Matrix proteomics applications

Randic, M., Witzmann, F., Vracko, M. andBasak, S.C. (2001) On characterization of proteomics maps and chemically induced changes in proteomes using matrix invariants application to peroxisome proliferations. Med. Chem. Res., 10, 456-479. 

Upon use of structurally modified variants as internal standards for the particular analytes, the relative quantificahon of oligonucleotides, peptides, and small proteins was demonstrated [44]. The potential of the ILM to allow quantitative analyses of peptides without the use of internal standards was presented recently [43]. Linear correlahons between peptide amount and signal intensities could be found upon applicahon of increased matrix-to-analyte ratios between 25,000 and 250,000 (mokmol). The dynamic range of linearity thus spanned one order of magnitude. Unfortunately, the importance of the M/A ratio prevents the use of this method in samples with unknown orders of concentration, for example, in a proteomics environment. On the other hand, the method is applicable for the screening of enzyme-catalyzed reactions because the starting concentrahons of the peptides are generally known in such assays. 

Applying mass-balance and thermodynamic constraints typically leaves one without a precisely defined (unique) solution for reaction fluxes and reactant concentration, but instead with a mathematically constrained feasible space for these variables. Exploration of this feasible space is the purview of constraint-based analysis. It has so far been left unstated that any application in this area starts with the determination of the reactions in a system, from which the stoichiometric matrix arises. This first step, network reconstruction, integrates genomic and proteomic data to determine carefully the enzymes present in an organism, cell, or subcellular compartment. The network reconstruction process is described elsewhere [107]. 

In the proteomic analysis of the brain, two-dimensional gels for protein separation, followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry for protein identification, have mainly been employed. This classical proteomics approach allows for the quantification of changes in protein levels and modifications. Simultaneously, it is a robust, well-established method that finds wide application in the study of biological systems. In this article, we provide a description of the protocols of the proteomic analysis used in our laboratory and a summary of the major findings from our group and other neuroproteomics groups. 

The methods for each study are divided into the initial protein separation step, a second separation step if applicable, the type of mass analysis, and the software used for peptide identification. ID = one dimensional polyacrylamide gel electrophoresis, 2D = two dimensional polyacrylamide gel electrophoresis, MS = mass spectrometry (peptide mass fingerprinting), MS/MS = tandem mass spectrometry, MALDI-TOF = matrix assisted laser desorption/ionization-time of flight, MS FIT = software from Protein Prospector, http //prospector.ucsf edu/, ESI = electrospray ionization, Q-TOF = quadrupole-time of flight, PPSS2 =Protana s Proteomic Software Suite (ProtanaEngineering, Odense, Denmark), Mascot = Matiix Science, http //www.matrixscience.com/, TOF-TOF = MALDI plus TOF tandem mass spectrometry, RP-HPLC = reverse phase high performance liquid chromatography, Q-IT = quadrupole ion trap, LIT = linear ion trap. Bioworks = Thermo Electron Corporation. 

Mirgorodskaya, E., Braeuer, C., Fucini, P, Lehrach, FI. and Gobom, J. (2005a) Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry Sample preparation, data anlysis, and application to the analysis of complex peptide mixtures. Proteomics 5, 399-408. 

Other Methods of Ionization. There are several other methods for ionization in addition to ESI and MALDI. However, most of them are not commonly used in proteomics. Some of these include chemical ionization, electron ionization, fast atom bombardment (FAB), and many others. Most of these lead to disintegration or fragmentation of analyte molecules and are not commonly used in proteomics. However, FAB has some application in the analysis of proteins and peptides, because this is a soft ionization procedure and does not cause the fragmentation of molecules under analysis. In the FAB method, a nonvolatile matrix such as m-nitrobenzyle alcohol is used to hold the analyte molecules. Analyte molecules are vaporized and ionized by bombardment with the high-energy beam of xenon or cesium from a probe inserted directly into the device containing the sample. Ionized molecules thus obtained are then subjected to separation by the mass... 

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