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A matrix consists of crystallised molecules. The most common of which are 3,5-dimethoxy-4-hydroxycinnamic acid, α-cyano-4-hydroxycinnamic acid, and 2,5-dihydroxybenzoic acid.

They are of a fairly low molecular weight (to allow facile vaporization), but are large enough (with a low enough vapour pressure) not to evaporate during sample preparation or while standing in the spectrometer.  

They are acidic, therefore act as a proton source to encourage ionization of the analyte.  

They have a strong optical absorption in the UV, so that they rapidly and efficiently absorb the laser irradiation.  

They are functionalized with polar groups, allowing their use in aqueous solutions.

How is the Matrix prepared?

The matrix is normally prepared by making a saturate solution of the solid in highly purified water and an organic solvent (normally acetonitrile or ethanol). Trifluoroacetic acid may also be added to encourage ionisation. For best results the matrix should be freshly prepared before use.

How is the sample added to the matrix?

The matrix is normally spotted onto the MAULDI target in solution and the solvent allowed to evaporate to produce a crystalline matrix. Sample may be added to the matrix solution before spotting onto the target, added to the spot of matrix solution on the target in a suitable solvent or added to matrix after it has crystallised on the target in a suitable solvent.

What types of compounds may be analysed by MALDI?

peptides, nucleotides, oligonucleotides, oligosaccharides, proteins, and lipids, have all been reported as having been analysed by MALDI/MS. The use of the correct matrix for analysis of the samlple is important. A guide as to which matrix to use is given below.

In proteomics, MALDI may be used for the identification of proteins isolated through gel electrophoresis: SDS-PAGE and two-dimensional gel electrophoresis. One method used is to identify proteins by MALDI/MS is by identification from fingerprints; our system is linked to external databases to aid protein identification.

Some synthetic macromolecules, such as catenanes and rotaxanes, dendrimers and hyperbranched polymers, which have molecular weights extending into the thousands or tens of thousands, are amenable to analysis by MALDI mass spectrometry, where most other ionization techniques have difficulty producing molecular ions . 

2,5-dihydroxy benzoic acid

Common Names :- HB, 2,5-DHB, Gentisis Acid

Solvents :-             water,aetonitrile, methanol, acetone, chloroform

Applications:-         peptides, necleotides, oligononucleotides, oligosaccharidrs

3,5-dimethoxy-4-hydroxycinnamic acid

Common Names :- sinapic acid, snapinic, SA

Solvents :-  acetonitrile, water, acetone, chloroform

Applications:-  peptides, proteins, lipids

4-hydroxy-3-methoxycinnamic acid

Common Name :-   ferulic acid

Solvents :-  acetonitrile, water, propanol

Applications:-         proteins

α-cyano-4-hydroxycinnamic acid

Common Name :-  CHCA

Solvents :-  acetonitrile, water, ethanol, acetone

Applications:-        peptides, lipids, neucleotides

3-hydroxy picolinic acid

Common Name :-  HPA

Solvents :-  ethanol

Applications:  oligononucleotides

Only matrices usable at the 337nm wave length of the Nitrogen Laser used in the AutoFlex Mass Spectrometer have been Included.

What type of data is obtained from the MALDI Spectrometer?

The data obtained from the MALDI experiment conducted on the AutoFlex is usually nominal mass data and is used for qualitative analysis of the sample. The accuracy of the masses measured will depend on the accuracy of the instrument calibration.

As far as possible samples for MALDI mass spectrometry should not contain inorganic salts. Inorganic salts may be part of protein extracts, for best results it is advisable to remove any such salts by solid phase extraction or washing the final target spots with water. Both methods can also be used to remove salts and other impurities from other types of sample. Samples to be run by MALDI should as far as possible not be prepared in glass apparatus so that they do not pick up alkali and alkaline earth metal ions from the glass which would interfere with MALDI ionisation.

How much sample will I need?

This question is hard to answer. It will depend on the type of sample and matrix being used, the purity of the sample, and the type of MALDI target used. In general an Anchor Chip Target usually produces the best sensitivity for proteins, but unfortunately only one of these is available in the Facility. In general the sample size should be at least 10 fmols.

What is the maximum resolution of the instrument?

With good sample preparation and careful operation of the instrument it is possible to obtain a resolution of about 10,000. The mass range of the instrument extend to about 60,000 Daltons if the reflectron is not used. Working at this level it is not possible to get sufficient resolution to separate the isotope peaks of an ion and it will appear as a hump covering a small range of masses.

How long will it take to run a sample?

MALDI spectra are normally built up by summing the results from a series of scans of the laser. The AutoFlex instrument has the facility to produce a spectrum by summing the results of two or more series of laser scans. The more series of scans that are summed the longer the running of the spectrum is likely to take. If the sample has been well prepared and the analyte is present in reasonable concentration it should be possible to run a MALDI spectrum in ten to fifteen minutes. Time must also be allowed for running of any calibration samples and blanks that may be required.