Efficient methods to generate reproducible mass spectra in matrix-assisted laser desorption ionization of peptides

Large-Area Graphene Films as Target Surfaces for Highly Reproducible Matrix-Assisted Laser Desorption Ionization Suitable for Quantitative Mass Spectrometry

Due to the known sweet-spot issues that intrinsically arise from inhomogeneous formation of matrix-analyte crystals utilized as samples in matrix-assisted laser desorption ionization (MALDI) mass spectrometry, its reproducibility and thus its applications for quantification have been somewhat limited. In this paper, we report a simple strategy to improve the uniformity of matrix-analyte crystal spots, which we realized by adapting large-area graphene films, i.e., non-inert, interacting surfaces, as target surfaces. In this example, the graphitic surfaces of the graphene films interact with excess matrix molecules during the sample drying process, which induces spontaneous formation of optically uniform MALDI sample crystal layers on the film surfaces. Further, mass spectrometric imaging reveals that the visible uniformity is indeed accompanied by reproducible MALDI ionization over an entire sample spot, which greatly suppresses the appearance of sweet spots. The results of this study confirm that the proposed method achieves good linear responses of ion intensity to the analyte concentration (R² > 0.99) with small relative standard deviations (σ < 10%), which is a range applicable for quantitative measurements using MALDI mass spectrometry. Graphical Abstract ᅟ.

Gain Switching for a Detection System to Accommodate a Newly Developed MALDI-Based Quantification Method

In matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF), matrix-derived ions are routinely deflected away to avoid problems with ion detection. This, however, limits the use of a quantification method that utilizes the analyte-to-matrix ion abundance ratio. In this work, we will show that it is possible to measure this ratio by a minor instrumental modification of a simple form of MALDI-TOF. This involves detector gain switching. Graphical Abstract ᅟ.

Recommendations for quantitative analysis of small molecules by matrix-assisted laser desorption ionization mass spectrometry

Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been used for quantitative analysis of small molecules for many years. It is usually preceded by an LC separation step when complex samples are tested. With the development several years ago of "modern MALDI" (automation, high repetition laser, high resolution peaks), the ease of use and performance of MALDI as a quantitative technique greatly increased. This review focuses on practical aspects of modern MALDI for quantitation of small molecules conducted in an ordinary way (no special reagents, devices or techniques for the spotting step of MALDI), and includes our ordinary, preferred methods The review is organized as 18 recommendations with accompanying explanations, criticisms and exceptions.

Quantitative transfer of polar analytes on a solid surface to a liquid matrix in MALDI profiling

In profiling of a specimen by matrix-assisted laser desorption ionization (MALDI) using a solid matrix, the solvent of the matrix solution extracts an analyte(s). A quantitative profiling cannot be achieved if the solvent evaporates before the complete extraction of the analyte. The extraction can become more quantitative when a liquid matrix dissolved in a solvent is used, which remains a liquid even after the evaporation of the solvent. To check this, radii of an analyte circle (r_A ), a matrix solution drop (r_D ) and a liquid matrix (r_M ) remaining after the solvent evaporation were controlled. Three types of samples were prepared, case A (r_A , r_D  < r_M ), case B (r_D  ≤ r_M  < r_A ) and case C (r_M  < r_D  < r_A ). In case A, the analyte amount in the matrix layer determined by MALDI was the same as the prepared amount inside the analyte circle. In case B, the analyte amount was the same as the amount inside the matrix circle. Only the analytes in contact with the liquid matrix layer, not more and not less, are transferred to the matrix layer. In case C, the analyte amount was greater than the amount inside the matrix circle, presumably because some of the analyte outside the matrix circle was dissolved by the solvent of the matrix solution. Copyright © 2016 John Wiley & Sons, Ltd.

Quantification of Carbohydrates and Related Materials Using Sodium Ion Adducts Produced by Matrix-Assisted Laser Desorption Ionization

The utility of sodium ion adducts produced by matrix-assisted laser desorption ionization for the quantification of analytes with multiple oxygen atoms was evaluated. Uses of homogeneous solid samples and temperature control allowed the acquisition of reproducible spectra. The method resulted in a direct proportionality between the ion abundance ratio I([A + Na]⁺)/I([M + Na]⁺) and the analyte concentration, which could be used as a calibration curve. This was demonstrated for carbohydrates, glycans, and polyether diols with dynamic range exceeding three orders of magnitude. Graphical Abstract ᅟ.

Discovery of a solvent effect preventing quantitative profiling by matrix-assisted laser desorption/ionization and its treatment

RATIONALE

In analyte profiling by matrix-assisted laser desorption/ionization (MALDI), drawing a quantitative profile map is an outstanding problem. Recently, we developed a method to quantify an analyte by MALDI, which is needed to solve the problem. Another requirement for quantitative profiling is the quantitative sample-to-matrix analyte transfer, which is investigated in this work.

METHODS

MALDI-time-of-flight (TOF) spectra were acquired for samples produced by two methods. In one, a sample solution containing a matrix and an analyte was loaded with a pipet and dried. In the other, a sample was prepared by a consecutive process, i.e., loading-drying of an analyte solution followed by that of a matrix solution. Two different micro-spotters were used in the second method. Various mixtures of organic solvents with water were used to prepare matrix solutions.

RESULTS

The organic solvent, matrix, and analyte used in the study did not affect the analyte transfer efficiency, whereas it improved as the water content in the solvent increased. It also improved as the liquid droplet emitted by a micro-spotter got larger. Use of a more polar solvent or a larger droplet increases the contact time between a solution droplet and the sample surface, which seems to be responsible for the improvement in the transfer efficiency.

CONCLUSIONS

Sample-to-matrix analyte transfer occurred efficiently when polar solvents and/or large liquid droplets were used to produce solid samples for MALDI profiling with a micro-spotter. A long contact time between the sample surface and a matrix solution droplet is one of the requirements for quantitative profiling. Copyright © 2015 John Wiley & Sons, Ltd.

Investigations of Some Liquid Matrixes for Analyte Quantification by MALDI

Sample inhomogeneity is one of the obstacles preventing the generation of reproducible mass spectra by MALDI and to their use for the purpose of analyte quantification. As a potential solution to this problem, we investigated MALDI with some liquid matrixes prepared by nonstoichiometric mixing of acids and bases. Out of 27 combinations of acids and bases, liquid matrixes could be produced from seven. When the overall spectral features were considered, two liquid matrixes using α-cyano-4-hydroxycinnamic acid as the acid and 3-aminoquinoline and N,N-diethylaniline as bases were the best choices. In our previous study of MALDI with solid matrixes, we found that three requirements had to be met for the generation of reproducible spectra and for analyte quantification: (1) controlling the temperature by fixing the total ion count, (2) plotting the analyte-to-matrix ion ratio versus the analyte concentration as the calibration curve, and (3) keeping the matrix suppression below a critical value. We found that the same requirements had to be met in MALDI with liquid matrixes as well. In particular, although the liquid matrixes tested here were homogeneous, they failed to display spot-to-spot spectral reproducibility unless the first requirement above was met. We also found that analyte-derived ions could not be produced efficiently by MALDI with the above liquid matrixes unless the analyte was sufficiently basic. In this sense, MALDI processes with solid and liquid matrixes should be regarded as complementary techniques rather than as competing ones.

Acquisition of the depth profiles and reproducible mass spectra in matrix-assisted laser desorption/ionization of inhomogeneous samples

RATIONALE

In our previous analysis of the matrix-assisted laser desorption/ionization (MALDI) spectra of peptides, we treated their depth profiles in solid samples as homogeneous. Here, we wanted to determine if the reproducible MALDI spectra and linear calibration curves reported previously would be obtained even when the depth profiles were inhomogeneous.

METHODS

We derived a formula relating shot-number-dependent ion abundance data in temperature-controlled MALDI with the analyte depth profile in a solid sample. We prepared samples containing peptides, amino acids, and serotonin in α-cyano-4-hydroxycinnamic acid matrix by vacuum-drying and micro-spotting methods, recorded their MALDI spectra, and analyzed them with the aforementioned formula.

RESULTS

For the samples prepared by vacuum-drying, the analyte depth profiles were inhomogeneous and maximized at the sample surface. Although the MALDI spectra changed as the shot continued, their sum over the entire set of spectra acquired from a spot was reproducible. Similarly, a high-quality calibration curve could be obtained with the spectral data summed over the entire set. Depth profiles were homogeneous for samples prepared by micro-spotting.

CONCLUSIONS

A method has been developed to obtain a reproducible MALDI spectrum and a linear calibration curve for an analyte with an inhomogeneous depth profile in a solid sample.

Quick quantification of proteins by MALDI

Previously, we reported that the matrix-assisted laser desorption ionization spectrum of a peptide became reproducible when an effective temperature was held constant. Using a calibration curve drawn by plotting the peptide-to-matrix ion abundance ratio versus the peptide concentration in a solid sample, a peptide could be quantified without the use of any internal standard. In this work, we quantified proteins by quantifying their tryptic peptides with the aforementioned method. We modified the digestion process; e.g. disulfide bonds were not cleaved, so that hardly any reagent other than trypsin remained after the digestion process. This allowed the preparation of a sample by the direct mixing of a digestion mixture with a matrix solution. We also observed that the efficiency of the matrix-to-peptide proton transfer, as measured by its reaction quotient, was similar for peptides with arginine at the C-terminus. With the reaction quotient averaged over many such peptides, we could rapidly quantify proteins. Most importantly, no peptide standard, not to mention its isotopically labeled analog, was needed in this method.

A Thermal Mechanism of Ion Formation in MALDI

An important recent discovery concerning the fundamentals of matrix-assisted laser desorption/ionization (MALDI) is that the abundance of each ion appearing in a spectrum is fixed, regardless of the experimental condition, when an effective temperature associated with the spectrum is fixed. We describe this phenomenon and the thermal picture for the ion formation in MALDI derived from it. Accepting that matrix-to-analyte proton transfer is in quasi-equilibrium as supported by experimental data, the above thermal determination occurs because the primary (matrix) ion formation processes are thermally governed. We propose that the abundances of the primary ions are limited by the autoprotolysis-recombination process regardless of how they are initially produced. Finally, we note that primary ion formation, secondary (analyte) ion formation, and their dissociations occur sequentially while the effective temperature of the matrix plume falls steadily due to cooling associated with expansion.

Spectral reproducibility and quantification of peptides in MALDI of samples prepared by micro-spotting

Previously, we reported that MALDI spectra of peptides became reproducible when temperature was kept constant. Linear calibration curves derived from such spectral data could be used for quantification. Homogeneity of samples was one of the requirements. Among the three popular matrices used in peptide MALDI [i.e., α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (DHB), and sinapinic acid (SA)], homogeneous samples could be prepared by conventional means only for CHCA. In this work, we showed that sample preparation by micro-spotting improved the homogeneity for all three cases.

Dual track time-of-flight mass spectrometry for peptide quantification with matrix-assisted laser desorption/ionization

RATIONALE

Previously, we reported a method (Anal. Chem. 2012, 84, 10332) for peptide quantification based on matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). In the method, the peptide-to-matrix ion abundance ratio was utilized. Implementation of the method with a commercial MALDI-TOF can be somewhat inconvenient because matrix-derived ions are routinely deflected away to avoid detector saturation. A solution for this inconvenience is required.

METHODS

We installed a detector to acquire the TOF spectrum of the ions thrown away to avoid detector saturation. By sending the matrix- and peptide-derived ions along two different tracks and detecting them with different detectors, the inconvenience mentioned above could be avoided.

RESULTS

Excellent linearity of the calibration curves obtained by the dual track TOF spectrometry is demonstrated. The method also allows for the acquisition of the tandem mass spectrum of a selected peptide, which can be useful for its identification.

CONCLUSIONS

We devised the dual track MALDI-TOF MS method to avoid detector saturation and demonstrated that the quantification and identification of peptides can be performed simultaneously.

Why do the abundances of ions generated by MALDI look thermally determined?

In a previous study (J. Mass Spectrom. 48, 299-305, 2013), we observed that the abundance of each ion in a matrix-assisted laser desorption ionization (MALDI) spectrum looked thermally determined. To find out the explanation for the phenomenon, we estimated the ionization efficiency and the reaction quotient (QA) for the autoprotolysis of matrix, M + M → [M + H](+) + [M - H](-), from the temperature-controlled laser desorption ionization spectra of α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB). We also evaluated the equilibrium constants (KA) for the autoprotolysis at various temperatures by quantum chemical calculation. Primary ion formation via various thermal models followed by autoprotolysis-recombination was compatible with the observations. The upper limit of the effective temperature of the plume where autoprotolysis-recombination occurs was estimated by equating QA with the calculated equilibrium constant. Figure ᅟ