Matrix selection, MALDI

Matrix selection and optimization of the sample preparation protocol are the most important steps in the analysis because the quality of the results depends on good sample preparation. However, the preparation procedures are still empirical. The MALDI matrix selection is based on the laser wavelength used. In addition, the most effective matrix is strongly related to the class of analyte and may differ for analytes that have apparently similar structures. The MALDI matrices must meet a number of requirements simultaneously. These are strong absorbance at the laser wavelength, low enough mass to be sublimable,... 

Also for MALDI, there is a special case worth mentioning. Surface-enhanced laser desorption/ionization (SELDI) is a technique that utilizes special sample plates [196, 197]. These have different modified surfaces, for example, hydrophobic, anionic, or antibody treated. Which type of surface to select depends on the application. After application of analyte the surface is washed according to a protocol leaving only the desired components on the target. Finally, a MALDI matrix is applied before analysis in the spectrometer. See Chapter 12 for an application example of SELDI. 

Figure 14.1 Schematic view of a mass spectrometer. Its basic parts are ion source, mass analyzer, and detector. Selected principles realized in modern mass spectrometers are assigned El—electron impact. Cl—chemical ionization, FAB—fast atom bombardment, ESI—electrospray ionization, MALDI—matrix-assisted laser desorption/ionization. Different combinations of ion formation with mass separation can be realized.

Figure A.3A.1 Flow chart illustrating the selection of a suitable ionization technique for the mass spectrometric analysis of a sample. Abbreviations APCI, atmospheric pressure chemical ionization Cl, chemical ionization El, electron impact FAB, fast atom bombardment MALDI, matrix-assisted laser desorption/ionization.

Although CHCA works well with most drug molecules, there is no universal MALDI matrix. However, as with the internal standard, it is not practical to optimize matrix selection for each compound in broad drug discovery applications. 

The matrix selection and deposition for MALDI-IMS is another crucial step in the sample preparation protocol. The matrix, solvent, concentration of matrix, and the protocol of coating matrix have to be optimized first and then used for the real samples detection. 

Matrix selection The successful detection of analyte molecules depends on the correct choice of the MALDI matrix. The matrix must not react with the analyte in the tissue sections. The MALDI matrices generally used for MALDI-TOF-MS are CF1CA, SA, and DF1B. For small molecule drugs, CHCA and DF1B are the most widely used matrices [125],... 

Since its inception about 15 year ago, MALDI-IMS has been developed into a powerful and versatile tool for biomedical research. It allows for the investigation of the spatial distribution of molecules at complex surfaces. The combination of molecular speciation with local analysis makes a chemical microscope that can be used for the direct biomolecular characterization of histological tissue section surface. However, successful detection of the analytes of interest at the desired spatial resolution requires careful attention to several steps in the IMS protocol matrix selection, matrix coating, data acquisition, and data processing. MALDI-IMS is increasingly playing an important role in the drug discovery and development and disease treatment. 

Recently, EWOD actuation chips were developed into a multiplexed device that was used to simultaneously cleanup four samples. A sequence of seven actuation steps were performed for each sample (1) generation of sample droplets (0.02 p.L), (2) transport and drying of sample droplets, (3) generation of rinsing droplets, (4) transport of rinsing droplets to the sample sites for selective dissolution of urea, (5) transport and disposal of the rinsing droplets, (6) generation of MALDI matrix solution droplets, and (7) delivery of matrix droplets to the dried peptide spots. 

After the selection of the MALDI matrix, cationization salt and solvent, several options are available for transferring the mixture onto the MALDI target. 

Lehrle, R. S. and Sarson, D. S., Degradation and Selective Desorption of Polymer Can Cause Uncertainty in MALDI (Matrix-assisted Laser Desorption Ionisation) Measurements, Polym, Deg, and Stab., 51, 197, 1996. 

Matrix-assisted iaser desorption/ionization (MALDI). This is another ionization method for the analysis of large molecules such as peptides, proteins, and nucleic acids, as well as some synthetic polymers. In MALDI, the analyte is first cocrystallized with an excess of a matrix, e.g., sinapinic acid or dihydroxybenzoic acid, that has a constituent aromatic component able to absorb photons from a UV laser beam. When the dried analyte matrix mixture is exposed (inside the vacuum chamber) to a sudden input of energy from a laser pulse the matrix evaporates, essentially instantaneously, carrying with it the analyte molecules. The matrix forms reagent ions that protonate the analytes. The selection of the matrix is critical as different compound classes exhibit substantial, matrix-dependent differences in ionization efficiency. The MALDI matrix should not be confused with the alternative use of the term matrix that is used to denote the medium in which biological and/or environmental components are presented, e.g., blood plasma, urine, sediment. 

MALDI is the dominant ionization source choice for MSI however, it is not without drawbacks. The application of MALDI matrix on top of the tissue surface complicates the analysis by adding potentially isobaric matrix cluster ions that may obscure the drug compound. Careful selection of MALDI matrix can reduce the matrix effect. An alternative would be to either use the water native to the tissue as a matrix such as with IR-MALDI or altogether eliminate the need for matrix. DESI is an atmospheric pressure technique that permits the direct analysis of surface samples, including tissue sections, with minimal sample preparation (Takats et al., 2004 Cooks et al., 2006). In contrast to MALDI—MSI, no matrix is required however, the spatial resolution for DESI—MSI is worse when compared to MALDI or SIMS imaging experiments. 

Demeure, K., Quinton, L, Gabelica, V., and De Pauw, E. (2007) Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay. Anal. Chem., 79, 8678-8685. 

Laser desorption generates high mass ions by irradiating a solid with a pulsed laser beam. In the case of matrix-assisted laser desorption, a solid mixture of an analyte is dissolved in a suitable matrix compound and the laser pulse desorbs and indirectly ionizes the analyte molecules. The selection of appropriate MALDI matrix, cationization salt, sample concentration, and sample preparation technique are critical success factors for obtaining a reliable mass spectrum that influence the polymer distribution. An alternative technique used to eliminate matrix and cationization salt effects is direct LDI, which is generally used for polymer samples with relatively low molecular weights. 

Collectively, IM-MS clearly provides separation of lipid classes according to their charge properties, individual molecular species of a lipid class based on their molecular size (including chain length and unsaturation), and isobaric/isomeric species possessing different conformational structures [83]. This in situ drift time/collision cross section variation could be used as an additional variable to the other separation variables (e.g., intrasource separation, LC-MS elution, and optimal selection of MALDI matrix for ionization) described earlier as an aid to providing 3D analysis of complex lipid mixtures. 

Requirements for MWD determination by means of MS techniques are (i) absence of discrimination (ii) soft ionisation (DCI, FAB, FD, ESI, LD, MALDI) (Hi) equal ionisation efficiency for high- and low-MW molecules (iv) transmission efficiency (even very heavy molecules should reach the detector) (v) detection efficiency and (vi) calibration. Soft ionisation techniques have all been applied to assorted polymers to obtain average MWDs. Of these, LDI is recommended because it is easily interfaced to both ToF-MS (capable of very high m/z detection) and FTICR (offering high mass resolution and accuracy). Sample preparation with matrix selection (out of 20-30 matrices) and the need for a great excess of matrix (10" 1) are critical for success of MALDI-MS. Failures for correct MWD with MALDI are due to polydispersity (PD) discrimination (especially for PD > 1.1), crystallisation and ionisation processes. Mass discrimination effects observed for polymers have been attributed to sample... 

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