved in linear time-of-flight mode. This is close to the resolution limit set by the detector system and above instrument specification for matrix-assisted laser desorption/ionization mass spectra.     

Determination of the binding sites for oxaliplatin on insulin using mass spectrometry-based approaches

Using insulin as a model protein for binding of oxaliplatin to proteins, various mass spectrometric approaches and techniques were compared. Several different platinum adducts were observed, e.g. addition of one or two diaminocyclohexane platinum(II) (Pt(dach)) molecules. By top-down analysis and fragmentation of the intact insulin–oxaliplatin adduct using nano-electrospray ionisation quadrupole time-of-flight mass spectrometry (nESI-Q-ToF-MS), the major binding site was assigned to histidine5 on the insulin B chain. In order to simplify the interpretation of the mass spectrum, the disulphide bridges were reduced. This led to the additional identification of cysteine6 on the A chain as a binding site along with histidine5 on the B chain. Digestion of insulin–oxaliplatin with endoproteinase Glu-C (GluC) followed by reduction led to the formation of five peptides with Pt(dach) attached. Identification of several of the binding sites was obtained using matrix-assisted laser desorption/ionization (MALDI)-ToF-ToF-MS and liquid chromatography-nESI-Q-ToF-MS. Upon comparing the top-down and bottom-up approaches, the suitability of the bottom-up approach for determining binding sites was questioned, as the release and possible re-association of Pt(dach) were demonstrated upon enzymatic digestion. The associated advantages and disadvantages of ESI and MALDI were also pointed out.     

Factors that influence the observed fast fragmentation of peptides in matrix-assisted laser desorption

Fragmentation processes that occur very early during matrix-assisted laser desorption ionization (MALDI) of peptides are examined by utilization of delayed pulsed ion extraction with a linear time-of-flight mass spectrometer. The oxidized B chain of bovine insulin (MW=3495. 95 u), which produces a wide range of fragment ions, is utilized as a probe to examine the effects of several experimental parameters on this process. Experimental evidence suggests that this MALDI process is not prompt fragmentation and involves metastable ion decay that is quite different from that which is observed with postsource decay experiments. This conclusion is based upon the significant differences observed in the fragmentation products produced by the two techniques. This metastable ion decay process also appears to be over within the minimum pulse delay period (320 ns) that is possible with the current pulsed ion extraction hardware. These two observations suggest that either different activation processes are involved in the two techniques or that the much different time frame of the methods influences the observed ion decay pathways. This fast MALDI metastable ion fragmentation also is shown to be influenced by both the MALDI matrix and the laser fluence.     

Characterization of plasma polymerized C, H, and O containing compounds by MALDI mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is used for the first time to characterize radio frequency plasma-deposited polymers and for investigation of the plasma polymerization process. The MALDI mass spectra of the plasma polymers of allyl alcohol, di(ethylene glycol) vinyl ether and ethylene glycol butyl vinyl ether are all reported using solvent-based MALDI sample preparation approaches. The MALDI mass spectra of each of the three plasma polymers contain distinctive polymer series ion signals having molecular weight distributions below 2000 Da. Unexpectedly, however, the ion signals from each of the three plasma polymers show a common polymer repeat unit of 44 Da, for which the chemical formula is most likely -(C(2)H(4)O)-, and no evidence of the expected radical chain polymerization polymer is detected. These results are discussed in terms of the likely involvement of gas-phase radical species having different stabilities in the radio frequency plasma environment.     

Tunable fragmentation of organic molecules in laser ablation glow discharge time-of-flight mass spectrometry

A DC-pulsed glow discharge (GD) has distinct temporal regimes which are characterized by “softer” or “harder” ionization of analytes introduced into the discharge. It is thus possible to obtain both molecular weight and structural fragment information from the same spectra. In order to extend the capabilities of this technique a laser ablation (LA) sampling system was coupled to a DC-pulsed GD and to a time-of-flight (TOF) mass spectrometer (MS) for characterizing organic samples such as oleic acid, reserpine, two different peptides, and a polymer. Both hard and soft ionization regimes were studied. These LAGD-TOFMS results were compared to matrix-assisted laser desorption ionization (MALDI) spectra using the same compounds (i.e., analytes, concentration, and matrix). It was found that LAGD offers tunable ionization and provides a reduced matrix dependence. However, the sensitivity achieved by the prototype LAGD-TOFMS was significantly lower when compared with commercially available MALDI-TOFMS instrumentation. Since LAGD-TOFMS is rather new, some technical details to increase its sensitivity are discussed.     

“Meta Elimination,” a Diagnostic Fragmentation in Mass Spectrometry

The diagnostic value of the “ortho effect” for unknown identification by mass spectrometry is well known. Here, we report the existence of a novel “meta effect,” which adds to the repertoire of useful mass spectrometric fragmentation mechanisms. For example, the meta-specific elimination pathway described in this report enables unequivocal identification of meta isomers from ortho and para isomers of carboxyanilides. The reaction follows a specific path to eliminate a molecule of meta-benzyne, from the anion produced after the initial decarboxylation of the precursor. Consequently, in the CID spectra of carboxyanilides, a peak for the (R-CO-NH)^– anion is observed only for the meta isomers. For example, the peaks observed at m/z 58, 86, 120, 128, and 170 from acetamido-, butamido-, benzamido, heptamido-, and decanamido-benzoates, respectively, were specific only to the spectra of meta isomers.     

A fast,reproducible and low‐cost method for sequence deconvolution of ‘on‐bead’ peptides via ‘on‐target’ maldi‐TOF/TOF mass spectrometry

A novel approach to high‐throughput sequence deconvolution of on‐bead small peptides (MW < 2000 Da) using on‐target MALDI‐TOF/TOF instrumentation is presented. Short peptides of pentamer and octamer length, covalently attached to TentaGel polystyrene beads through a photolabile linker, were placed onto the MALDI target, apportioned with suitable matrix (2,5‐dihydroxybenzoic acid) and then hit with the instrument laser (Nd : YAG, 355 nm). This induced easy and highly reproducible photochemical cleavage, desorption (MS mode) and fragmentation (MS/MS mode). Peptide fragments were identified with a mass accuracy of 0.1 Da of the expected values. This technique significantly accelerates the sequence determination of positive peptide hits obtained from random combinatorial libraries when screening against biological targets, paving the way for a rapid and efficient method to identify molecular imaging ligands specific to pathological targets in cancer and other diseases. Copyright © 2009 John Wiley & Sons, Ltd.     

Determining the time needed for the vortex method for preparing solvent-free MALDI samples of low molecular mass polymers

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is an important technique to characterize many different materials, including synthetic polymers. MALDI mass spectral data is used to determine the polymer average molecular weights, repeat units, and end groups. The development of the vortex method of solvent-free sample preparation showed that remarkably short mixing times could prepare samples that yielded high quality MALDI mass spectra. In this paper, we use microscopy images and MALDI mass spectra to evaluate the mixing time required by the vortex method to produce mass spectra for low molecular mass polymer samples. Our results show that mixing times of as little as 10 s can generate homogeneous thin films that produce high quality mass spectra with S/N ∼ 100. In addition, ultrashort mixing times of only 2 s still produce samples with mostly smooth morphology and mass spectra with S/N ∼ 10.     

Selection of internal standards for quantitative analysis by matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry

 The selection of an appropriate internal standard (IS) for quantification by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is critical for the successful application of quantitative MALDI. Selection of the IS depends on the chemical similarity of the analyte and IS and the mass separation of the analyte and IS as a function of instrumental peak resolution. For the quantification of bovine insulin, a series of internal standards including horse heart cytochrome C, bovine insulin chain B, des-pentapeptide human insulin, and des-octapeptide porcine insulin was investigated. Des-pentapeptide human insulin was found to be the most appropriate internal standard (relative standard deviation of the standard curve slope=2.99%, correlation coefficient=0.988 in the range of 0.5–0.4 μmol/L). Two methods for measuring of the MALDI signal intensity were evaluated, direct peak integration following subtraction of a linear background and non-linear least squares curve fitting. The results obtained with these methods were equivalent. Received: 10 November 1995 / Revised: 4 March 1996 / Accepted: 6 March 1996     

Development of a MALDI two-layer volume sample preparation technique for analysis of colored conidia spores of <Emphasis Type="Italic">Fusarium</Emphasis> by MALDI linear TOF mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) has been proved to be a powerful tool for the identification and characterization of microorganisms based on their surface peptide/protein pattern. Because of the complexity of microorganisms, there are no standardized protocols to acquire reproducible peptide/protein profiles for a broad range of microorganisms and for fungi in particular. Small variations during MALDI MS sample preparation affect the quality of mass spectra quite often. In this study, we were aiming to develop a sample preparation method for the analysis of colored, a quite often observed phenomenon, and mycotoxin-producing Fusarium conidia spores using MALDI–TOF MS. Different washing solvent systems for light- and deep-colored (from slightly orange to red-brown) conidia spores and connected sample deposition techniques were evaluated based on MS reproducibility and number and intensities of peaks. As a method of choice for generation of reproducible and characteristic MALDI–TOF mass spectra, the use of a washing process for colored Fusarium conidia spores with acetonitrile/0.5% formic acid (7/3) was found and subsequently combined with two-layer volume technique (spores/matrix (ferulic acid) solution was deposited onto a MALDI target, and after solvent evaporation, a second matrix layer was deposited). With the application of this sample preparation method, for deep-colored Fusarium species, 19 abundant molecular ions in the m/z range 2,000–10,000 were always detected with an S/N ratio of 3:1 or better. Finally this optimized sample preparation for the first time provided mass spectrometric fingerprints of strongly colored Fusarium conidia spores resulting in the possibility of differentiation of such spores at the species level.      

MALDI-TOF mass signatures for differentiation of yeast species,strain grouping and monitoring of morphogenesis markers

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is demonstrated to be a potentially useful tool for the rapid identification of yeasts, the grouping of Candida albicans strains, and the monitoring of germ tube-specific markers. Co-crystallized with sinapinic acid as the MALDI matrix, intact yeast cells yielded a sufficient number of medium-sized ions (4–15 kDa) in MALDI mass spectra to provide “mass signatures” that were diagnostic of strain type. For most isolates, the mass signatures were affected by the growth medium, length of incubation and the cell preparation method. While the overall past success of this methodology for fungal cells has been relatively low compared to its application to bacteria, fixing the yeast cells in 50% methanol inactivated the cells, reduced cell aggregation in aqueous suspension solution, and more importantly, it significantly improved the mass signature quality. This simple but critical advance in sample treatment improved mass spectrometric signal-to-noise ratios and allowed the identification of yeasts by a mass signature approach. Under optimized conditions, Candida species (C. albicans, C. glabrata, C. krusei, C. kefyr), Aspergillus species (A. terreus, A. fumigatus, A. syndowii) and other yeast genera (Cryptococcus neoformans, Saccharomyces cerevisiae and a Rhodotorula sp.) could be distinguished. Within the C. albicans species, several common ions in the m/z 5,000–10,000 range were apparent in the mass spectra of all tested strains. In addition to shared ions, the mass spectra of individual C. albicans strains permitted grouping of the strains. Principal component analysis (PCA) was employed to confirm spectral reproducibility and C. albicans strain grouping by mass signatures. Finally, C. albicans germ tubes produced MALDI-TOF mass signatures that differed from yeast forms of this species. This is a rapid, sensitive and simple method for identifying yeasts, grouping strains and following the morphogenesis of C. albicans. Figure       

Small molecule analysis by MALDI mass spectrometry

This review focuses on the application of matrix assisted laser desorption/ionization (MALDI) mass spectrometry to the characterization of molecules in the low mass range (<1500 Da). Despite its reputation to the contrary, MALDI is a powerful technique to provide both qualitative and quantitative determination of low molecular weight compounds. Several approaches to minimize interference via sample preparation and matrix selection are discussed, as well as coupling of MALDI to liquid and planar chromatographic techniques to extend its range of applicability.     

Synthesis of a “memory tripeptide” (Arg—Glu—Arg,RER) and the Kabachnik—Fields reaction with di- and tripeptides as a method for the synthesis of phosphorus-containing peptide analogs

Methods for the synthesis of potential “twin-drugs” containing fragments of the glutamate receptor antagonist and cognitive function enhancing oligopeptides were developed. The “memory tripeptide” Arg—Glu—Arg (RER) containing the tripeptide sequence of a protein APP_328–330, a gB-amyloid precursor, was synthesized. A method for the synthesis of gA-aminophosphonates with oligopeptides as the amine component of the one-pot three-component Kabachnik—Fields reaction was developed. A method for the synthesis of phosphonopeptides by the introduction of gA-aminophosphonates into the peptide chain was proposed.     

Fragmentation of phosphopeptides by atmospheric pressure MALDI and ESI/ion trap mass spectrometry

An investigation of phosphate loss from phosphopeptide ions was conducted, using both atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI) and electrospray ionization (ESI) coupled to an ion trap mass spectrometer (ITMS). These experiments were carried out on a number of phosphorylated peptides in order to investigate gas phase dephosphorylation patterns associated with phosphoserine, phosphothreonine, and phosphotyrosine residues. In particular, we explored the fragmentation patterns of phosphotyrosine containing peptides, which experience a loss of 98 Da under collision induced dissociation (CID) conditions in the ITMS. The loss of 98 Da is unexpected for phosphotyrosine, given the structure of its side chain. The fragmentation of phosphoserine and phosphothreonine containing peptides was also investigated. While phosphoserine and phosphothreonine residues undergo a loss of 98 Da under CID conditions regardless of peptide amino acid composition, phosphate loss from phosphotyrosine residues seems to be dependent on the presence of arginine or lysine residues in the peptide sequence.     

Electron Transfer Dissociation (ETD) of Peptides Containing Intrachain Disulfide Bonds

The fragmentation chemistry of peptides containing intrachain disulfide bonds was investigated under electron transfer dissociation (ETD) conditions. Fragments within the cyclic region of the peptide backbone due to intrachain disulfide bond formation were observed, including: c (odd electron), z (even electron), c-33 Da, z + 33 Da, c + 32 Da, and z–32 Da types of ions. The presence of these ions indicated cleavages both at the disulfide bond and the N–Cα backbone from a single electron transfer event. Mechanistic studies supported a mechanism whereby the N–Cα bond was cleaved first, and radical-driven reactions caused cleavage at either an S–S bond or an S–C bond within cysteinyl residues. Direct ETD at the disulfide linkage was also observed, correlating with signature loss of 33 Da (SH) from the charge-reduced peptide ions. Initial ETD cleavage at the disulfide bond was found to be promoted amongst peptides ions of lower charge states, while backbone fragmentation was more abundant for higher charge states. The capability of inducing both backbone and disulfide bond cleavages from ETD could be particularly useful for sequencing peptides containing intact intrachain disulfide bonds. ETD of the 13 peptides studied herein all showed substantial sequence coverage, accounting for 75%–100% of possible backbone fragmentation.