MALDI peptide analysis

Dai, Y., Whittal R.M., and Li, L., Two-layer sample preparation a method for MALDI-MS analysis of complex peptide and protein mixtures, Anal. Chem., 71, 1087, 1999. 

S. L. Cohen and B. T. Chait Influence of Matrix Solution Conditions on the MALDI-MS Analysis of Peptides and Proteins. Anal. Chem., 68(1996) 31-37. 

J. Gobom, M. Schuerenberg, M. Mueller, D. Theiss, H. Lehrach, and E. Nordhoff. a-Cyano-4-hydroxycinnamic Acid Affinity Sample Preparation. A Protocol for MALDI-MS Peptide Analysis in Proteomics. Anal. Chem., 73(2001) 434-438. 

The peptide mixture on the MALDI target can be exposed to a chemical derivatization to confirm the identity of a peptide by the mass shift associated with the sequence-specific derivatization. A large number of possible derivatization reactions can be combined with the MALDI-TOF analysis. Their usefulness depends critically on the kinetics of the derivatization reaction, whether the reaction is complete with small amounts of peptides and whether only one product is generated. A visible MALDI signal can be generated from low atomole of peptide present under the laser beam (Vorm et al., 1994), but these amounts are often not sufficient... 

Low W, Kang J, Di Gruccio M, Kirby D, Perrin M, et al. 2004. MALDI-MS analysis of peptides modified with photolabile arylazido groups. J Am Soc Mass Spectrom 15 1156. 

An approach to multiplexing analysis was presented by Min et al. [23], who de-velopped a SAMDI-based assay scheme to screen for the activity of different kinases. In this assay scheme, peptide substrates were used that are specific for one type of kinase. A mixture of four substrates was immobilized on the SAM. After incubation with an appropriate kinase, the target surface was rinsed, thus stopping the reaction. Matrix was deposited on the surface and MALDI-MS analysis was carried out (Fig. 8.13). By monitoring the signal intensities for the substrates... 

Combariza MY, SavariarEN, Vutukuri DR, Thayumanavan S, Vachet RW. Polymeric inverse micelles as selective peptide extraction agents for MALDI-MS analysis. Anal Chem 2007 79 7124-7130. 

Many of the advantages that MALDI offers for peptide analysis are equally applicable to proteins. Protein analysis is similar to peptide analysis, in which ionization usually occurs through the addition of one, two, or three protons. However, since proteins are significantly bigger than peptides, ion detection is typically less efficient. Therefore, while peptides are measured at the femtomole or even attomole level with MALDI, proteins are usually measured at the high femtomole to low picomole level. 

Cohen, S. L., and Chait, B. T. (1996). Influence of matrix solution conditions on the MALDI MS analysis of peptides and proteins. Anal. Chem. 68 31-37. 

The most widely used mass spectrometric identification procedure is MALDI-Tof analysis of the entire peptide mixture. Gas-phase matrix interaction with peptide ions in MALDI-Tof results in singly charged ions, giving a mass profile that is highly characteristic of the protein from which the peptides are derived. These peptide masses (actually protonated peptide molecular ions, MH+) can be used to search databases (either protein or nucleic acid databases) to identify the proteins. The two most important factors in successfully identifying proteins by this approach are the number of matching peptide masses and the accuracy of the peptide mass determination. 

One of the requirements in MALDI-MS analysis is the use of a liquid matrix. The electrowetting-on-dielectric (EWOD) method has been used to move and mix droplets containing proteins and peptides with the liquid matrix, all of which were situated at specific locations on an array of electrodes. With this method, insulin (1.75 pM), insulin chain B (2 pM), cytochrome c (1.85 pM), and myoglobin (1.45 pM) have been analyzed [518]. 

Inspection of the UV chromatogram from the LC-ESI MS analysis of the tryptic digest of the protein revealed a peak not present in the digestion of wild-type TTR, at retention time 25.95 min. The [M + H]+ of this variant peptide (m/z 1392.6) was consistent with a 27 Da increment to the normal tryptic peptide T4, 22GSPAINVAVHVFR34. The location of the mutation was confirmed by MALDI MS analysis of the chromatographic fraction collected between retention times 25.0-27.5 min. In the MALDI mass spectrum, peaks at m/z 1365.2 (wild-type T4) and m/z 1392.1 (variant T4) are both present (Fig. 8). This observation confirmed that the mass difference between the variant and the wild type peptides is indeed +27 Da. The only possible amino acid substitution that would give rise to a +27 Da shift in that peptide is Ser23 —> Asn. 

Mueller, M., Theiss, D., Lehragh, H., Nordhoff, E. (2001). a-Cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal. Chem. 73, 434 38. 

It was noticed that a gel band located in between band V and band VI was observed and labeled as the 31-kDa band. This band is one of the three major bands (II, Ilia, and 31 kDa) observed only in the empty capsids, which was not detected in complete viral particles [136]. MALDI-MS analysis of trypsin digested 31-kDa band followed by database search using MS-Fit (peptide mass... 

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