High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Liquid ultraviolet matrix-assisted laser desorption/ionization - mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet -- matrix-assisted laser desorption/ionisation -- mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. The low-femtomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydroxybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and low-mass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

Liquid ultraviolet matrix-assisted laser desorption/ionization mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet - matrix-assisted laser desorption/ ionisation - mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. U. Am. Soc. Mass Spectrom. 1998, 9, 166-174). The low-ferntomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydrox-ybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and lowmass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Analytical and compositional aspects of isoflavones in food and their biological effects

This paper provides an overview of analytical techniques used to determine isoflavones (IFs) in foods and biological fluids with main emphasis on sample preparation methods. Factors influencing the content of IFs in food including processing and natural variability are summarized and an insight into IF databases is given. Comparisons of dietary intake of IFs in Asian and Western populations, in special subgroups like vegetarians, vegans, and infants are made and our knowledge on their absorption, distribution, metabolism, and excretion by the human body is presented. The influences of the gut microflora, age, gender, background diet, food matrix, and the chemical nature of the IFs on the metabolism of IFs are described. Potential mechanisms by which IFs may exert their actions are reviewed, and genetic polymorphism as determinants of biological response to soy IFs is discussed. The effects of IFs on a range of health outcomes including atherosclerosis, breast, intestinal, and prostate cancers, menopausal symptoms, bone health, and cognition are reviewed on the basis of the available in vitro, in vivo animal and human data.

Sample preparation: a crucial factor for the analytical performance of rationally designed MALDI matrices

Evidence is presented that the performance of the rationally designed MALDI matrix 4-chloro-α-cyanocinnamic acid (ClCCA) in comparison to its well-established predecessor α-cyano-4-hydroxycinnamic acid (CHCA) is significantly dependent on the sample preparation, such as the choice of the target plate. In this context, it becomes clear that any rational designs of MALDI matrices and their successful employment have to consider a larger set of physicochemical parameters, including sample crystallization and morphology/topology, in addition to parameters of basic (solution and/or gas-phase) chemistry.

On mathematical and physical principles of transformations of the coherent radar backscatter matrix

The congruential rule advanced by Graves for polarization basis transformation of the radar backscatter matrix is now often misinterpreted as an example of consimilarity transformation. However, consimilarity transformations imply a physically unrealistic antilinear time-reversal operation. This is just one of the approaches found in literature to the description of transformations where the role of conjugation has been misunderstood. In this paper, the different approaches are examined in particular in respect to the role of conjugation. In order to justify and correctly derive the congruential rule for polarization basis transformation and properly place the role of conjugation, the origin of the problem is traced back to the derivation of the antenna height from the transmitted field. In fact, careful consideration of the role played by the Green’s dyadic operator relating the antenna height to the transmitted field shows that, under general unitary basis transformation, it is not justified to assume a scalar relationship between them. Invariance of the voltage equation shows that antenna states and wave states must in fact lie in dual spaces, a distinction not captured in conventional Jones vector formalism. Introducing spinor formalism, and with the use of an alternate spin frame for the transmitted field a mathematically consistent implementation of the directional wave formalism is obtained. Examples are given comparing the wider generality of the congruential rule in both active and passive transformations with the consimilarity rule.

A criterion for unitary similarity of upper triangular matrices in general position

Each square complex matrix is unitarily similar to an upper triangular matrix with diagonal entries in any prescribed order. Let A = [a(ij)] and B = [b(ij)] be upper triangular n x n matrices that are not similar to direct sums of square matrices of smaller sizes, or are in general position and have the same main diagonal. We prove that A and B are unitarily similar if and only if parallel to h(A(k))parallel to = parallel to h(B(k))parallel to for all h is an element of C vertical bar x vertical bar and k = 1, ..., n, where A(k) := [a(ij)](i.j=1)(k) and B(k) := [b(ij)](i.j=1)(k) are the leading principal k x k submatrices of A and B, and parallel to . parallel to is the Frobenius norm. (C) 2011 Elsevier Inc. All rights reserved.

A canonical form for nonderogatory matrices under unitary similarity

A square matrix is nonderogatory if its Jordan blocks have distinct eigenvalues. We give canonical forms for (1) nonderogatory complex matrices up to unitary similarity, and (2) pairs of complex matrices up to similarity, in which one matrix has distinct eigenvalues. The types of these canonical forms are given by undirected and, respectively, directed graphs with no undirected cycles. (C) 2011 Elsevier Inc. All rights reserved.

Matrix effects observed during pesticides residue analysis in fruits by GC

The influence of the sample matrix in the CC-electron-capture detection analysis of the pesticides dimethoate, diazinon, chlorothalonil.. parathion methyl and fenitrothion in fruits samples has been studied. Experiments have been carried out where the pesticide responses in standard solutions prepared in selected solvent were compared with their response when present in apple, mango, papaya, banana, pineapple and melon extracts. The presence of matrix effects (MEs) and their extent were shown to be simultaneously influenced by several factors (matrix concentration, matrix type, pesticide concentration, analytical range). Pronounced MEs were observed particularly for dimethoate and diazinon in all matrices tested; in lower concentrations, all pesticides presented significant ME. The other pesticides presented variable ME. Higher ME enhancement was detected at lower pesticide concentration levels of and/or at higher matrix concentration solutions. The ME detected for fenitrothion, in the analytical range evaluated, were dependent on matrix type. For each pesticide, solvent and matrix-matched calibrations were compared for all fruit samples, and it could be concluded that quantitation based on standard solutions prepared in blank matrix extract (matrix-matched calibration) should be used to compensate the MEs and to obtain more accurate results for the pesticides studied.

Headspace solid-phase microextraction combined with mass spectrometry as a powerful analytical tool for profiling the terpenoid metabolomic pattern of hop-essential oil derived from Saaz variety

Hop(HumuluslupulusL.,Cannabaceaefamily)isprizedforitsessentialoilcontents,usedin beer production and, more recently, in biological and pharmacological applications. In this work,a methodinvolvingheadspace solid-phase microextractionand gas chromatography– mass spectrometry was developed and optimized to establish the terpenoid (monoterpenes and sesquiterpenes) metabolomic pattern of hop-essential oil derived from Saaz variety as a mean to explore this matrix as a powerful biological source for newer, more selective, biodegradable and naturally produced antimicrobial and antioxidant compounds. Different parameters affecting terpenoid metabolites extraction by headspace solid-phase microextraction were considered and optimized: type of fiber coatings, extraction temperature, extraction time, ionic strength, and sample agitation. In the optimized method, analytes were extracted for 30 min at 40 C in the sample headspace with a 50/30 m divinylbenzene/carboxen/polydimethylsiloxane coating fiber. The methodology allowed the identification of a total of 27 terpenoid metabolites, representing 92.5% of the total Saaz hop-essential oil volatile terpenoid composition. The headspace composition was dominated by monoterpenes (56.1%, 13 compounds), sesquiterpenes (34.9%, 10), oxygenated monoterpenes (1.41%, 3), and hemiterpenes (0.04%, 1) some of which can probably contribute to the hop of Saaz variety aroma. Mass spectrometry analysis revealed that the main metabolites are the monoterpene -myrcene (53.0±1.1% of the total volatile fraction), and the cyclic sesquiterpenes, -humulene (16.6 ± 0.8%), and -caryophyllene (14.7 ± 0.4%), which together represent about 80% of the total volatile fraction from the hop-essential oil. Thesefindingssuggestthatthismatrixcanbeexploredasapowerfulbiosourceofterpenoid metabolites.

Comparison between Two Methods to Calculate the Transition Matrix of Orbit Motion

Two methods to evaluate the state transition matrix are implemented and analyzed to verify the computational cost and the accuracy of both methods. This evaluation represents one of the highest computational costs on the artificial satellite orbit determination task. The first method is an approximation of the Keplerian motion, providing an analytical solution which is then calculated numerically by solving Kepler's equation. The second one is a local numerical approximation that includes the effect of J(2). The analysis is performed comparing these two methods with a reference generated by a numerical integrator. For small intervals of time (1 to 10s) and when one needs more accuracy, it is recommended to use the second method, since the CPU time does not excessively overload the computer during the orbit determination procedure. For larger intervals of time and when one expects more stability on the calculation, it is recommended to use the first method.

The role of matrix effects on the quantification of abscisic acid and its metabolites in the leaves of Bauhinia variegata L. using liquid chromatography combined with tandem mass spectrometry

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A new potentiometric ibuprofenate ion sensor immobilized in a graphite matrix for determination of ibuprofen in tablets

The characteristics, performance, and application of an electrode, namely, Pt vertical bar Hg vertical bar Hg-2(IBP)(2)vertical bar Graphite, where IBP stands for ibuprofenate ion, are described. This electrode responds to IBP with sensitivity of (58.6 +/- 0.9) mV decade 1 over the range 5.0 x 10(-5)-1.0 x 10(-1) mol L-1 at pH 6.0-9.0 and a detection limit of 3.8 x 10(-5) mol L-1. The electrode is easily constructed at a relatively low cost with fast response time (within 1530 s) and can be used for a period of 5 months without any considerable divergence in potentials. The proposed sensor displayed good selectivity for ibuprofen in the presence of several substances, especially concerning carboxylate and inorganic anions. It was used for the direct assay of ibuprofen in commercial tablets by means of the standard additions method. The analytical results obtained by using this electrode are in good agreement with those given by the United States Pharmacopeia procedure. (c) 2006 Elsevier B.V. All rights reserved.

Effect of a pilot washing system on dicofol levels in orange matrix

An efficient analytical method is described for the analysis of dicofol residues in pulp and orange peel. Samples are mixed with Celite and transferred to chromatographic columns prepacked with silica gel. Dicofol is eluted with ethyl acetate, and the extracts are analyzed by gas chromatography with electron capture detection. Mean recoveries for dicofol at levels of 0.5, 2.0, 5.0, and 10 mg/kg ranged from 87 to 95% with relative standard deviation values between 2.6 and 9.0%. To investigate the effect of a pilot washing system on dicofol residues in oranges, the analytical procedure was applied to samples submitted to different treatments with commercial formulations under field and laboratory conditions. The orange samples with and without washing were analyzed in duplicate, and the results indicated that washing under the described conditions did not allow a complete removal of dicofol residues from orange peel.