Matrix assisted laser desorption ionization Proteomics

Bernardo, K. Pakulat, N. Macht, M. Krut, O. Seifert, H. Fleer, S. Hunger, F. Kronke, M. Identification and discrimination of Staphylococcus aureus strains using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Proteomics 2002, 2, 747-753. 

Conway, G. C. Smole, S. C. Sarracino, D. A. Arbeit, R. D. Leopold, P. E. Phylo-proteomics Species identification of Enterobacteriaceae using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Mol. Microbiol. Biotech-nol. 2001, 3,103-112. 

Verhaert, P., Uttenweiler-Joseph, S., de Vries, M., Loboda, A., Ens, W., Standing, K.G. (2001). Matrix-assisted laser desorption/ionization quadrupole time-of-flight mass spectrometry an elegant tool for peptidomics. Proteomics 1, 118-131. 

Proteomics ultimately hinges upon protein identification to reveal the meaning behind the masses, spots, or peaks detected by other means. Because fraction collection is a natural component of HPLC separations, intact proteins can be readily collected either for direct analysis or for proteolytic digestion and identification using peptide mass fingerprinting (PMF) in conjunction with matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). 

Many diseases are characterized by the expression of specific proteins1 in some cases, malignant cells yield unique protein profiles when total cellular protein extracts are analyzed by proteomic methods such as two-dimensional gel electrophoresis or matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS).2 High-throughput proteomic studies may be useful to differentiate normal cells from cancer cells, to identify and define the use of biomarkers for specific cancers, and to characterize the clinical course of disease. Proteomics can also be used to isolate and characterize potential drug targets and to evaluate the efficacy of treatments. 

B. Warscheid and C. Fenslau. A Targeted Proteomics Approach to the Rapid Identification of Bacterial Cell Mixtures by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Proteomics, 4(2004) 2877-2892. 

Spengler B (2001) The basics of matrix-assisted laser desorption ionization time-of flight mass spectrometry and post source decay. In James P (ed) (2001) Proteome research Mass spectrometry. Springer, New York, p 33... 

Kim J, Kim SH, Lee SU et al. Proteome analysis of human liver tumor tissue by two-dimensional gel eleetrophoresis and matrix-assisted laser desorption/ionization-mass spectrometry for identification of disease-related proteins. Electrophoresis 2002 23 4142 156. 

Sinha, P. Poland, J. Schnolzer, M. Rabilloud, T. A new silver staining apparatus and procedure for matrix-assisted laser desorption/ionization-time of flight analysis of proteins after two-dimensional electrophoresis. Proteomics (Germany) 2001, 1(7), 835-840. 

Matrix-assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption ionization (SELDI) have been used online with TOF-MS for protein differential profiles of intact or hydrolyzed biological matrices in proteomics. The potential use of affinity chips, grafted with specific Ab towards the drug compound for MALDI or SELDI, will bring sensitive and selective tools for macromolecules. Specific Ab towards either the intact protein or several signature peptides... 

The use and development of high-resolving separation techniques as well as highly accurate mass spectrometers is nowadays essential to solve the proteome complexity. Currently, more than a single electrophoretic or chromatographic step is used to separate the thousands of proteins found in a biological sample. This separation step is followed by analysis of the isolated proteins (or peptides) by mass spectrometry (MS) via the so-called soft ionization techniques, such as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) combined with the everyday more powerful mass spectrometers. Two fundamental analytical strategies can be employed the bottom-up and the top-down approach. 

D. Goldberg, M. Sutton-Smith, J. C. Paulson, and A. Dell, Automatic annotation of matrix-assisted laser desorption/ionization V-glycan spectra, Proteomics, 5 (2005) 865-875. 

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. 

Li, N., Shaw, A.R., Zhang, N.,Mak,A. andLi, L.(2004)Lipidraftproteomics analysis of in-solution digest of sodium dodecyl sulfate-solubilized lipid raft proteins by liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry. Proteomics 4, 3156-3166. 

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. 

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