Fragmentation of MALDI Ions

In contrast, no such difference in basicity between the negatively charged ions of matrix molecules and peptides exists, because both are typically carboxylate anions with very close proton affinities. Peptide anion generation competes with simple dissociation of the neutral analyte-matrix anion adduct and limits the yield of analyte anions (see Eq. 1.8 for the CPCD model and Eq. 1.10 for the lucky survivor ). 

Similar arguments hold for the polyanionic nucleic acids. While the addition of ammonium ions results in a quantitative detection of the free acids as singly charged cations or anions, substitution of the ammonium ions by tetraaUcyl ammonium ions leads to the observation of adduct ions, increasing in intensity with increasing length of the alkyl chains. 

Both models - protonation of neutral analytes in the gas phase according to the CPCD model as well as the revised lucky survivor - are discussed in detail in Refs [3, 24, 65]. 

For analytes of very low proton affinity, such as neutral carbohydrates and many synthetic polymers, cationization by Na, K or other metal cations is usually observed in MALDI (see Chapters 6-8). The cationization in all likelihood takes place in the expanding plume, and requires a codesorption of the analyte and the cations. Hence, the best results are obtained from sample locations where both species exist in close neighborhood, such as in the center of DHB-dried droplet preparations. Specific protocols have been developed for the MALDI of such analytes [66, 67]. 

The fragmentation of MALDI ions is a mixed blessing, as in all of MS. It can, on the one hand, lead to a substantial loss of spectra quality such as loss of mass resolution or even complete loss of the signal of the intact parent ion, as has been 

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Figure 2 shows the chromatogram of the starting reaction product, Ce C82(CF3)x. Three Ce C82(CF3)5 isomers were isolated from fractions A, B, D and pure Ce2 Cgo was isolated from fraction D. In contrast to the reaction of Y-EMFs with silver (I) trifluoroacetate, which affords two Y C82(CF3)5 isomers and Y2 Cg0(CF3)13 derivatives [12], the reaction with Ce-EMFv affords three Ce Cg2(CF3)5 isomers and Ce2 Cg0 does not react and can be isolated as an individual compound. The F1PLC chromatogram and the Sg-MALDI spectrum of isolated Ce Cg2(CF3)5 (isomer III) are presented in Fig. 3. The mass spectrum shows only the peak with m/z=1469 attributable to Ce Cg2(CF3)5+. The fragmentation of this ion results in the loss of the CF3 groups up to the formation of the Ce C82+ ion. The 99 % purity of Ce C82(CF3)5 (isomers I, II and III) and Y Cg2(CF3)5 (isomers I and II) was determined by HPLC and Sg-MALDI analysis.

In comparison with MALDI, ESI represents an even softer ionization technique and causes no fragmentation of analyte ions. 

Katta, V., Chow, D. T., and Trohde, M., Application of In-Source Fragmentation of Protein Ions for Direct Sequence Analysis by Delayed Extraction MALDI-TOF Mass Spectrometry Anal. Chem., 70, 4410, 1998. 

There have been considerable advances in mass spectrometry in the last 10 years. Advanced techniques such as matrix-assisted laser desorption ionization (MALDI), electrospray ionization (ESI), thermospray ionization, plasma desorption, and ion spray have been improved and are widely used to obtain the mass spectra of polar and nonpolar compounds with the mass of several thousand Daltons. New MS-MS techniques can provide structural information based on fragmentation of selected ions and are of great value both for qualitative and quantitative analyses especially in difficult matrices. There is no method of ionization that is ideal for all samples. Often the analyst and pigment chemist must work togeth-... 

For PMMA/additive dissolutions, it was not possible to identify any additive characteristic mass peaks, either by direct laser desorption or with matrix-assistance (dithranol, DHBA or sinapinic acid, 4-hydroxy-3,5-dimethoxy-cinnamic acid). This has again been ascribed to very strong interaction between PMMA and additives, which suppresses desorption of additive molecules. Also, partial depolymerisation of pho-tolytically labile PMMA by laser irradiation may play a role, which leads to saturation of the detector by PMMA fragment-ions and disappearance of additive mass peaks below noise level. Meyer-Dulheuer [55] has also reported MALDI-TOFMS analysis of a coating/2-ethylhexyldiphenylphosphate sample. Quantitative determination of the additives by means of MALDI-ToFMS proved impossible. Possibly the development of reproducible (automated) sample handling procedures or thin films might overcome this problem. 

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