Enhanced MALDI MS sensitivity by weak base additives and glycerol sample coating.

The concept of rationally designing MALDI matrices has been extended to the next "whole sample" level. These studies have revealed some unexpected and exploitable insights in improving MALDI sensitivity. It is shown that (i) additives which only provide additional laser energy absorption are best to be avoided; (ii) the addition of proton donors in the form of protonated weak bases can be highly beneficial; (iii) the addition of glycerol for coating crystalline samples is highly recommended. Overall, analytical sensitivity has been significantly increased compared to the current "gold" standards in MALDI MS, and new insights into the mechanisms and processes of MALDI have been gained.

2,5-dihydroxybenzoic acid salts for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric lipid analysis: simplified spectra interpretation and insights into gas-phase fragmentation.

RATIONALE: In the last decades the interest in lipids as important components of membranes has considerably increased. Nowadays, lipids are often routinely analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In this regard, many relevant aspects are so far unknown, e.g., gas-phase stabilities, adduct formation and fragmentation. To fill this gap, MALDI matrix salts are presented which allow for simplified lipid analysis and elucidation of the underlying gas-phase fragmentation mechanisms. METHODS: MALDI-TOF MS was used due to its beneficial properties for lipid investigations, e.g., high sensitivity, simple sample preparations, and a high tolerance to contaminants. The lipid hydrolysis, ionization and fragmentation properties of synthesized near neutral Na(+) and NH4 (+) salts of the commonly used MALDI matrix 2,5-dihydroxybenzoic acid were compared to that of DHB free acid itself as well as to base addition to DHB during dried-droplet sample preparation. RESULTS: Many lipid classes such as sterols, triacylglycerols, phosphatidylcholines and -ethanolamines undergo initial protonation with subsequent prompt partial up to quantitative fragmentation when analyzed with classical acidic matrices by MALDI-TOF MS. Neutral matrix salts can prevent initial analyte fragmentation by suppression of analyte protonation. Additionally, intramolecular gas-phase fragmentation reactions can be inhibited due to analyte stabilization by cation chelation. Base addition during sample preparation leads not only to in situ generation of matrix salts but also to analyte hydrolysis. CONCLUSIONS: Neutral DHB salts avoid separation of lipid species into several ionization states when used as matrices in MALDI-TOF MS. This allows for simplified lipid spectra interpretation. Due to the high cationization efficiency of DHB matrix salts, certain lipid classes become detectable which cannot be analyzed easily using standard acidic DHB.

Improving peptide relative quantification in MALDI-TOF MS for biomarker assessment.

Proteomic profiling by MALDI-TOF MS presents various advantages (speed of analysis, ease of use, relatively low cost, sensitivity, tolerance against detergents and contaminants, and possibility of automation) and is being currently used in many applications (e.g. peptide/protein identification and quantification, biomarker discovery, and imaging MS). Earlier studies by many groups indicated that moderate reproducibility in relative peptide quantification is a major limitation of MALDI-TOF MS. In the present work, we examined and demonstrate a clear effect, in cases apparently random, of sample dilution in complex samples (urine) on the relative quantification of peptides by MALDI-TOF MS. Results indicate that in urine relative abundance of peptides cannot be assessed with confidence based on a single MALDI-TOF MS spectrum. To account for this issue, we developed and propose a novel method of determining the relative abundance of peptides, taking into account that peptides have individual linear quantification ranges in relation to sample dilution. We developed an algorithm that calculates the range of dilutions at which each peptide responds in a linear manner and normalizes the received peptide intensity values accordingly. This concept was successfully applied to a set of urine samples from patients diagnosed with diabetes presenting normoalbuminuria (controls) and macroalbuminuria (cases).

Matching the laser wavelength to the absorption properties of matrices increases the ion yield in UV-MALDI mass spectrometry.

A high analytical sensitivity in ultraviolet matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is only achieved if the laser wavelength corresponds to a high optical absorption of the matrix. Laser fluence and the physicochemical properties of the compounds, e.g., the proton affinity, also influence analytical sensitivity significantly. In combination, these parameters determine the amount of material ejected per laser pulse and the ion yield, i.e., the fraction of ionized biomolecules. Here, we recorded peptide ion signal intensities as a function of these parameters. Three cinnamic acid matrices were investigated: α-cyano-4-hydroxycinnamic acid, α-cyano-4-chlorocinnamic acid, and α-cyano-2,4-difluorocinnamic acid. In addition, 2,5-dihydroxybenzoic acid was used in comparison experiments. Ion signal intensities "per laser shot" and integrated ion signal intensities were acquired over 900 consecutive laser pulses applied on distinct positions on the dried-droplet sample preparations. With respect to laser wavelength, the two standard MALDI wavelengths of 337/355 nm were investigated. Also, 305 or 320 nm was selected to account for the blue-shifted absorption profiles of the halogenated derivatives. Maximal peptide ion intensities were obtained if the laser wavelength fell within the peak of the absorption profile of the compound and for fluences two to three times the corresponding ion detection threshold. The results indicate ways for improving the analytical sensitivity in MALDI-MS, and in particular for MALDI-MS imaging applications where a limited amount of material is available per irradiated pixel.

Enzyme-cleavable tandem peptides for quantitative studies in MS-based proteomics.

A novel type of peptide standard is introduced that consists of two peptides combined in one synthetic molecule and separated by a proteolytic cleavage site. Upon enzymatic digestion, the two peptides are released in a molar one-to-one ratio. This method enables the generation of exact equimolar mixtures of two peptides of any nature and origin, thereby providing a valuable tool for the investigation of fundamental phenomena in MS. The applicability of the method is exemplified by the analysis of the effect of peptide sequence variations on the relative ionization efficiency in ESI- and MALDI-MS.

Ion yields in UV-MALDI mass spectrometry as a function of excitation laser wavelength and optical and physico-chemical properties of classical and halogen-substituted MALDI matrixes.

The laser wavelength constitutes a key parameter in ultraviolet-matrix-assisted laser desorption ionization-mass spectrometry (UV-MALDI-MS). Optimal analytical results are only achieved at laser wavelengths that correspond to a high optical absorption of the matrix. In the presented work, the wavelength dependence and the contribution of matrix proton affinity to the MALDI process were investigated. A tunable dye laser was used to examine the wavelength range between 280 and 355 nm. The peptide and matrix ion signals recorded as a function of these irradiation parameters are displayed in the form of heat maps, a data representation that furnishes multidimensional data interpretation. Matrixes with a range of proton affinities from 809 to 866 kJ/mol were investigated. Among those selected are the standard matrixes 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA) as well as five halogen-substituted cinnamic acid derivatives, including the recently introduced 4-chloro-α-cyanocinnamic acid (ClCCA) and α-cyano-2,4-difluorocinnamic acid (DiFCCA) matrixes. With the exception of DHB, the highest analyte ion signals were obtained toward the red side of the peak optical absorption in the solid state. A stronger decline of the molecular analyte ion signals generated from the matrixes was consistently observed at the low wavelength side of the peak absorption. This effect is mainly the result of increased fragmentation of both analyte and matrix ions. Optimal use of multiply halogenated matrixes requires adjustment of the excitation wavelength to values below that of the standard MALDI lasers emitting at 355 (Nd:YAG) or 337 nm (N(2) laser). The combined data provide new insights into the UV-MALDI desorption/ionization processes and indicate ways to improve the analytical sensitivity.

High-reactivity matrices increase the sensitivity of matrix enhanced secondary ion mass spectrometry.

Secondary ion mass spectrometry (SIMS) is a desorption/ionization method in which ions are generated by the impact of a primary ion beam on a sample. Classic matrix assisted laser desorption and ionization (MALDI) matrices can be used to increase secondary ion yields and decrease fragmentation in a SIMS experiment, which is referred to as matrix enhanced SIMS (ME-SIMS). Contrary to MALDI, the choice of matrices for ME-SIMS is not constrained by their photon absorption characteristics. This implies that matrix compounds that exhibit an insufficient photon absorption coefficient have the potential of working well with ME-SIMS. Here, we evaluate a set of novel derivatives of the classical MALDI matrices α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) for usability in ME-SIMS. This evaluation was carried out using peptide mixtures of different complexity and demonstrates significant improvements in signal intensity for several compounds with insufficient UV absorption at the standard MALDI laser wavelengths. Our study confirms that the gas-phase proton affinity of a matrix compound is a key physicochemical characteristic that determines its performance in a ME-SIMS experiment. As a result, these novel matrices improve the performance of matrix enhanced secondary ion mass spectrometry experiments on complex peptide mixtures.

Entianin, a novel subtilin-like lantibiotic from Bacillus subtilis subsp. spizizenii DSM 15029T with high antimicrobial activity.

Lantibiotics, such as nisin and subtilin, are lanthionine-containing peptides that exhibit antimicrobial as well as pheromone-like autoinducing activity. Autoinduction is specific for each lantibiotic, and reporter systems for nisin and subtilin autoinduction are available. In this report, we used the previously reported subtilin autoinduction bioassay in combination with mass spectrometric analyses to identify the novel subtilin-like lantibiotic entianin from Bacillus subtilis subsp. spizizenii DSM 15029(T). Linearization of entianin using Raney nickel-catalyzed reductive cleavage enabled, for the first time, the use of tandem mass spectrometry for the fast and efficient determination of an entire lantibiotic primary structure, including posttranslational modifications. The amino acid sequence determined was verified by DNA sequencing of the etnS structural gene, which confirmed that entianin differs from subtilin at 3 amino acid positions. In contrast to B. subtilis ATCC 6633, which produces only small amounts of unsuccinylated subtilin, B. subtilis DSM 15029(T) secretes considerable amounts of unsuccinylated entianin. Entianin was very active against several Gram-positive pathogens, such as Staphylococcus aureus and Enterococcus faecalis. The growth-inhibiting activity of succinylated entianin (S-entianin) was much lower than that of unsuccinylated entianin: a 40-fold higher concentration was required for inhibition. For succinylated subtilin (S-subtilin), a concentration 100-fold higher than that of unsuccinylated entianin was required to inhibit the growth of a B. subtilis test strain. This finding was in accordance with a strongly reduced sensing of cellular envelope stress provided by S-entianin relative to that of entianin. Remarkably, S-entianin and S-subtilin showed considerable autoinduction activity, clearly demonstrating that autoinduction and antibiotic activity underlie different molecular mechanisms.

Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila.

Thirteen novel PAX (peptide-antimicrobial-Xenorhabdus) peptides were identified in Xenorhabdus nematophila HGB081. Their structures including the absolute configuration were elucidated using a combination of labeling experiments, detailed MS/MS experiments, the advanced Marfey's method, and a detailed analysis of the biosynthesis gene cluster, which was identified as well.

4-Chloro-alpha-cyanocinnamic acid is an advanced, rationally designed MALDI matrix.

Matrix-assisted laser desorption ionization (MALDI) has become an enabling technology for the fields of protein mass spectrometry (MS) and proteomics. Despite its widespread use, for example, in protein identification via peptide mass fingerprinting, a comprehensive model for the generation of free gas-phase ions has not yet been developed. All matrices in use today, such as alpha-cyano-4-hydroxycinnamic acid (CHCA), have been found empirically and stem from the early days of MALDI. By systematic and targeted variation of the functional groups of the alpha-cyanocinnamic acid core unit, 4-chloro-alpha-cyanocinnamic acid (Cl-CCA) was selected and synthesized, and it exhibited outstanding matrix properties. Key features are a substantial increase in sensitivity and a considerably enhanced peptide recovery in proteomic analyses because of a much more uniform response to peptides of different basicity. Using Cl-CCA as a matrix for a 1 fmol bovine serum albumin (BSA) in-solution digest, the sequence coverage is raised to 48%, compared with 4% for CHCA. For a gel band containing 25 fmol of BSA, unambiguous protein identification becomes possible with Cl-CCA. These findings also imply ion formation via a chemical ionization mechanism with proton transfer from a reactive protonated matrix species to the peptide analytes. The considerable increase in performance promises to have a strong impact on future analytical applications of MALDI, because current sensitivity limits are overcome and more comprehensive analyses come into reach.

Peptide mass fingerprinting after less specific in-gel proteolysis using MALDI-LTQ-Orbitrap and 4-chloro-alpha-cyanocinnamic acid.

Peptide Mass Fingerprinting (PMF) of tryptically in-gel digested samples is a well-established protein identification technique for MALDI mass spectrometry but an in-depth PMF evaluation for in-gel digestions of less specific enzymes is still missing. This study demonstrates that the MALDI-LTQ-Orbitrap provides the mass accuracy to gain significant database search results via PMF for the less specific enzymes chymotrypsin and elastase. Additionally, the highly sensitive MALDI matrix ClCCA was compared to the most widely used matrix CHCA by means of the detected peptide number, peptide composition, pI and S/N distribution, sequence coverage, and Mascot score. Therefore, several proteins were in-gel digested by chymotrypsin and elastase. Trypsin and proteinase K were included as references for specific and nonspecific proteases, respectively. Compared to CHCA, ClCCA resulted in a better mapping in all cases of the more complex peptide mixtures generated by less specific enzymes. In summary, the MALDI-LTQ-Orbitrap combined with the matrix ClCCA makes PMF of less specific digests possible in an easy and fast way. Moreover, it opens more possibilities for PMF in the analysis of difficult tasks such as membrane proteins.

Using fluorescence dyes as a tool for analyzing the MALDI process.

In a recent paper (Setz, P. D.; Knochenmuss, R. Phys. Chem. A2005, 109, 4030-4037) energy-transfer from excited matrix molecules to fluorescent traps was used to study the role of pooling reactions for the ionization processes in matrix-assisted laser desorption ionization (MALDI) using 2,5-dihydroxybenzoic acid as matrix. Exciton trapping was shown to interfere with matrix ionization. These investigations were extended to analyze the influence of fluorescent traps on both matrix and analyte ions for alpha-cyano-4-hydroxycinnamic acid and further matrices. A strong influence of the fluorescent traps on both matrix and analyte ionization was revealed, depending on the matrix:trap ratio, and manifested itself differently for low and high mass analytes. The observations are rationalized by the intermediate formation of a "hot spot" due to an efficient conversion of electronic excitation energy to vibronic energy within the fluorescent traps. This process favors the desorption and ionization of small vaporizable analytes and compromises the cluster ablation process needed for larger analyte ions.

Color matters--material ejection and ion yields in UV-MALDI mass spectrometry as a function of laser wavelength and laser fluence.

The success of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) as a widely employed analytical tool in the biomolecular sciences builds strongly on an effective laser-material interaction that is resulting in a soft co-desorption and ionization of matrix and imbedded biomolecules. To obtain a maximized ion yield for the analyte(s) of interest, in general both wavelength and fluence need to be tuned to match the specific optical absorption profile of the used matrix. However, commonly only lasers with fixed emission wavelengths of either 337 or 355 nm are used for MALDI-MS. Here, we employed a wavelength-tunable dye laser and recorded both the neutral material ejection and the MS ion data in a wide wavelength and fluence range between 280 and 377.5 nm. α-Cyano-4-hydroxycinnamic acid (HCCA), 4-chloro-α-cyanocinnamic acid (ClCCA), α-cyano-2,4-difluorocinnamic acid (DiFCCA), and 2,5-dihydroxybenzoic acid (DHB) were investigated as matrices, and several peptides as analytes. Recording of the material ejection was achieved by adopting a photoacoustic approach. Relative ion yields were derived by division of photoacoustic and ion signals. In this way, distinct wavelength/fluence regions can be identified for which maximum ion yields were obtained. For the tested matrices, optimal results were achieved for wavelengths corresponding to areas of high optical absorption of the respective matrix and at fluences about a factor of 2-3 above the matrix- and wavelength-dependent ion detection threshold fluences. The material ejection as probed by the photoacoustic method is excellently fitted by the quasithermal model, while a sigmoidal function allows for an empirical description of the ion signal-fluence relationship.

Compelling evidence for Lucky Survivor and gas phase protonation: the unified MALDI analyte protonation mechanism.

This work experimentally verifies and proves the two long since postulated matrix-assisted laser desorption/ionization (MALDI) analyte protonation pathways known as the Lucky Survivor and the gas phase protonation model. Experimental differentiation between the predicted mechanisms becomes possible by the use of deuterated matrix esters as MALDI matrices, which are stable under typical sample preparation conditions and generate deuteronated reagent ions, including the deuterated and deuteronated free matrix acid, only upon laser irradiation in the MALDI process. While the generation of deuteronated analyte ions proves the gas phase protonation model, the detection of protonated analytes by application of deuterated matrix compounds without acidic hydrogens proves the survival of analytes precharged from solution in accordance with the predictions from the Lucky Survivor model. The observed ratio of the two analyte ionization processes depends on the applied experimental parameters as well as the nature of analyte and matrix. Increasing laser fluences and lower matrix proton affinities favor gas phase protonation, whereas more quantitative analyte protonation in solution and intramolecular ion stabilization leads to more Lucky Survivors. The presented results allow for a deeper understanding of the fundamental processes causing analyte ionization in MALDI and may alleviate future efforts for increasing the analyte ion yield.

Significant sensitivity improvements by matrix optimization: a MALDI-TOF mass spectrometric study of lipids from hen egg yolk.

Due to its sensitivity, the tolerance of impurities and the simplicity of performance, matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is increasingly used to analyze lipids from biological sources. Although its detailed role is not understood so far, the applied matrix has a pronounced effect on the achievable spectrum quality and particularly how sensitive the individual lipid classes are detectable. Different matrix compounds were recently established in the lipid field including 2,5-dihydroxybenzoic acid (DHB), 9-aminoacridine (9-AA), para-nitroaniline (PNA), 2-mercaptobenzothiazole (MBT), and 2-(2-aminoethylamino)-5-nitropyridine (AAN). It is the aim of this paper to compare the properties of these matrices with the newly synthesized matrix, alpha-cyano-2,4-difluorocinnamic acid (Di-FCCA). An organic extract from hen egg yolk was used as a simple and easily available test system. It will be shown that Di-FCCA is the matrix of choice to detect lipids in the positive-ion mode due to an achievable sensitivity gain of more than one order of magnitude compared to alternative matrices. In contrast, Di-FCCA is not suitable for negative-ion detection of phospholipids. Here, 9-AA is unequivocally the matrix of choice.

Comparison between the matrices alpha-cyano-4-hydroxycinnamic acid and 4-chloro-alpha-cyanocinnamic acid for trypsin, chymotrypsin, and pepsin digestions by MALDI-TOF mass spectrometry.

The performance of the recently developed 4-chloro-alpha-cyanocinnamic acid (Cl-CCA) matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) matrix was investigated in comparison to the most widely used matrix alpha-cyano-4-hydroxycinnamic acid (CHCA). For this purpose, in-solution digestions of standard proteins in the low femtomole range with the proteases trypsin, chymotrypsin, and pepsin were used as analytes. For all protein-protease combinations, Cl-CCA revealed to be highly superior in terms of number of identified peptides, obtained sequence coverages and peptide detection reproducibility. A deeper inspection of the detected peptide signals with regard to both physicochemical peptide properties (their isoelectric point) and mass spectrometric performance (signal-to-noise ratios and mass accuracies) showed that the progress achieved with Cl-CCA is due to the detection of numerous acidic to neutral peptides. Moreover, the higher Cl-CCA sensitivity allowed for the detection of numerous additional phosphopeptides, all of which were verified by means of MS/MS investigations. The occurrence of strong signals of doubly charged peptides which is exclusively observed for the Cl-CCA matrix can be traced back to the peptide amino-acid composition, that is, the presence of a high number of basic amino acids (Arg, Lys, and His) and is thus more pronounced for nontryptic protein digests. These observed improvements well agree with an increased protonation reactivity of Cl-CCA and are more pronounced with a decreasing level of protease specificity and decreasing sample amounts.

Comparison between vacuum sublimed matrices and conventional dried droplet preparation in MALDI-TOF mass spectrometry.

The properties of several cinnamic acid compounds used as matrices for matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) were investigated as standard dried droplet (DD) and vacuum sublimed preparations. The differences between both preparation methods were analyzed with regard to matrix grain size, internal ion energy, initial velocity, analyte intensity, and analyte incorporation depth. Some of the used cinnamic acid derivatives exhibit clearly reduced grain sizes as sublimed preparations compared with standard DD approaches. In these cases higher effective temperatures could be measured accompanied by increased analyte intensities, which can be explained by stronger volatilization processes caused by a hindered heat dissipation resulting in a raised analyte transfer into the gas phase. For all sublimed compounds, a strong increase of the initial ion velocity compared with DD preparations could be measured. Higher initial ion velocities correlate with a decrease in internal ion energy which might be attributed to the very uniform crystal morphology exhibited by sublimed compounds. For sublimed matrices without reduced grain size, at least slightly higher analyte intensities could be detected at raised laser fluences. Analyte accumulation in the uppermost matrix layers or the detected higher ion stability can be explanations for these results.