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The article contains sections titled: 1. Introduction 2. Immobilization Techniques 2.1. Introduction 2.2. Methods of Enzyme Immobilization 2.2.1. Carriers for Enzyme Immobilization 2.2.2. Methods for Insoluble Enzymes 2.2.2.1. Carrier Binding 2.2.2.2. Cross-Linking 2.2.2.3. Enzyme Copolymerization 2.2.2.4. Entrapment 2.2.3. Methods for Soluble Enzymes 2.3. Methods of Cell Immobilization 2.3.1. Introduction 2.3.2. Cell Supports 2.3.3. Immobilization Techniques 2.3.3.1. Cell Immobilization without a Support 2.3.3.2. Binding of Cells to a Carrier 2.3.3.3. Immobilization of Cells by Entrapment 2.4. Methods of Organelle Immobilization 2.5. Coimmobilization of Biocatalysts 3. Activity and Kinetics of Immobilized Biocatalysts 3.1. Effects of Immobilization on Enzyme Activity 3.2. Kinetics of Immobilized Biocatalysts 3.3. Assay of Immobilized Biocatalysts 4. Mass Transfer in Immobilized Biocatalyst Systems 4.1. External Mass Transfer 4.2. Prediction and Correlation of External Mass-Transfer Coefficients 4.2.1. Catalyst Beds 4.2.2. Particles in an Agitated Tank 4.3. Internal Mass Transfer 5. Design of Immobilized Biocatalyst Reactors 5.1. Batch Stirred-Tank Reactor 5.2. Plug-Flow Tubular Reactor 5.3. Continuous Stirred-Tank Reactor 5.4. Packed- or Fixed-Bed Reactors 5.5. Fluidized-Bed Reactors 5.6. Membrane Reactor Systems 5.7. Laboratory Reactors for Kinetic Measurements 5.7.1. Batch and Continuous Tank Reactors 5.7.2. Experimental Differential Recycle Reactor 6. Immobilization Media 6.1. Characteristics of Solid Supports 6.2. Characteristics of Semipermeable Separators 7. Application of Immobilized Biocatalysts 7.1. Analysis 7.2. Immobilized Enzymes in Therapeutic Medicine 7.3. Ethanol Production Using Immobilized Cells 7.4. Industrial Applications of Immobilized Biocatalysts 7.4.1. Production of High-Fructose Corn Syrup 7.4.2. Amino Acid Production 7.4.3. Environmental Applications 8. Economic Aspects 9. Safety, Environmental, and Legal Aspects 9.1. Immobilized Enzymes 9.2. Immobilized Cells

The repeatability of peptide identifications in shotgun proteome analyses employing strong cation-exchange-xion-pair RP HPLC hyphenated to ESI MS/MS was compared to an alternative scheme, comprising high-pH RP chromatography combined with low-pH ion-pair RP chromatography. Equivalent results were obtained with both methods in proteome analysis of Corynebacterium glutamicum. From a total number of 1350 to 1850 peptides identified in triplicate analyses of five consecutive fractions chosen from the first-dimension separation, 41-45% of the peptides were identified three times, whereas 16-22 and 37-39% of the peptides were identified only twice or once, respectively. A comparison of the repeatability of peptide identifications from complex samples upon 1- or 2-D chromatographic separation revealed that an additional separation dimension decreases the repeatability by approximately 25%.

In the present work, the metabolic network of primary metabolism of the slow-growing myxobacterium Sorangium cellulosum was reconstructed from the annotated genome sequence of the type strain So ce56. During growth on glucose as the carbon source and asparagine as the nitrogen source, So ce56 showed a very low growth rate of 0.23 d-(1), equivalent to a doubling time of 3 days. Based on a complete stoichiometric and isotopomer model of the central metabolism, 13C metabolic flux analysis was carried out for growth with glucose as carbon and asparagine as nitrogen sources. Normalized to the uptake flux for glucose (100%), cells recruited glycolysis (51%) and the pentose phosphate pathway (48%) as major catabolic pathways. The Entner-Doudoroff pathway and glyoxylate shunt were not active. A high flux through the TCA cycle (118%) enabled a strong formation of ATP, but cells revealed a rather low yield for biomass. Inspection of fluxes linked to energy metabolism revealed that S. cellulosum utilized only 10% of the ATP formed for growth, whereas 90% is required for maintenance. This explains the apparent discrepancy between the relatively low biomass yield and the high flux through the energy-delivering TCA cycle. The total flux of NADPH supply (216%) was higher than the demand for anabolism (156%), indicating additional reactions for balancing of NADPH. The cells further exhibited a highly active metabolic cycle, interconverting C3 and C4 metabolites of glycolysis and the TCA cycle. The present work provides the first insight into fluxes of the primary metabolism of myxobacteria, especially for future investigation on the supply of cofactors, building blocks, and energy in myxobacteria, producing natural compounds of biotechnological interest.

Efficient and accurate safety assessment of compounds is extremely important in the preclinical development of drugs especially when hepatotoxicty is in question. Multiparameter and time resolved assays are expected to greatly improve the prediction of toxicity by assessing complex mechanisms of toxicity. An integrated approach is presented in which Hep G2 cells and primary rat hepatocytes are compared in frequently used cytotoxicity assays for parent compound toxicity. The interassay variability was determined. The cytotoxicity assays were also compared with a reliable alternative time resolved respirometric assay. The set of training compounds consisted of well known hepatotoxins; amiodarone, carbamazepine, clozapine, diclofenac, tacrine, troglitazone and verapamil. The sensitivity of both cell systems in each tested assay was determined. Results show that careful selection of assay parameters and inclusion of a kinetic time resolved assay improves prediction for non-metabolism mediated toxicity using Hep G2 cells as indicated by a sensitivity ratio of 1. The drugs with EC50 values 100 μM or lower were considered toxic. The difference in the sensitivity of the two cell systems to carbamazepine which causes toxicity via reactive metabolites emphasizes the importance of human cell based in-vitro assays. Using the described system, primary rat hepatocytes do not offer advantage over the Hep G2 cells in parent compound toxicity evaluation. Moreover, respiration method is non invasive, highly sensitive and allows following the time course of toxicity. Respiration assay could serve as early indicator of changes that subsequently lead to toxicity.

Mass spectrometric (MS) isotopomer analysis has become a standard tool for investigating biological systems using stable isotopes. In particular, metabolic flux analysis uses mass isotopomers of metabolic products typically formed from (13)C-labeled substrates to quantitate intracellular pathway fluxes. In the current work, we describe a model-driven method of numerical bias estimation regarding MS isotopomer analysis. Correct bias estimation is crucial for measuring statistical qualities of measurements and obtaining reliable fluxes. The model we developed for bias estimation corrects a priori unknown systematic errors unique for each individual mass isotopomer peak. For validation, we carried out both computational simulations and experimental measurements. From stochastic simulations, it was observed that carbon mass isotopomer distributions and measurement noise can be determined much more precisely only if signals are corrected for possible systematic errors. By removing the estimated background signals, the residuals resulting from experimental measurement and model expectation became consistent with normality, experimental variability was reduced, and data consistency was improved. The method is useful for obtaining systematic error-free data from (13)C tracer experiments and can also be extended to other stable isotopes. As a result, the reliability of metabolic fluxes that are typically computed from mass isotopomer measurements is increased.

The separation of complex peptide mixtures in shotgun proteome analysis using a 2D separation scheme encompassing reversed-phase × ion-pair reversed-phase (IP-RP) liquid chromatography coupled online to electrospray ion trap mass spectrometry (MS) has been shown earlier to be superior in terms of separation efficiency and technical robustness compared to the classically used separation scheme encompassing strong cation exchange × IP-RP-chromatography in shotgun proteome analysis. In the present study, this novel separation scheme was coupled offline to matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF)/TOF-MS for the analysis of the same sample, a tryptic digest of the cytosolic proteome of the bacterium Corynebacterium glutamicum. Compared to the earlier study, the MALDI-based platform led to a significantly increased number of peptides (7,416 vs. 2,709) and proteins (1,208 vs. 468, without single peptide-based identifications), respectively. This represents the majority of all predicted cytosolic proteins in C. glutamicum. The high proteome coverage, as well as the large number of low-abundant proteins identified with this improved analytical platform, pave the way for new biological studies.

Identification of ancient biological samples from the 1991-discovered and more than 5300-year-old Tyrolean mummy, also called iceman or Oetzi, is very difficult. The species of origins of four animal-hair-bearing samples of the accoutrement of the mummy not yet diagnosed were identified by a special proteomics method. Ha 43/91/130 and Ha 6/91, two samples from his coat, and Ha 5/91, a sample from his leggings, were assigned to sheep. The upper leather of his moccasins, Ha 2/91, was made from cattle. Despite the enormous age of these samples with partial (bio)chemical alterations, reliable identification was possible using a recently developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometric ((MALDI-TOF MS)-based analytical method. The method is exclusively based on the analysis of proteins and uses minute amounts of peptides directly derived from tryptic hair digests without any separation or enrichment steps. Unknown species are identified by comparison of their peptide ion patterns with known spectra stored in existing databases. Hereby, the correlation distance, a form of Euclidean distance, and deduced parameters are used to measure similarities. If more than one potential hit remains, specific diagnostic peptide ions are used to stepwise exclude incorrect matches. These ions are specific for orders, families, subfamilies/genera and/or even species. Peptide mass fingerprinting data combined with those from collision-induced dissociation spectra (combined MS & MS/MS) were used for interpretation with the MASCOT search engine and the NCBI database to find the potential parentage of hair proteins. For this technique, selected precursor ions were identified as specific diagnostic peptide ions.

On-line fermentation gas analysis is of general interest because it permits the determination of metabolic rates in almost any biological process using living organisms. The consumption and production of gases (O2, CO2, CH4, etc.) and volatile compounds may be determined without causing any risk of infection. Elemental balancing permits the determination of other metabolic rates if the stoichiometry is known. This was studied with the production of poly-β-hydroxybutyrate (PHB) by Alcaligenes latus. Estimations were based on the measurement of gas partial pressure and flow-rates, pH and alkali consumption rate. Experiments with a small quadrupole mass spectrometer showed unacceptable error propagation. Therefore, dynamic error propagation for all rates was studied using simulation. It was found that, for example, a 1% relative offset-calibration error for oxygen can result in an error in PHB estimation of > 50%. It is suggested that this culture is used in combination with elemental balancing for thorough tests of the accuracy of on-line gas analysis equipment. An on-line process gas analyser based on a quadrupole mass spectrometer (Balzers PGM 407) gave the following precision values (abs. vol.−%) during cultivation of Bacillus subtilis: nitrogen (m/z 14), 0.024; oxygen (m/z 32), 0.020; argon (m/z 40), 0.0011; and carbon dioxide (m/z 44), 0.0034. These values, combined with automatic recalibration, would be sufficient for reasonable estimation of PHB, biomass and substrates.

A two-dimensional separation scheme for shotgun proteome analysis employing high-pH reversed-phase HPLC in the first and low-pH ion-pair reversed-phase HPLC in the second dimension (RP x IP-RP-HPLC) has been developed and evaluated. Compared to the classical strong cation exchange x ion-pair reversed-phase (SCX x IP-RP-HPLC) approach, the RP x IP-RP-HPLC system was characterized by a lower degree of orthogonality, which was, however, more than counterbalanced by higher separation efficiency, more homogeneous distribution of peptide elution, and easier experimental handling. Peptide fragment fingerprinting by electrospray-ionization tandem mass spectrometry (ESI-MS/MS) was employed for peptide detection and identification. About 13% more peptides and 7% more proteins could be identified with the alternative approach in 30% less analysis time, enabling the analysis of the proteome of Corynebacterium glutamicum with a coverage of 24.9% (745 proteins). Combining the identification results both of the SCX- x IP-RP-HPLC-ESI-MS/MS and RP- x IP-RP-HPLC-ESI-MS/MS methods, a total of 871 proteins were identified in a cytosolic protein preparation, which represented 29.1% of all proteins annotated in the genome of C. glutamicum.

Background The importance and power of isotope-based metabolic flux analysis and its contribution to understanding the metabolic network is increasingly recognized. Its application is, however, still limited partly due to computational inefficiency. 13C metabolic flux analysis aims to compute in vivo metabolic fluxes in terms of metabolite balancing extended by carbon isotopomer balances and involves a nonlinear least-squares problem. To solve the problem more efficiently, improved numerical optimization techniques are necessary. Results For flux computation, we developed a gradient-based hybrid optimization algorithm. Here, independent flux variables were compactified into [0, 1)-ranged variables using a single transformation rule. The compactified parameters could be discriminated between non-identifiable and identifiable variables after model linearization. The developed hybrid algorithm was applied to the central metabolism of Bacillus subtilis with only succinate and glutamate as carbon sources. This creates difficulties caused by symmetry of succinate leading to limited introduction of 13C labeling information into the system. The algorithm was found to be superior to its parent algorithms and to global optimization methods both in accuracy and speed. The hybrid optimization with tolerance adjustment quickly converged to the minimum with close to zero deviation and exactly re-estimated flux variables. In the metabolic network studied, some fluxes were found to be either non-identifiable or nonlinearly correlated. The non-identifiable fluxes could correctly be predicted a priori using the model identification method applied, whereas the nonlinear flux correlation was revealed only by identification runs using different starting values a posteriori. Conclusion This fast, robust and accurate optimization method is useful for high-throughput metabolic flux analysis, a posteriori identification of possible parameter correlations, and also for Monte Carlo simulations to obtain statistical qualities for flux estimates. In this way, it contributes to future quantitative studies of central metabolic networks in the framework of systems biology.

New methods for an extended physiological characterization of yeast at a microtiter plate scale were applied to 27 deletion mutants of Saccharomyces cerevisiae cultivated on glucose and galactose as sole carbon sources. In this way, specific growth rates, specific rates of glucose consumption and ethanol production were determined. Flux distribution, particularly concerning branching into the pentose phosphate pathway was determined using a new 13C-labelling method using MALDI-ToF-mass spectrometry. On glucose, the growth was predominantly fermentative whereas on galactose respiration was more active with correspondingly lower ethanol production. Some deletion strains showed unexpected behavior providing very informative data about the function of the corresponding gene. Deletion of malic enzyme gene, MAE1, did not show any significant phenotype when grown on glucose but a drastically increased branching from glucose 6-phosphate into the pentose phosphate pathway when grown on galactose. This allows the conclusion that MAE1 is important for the supply of NADPH during aerobic growth on galactose.

In this paper we present a method that allows dynamic flux analysis without a priori kinetic knowledge. This method was developed and validated using the pulse-feeding experimental data obtained in our previous study (Matsuda et al., 2005), in which incorporation of exogenously applied l-phenylalanine-d(5) into seven phenylpropanoid metabolites in potato tubers was determined. After identification of the topology of the metabolic network of these biosynthetic pathways, the system was described by dynamic mass balances in combination with power-law kinetics. After the first simulations, some reactions were removed from the network because they were not contributing significantly to network behaviour. As a next step, the exponents of the power-law kinetics were identified and then kept at fixed values during further analysis. The model was tested for statistical reliability using Monte Carlo simulations. Most fluxes could be identified with high accuracy. The two test cases, control and after elicitation, were clearly distinguished, and with elicitation fluxes to N-p-coumaroyloctopamine (pCO) and N-p-coumaroyltyramine (pCT) increased significantly, whereas those for chlorogenic acid (CGA) and p-coumaroylshikimate decreased significantly. According to the model, increases in the first two fluxes were caused by induction/derepression mechanisms. The decreases in the latter two fluxes were caused by decreased concentrations of their substrates, which in turn were caused by increased activity of the pCO- and pCT-producing enzymes. Flux-control analysis showed that, in most cases, flux control was changed after application of elicitor. Thus the results revealed potential targets for improving actions against tissue wounding and pathogen attack.

Growth, substrate consumption, metabolite formation, biomass composition and respiratory parameters of Kluyveromyces marxianus ATCC 26548 were determined during aerobic batch and chemostat cultivations, using mineral medium with glucose as the sole carbon source, at 30 degrees C and pH 5.0. Carbon balances closed within 95-101% in all experiments. A maximum specific growth rate of 0.56 h(-1), a biomass yield on glucose of 0.51 g g(-1), and a maximum specific consumption of oxygen of 11.1 mmol g(-1) h(-1) were obtained during batch cultures. The concentration of excreted metabolites was very low at the culture conditions applied, representing 6% of the consumed carbon at most. Acetate and pyruvate were excreted to a larger extent than ethanol under the batch conditions, and the protein content accounted for 54.6% of the biomass dry weight. Steady states were obtained during chemostats at dilution rates of 0.1, 0.25 and 0.5 h(-1). At the two former dilution rates, cells grew at carbon limitation and the biomass yield on glucose was similar to that obtained under the batch conditions. Metabolite formation was rather low, accounting for a total of 0.005 C-mol C-mol(-1) substrate. At 0.5 h(-1), although the biomass yield on glucose was similar to the value obtained under the above-mentioned conditions, the cultivation was not under carbon limitation. Under this condition, 2-oxoglutarate, acetate, pyruvate and ethanol were the prevalent metabolites excreted. Total metabolite formation only accounted to 0.056 C-mol C-mol(-1) of substrate. A very high protein and a low carbohydrate content (71.9% and 9.6% of biomass dry weight, respectively) were measured in cells under this condition. It is concluded that K. marxianus aligns with the so-called aerobic-respiring or Crabtree-negative yeasts. Furthermore, it has one of the highest growth rates among yeasts, and a high capacity of converting sugar into biomass, even when carbon is not the limiting nutrient. These results provide useful data regarding the future application of K. marxianus in processes aimed at the production of biomass-linked compounds, with high yields and productivities.

Understandig of the function of complex metabolic networks and methods for their rational design, e.g. for the overproduction of metabolites or for the abatement of metabolically related diseases, are still in its infancy compared to their real complexity. Using the increasing knowledge about genome sequences and its bioinformatic exploration, whole genome network analysis and design is increasingly possible, presently primarily using stoichiometric information. In a next higher level kinetic information that cannot be derived from genome analysis is used to describe also the dynamics of network. This allows a much more detailed understanding and application for design, as has been shown for the production of citric acid [1]. We will briefly describe the state-of-the-art and present and likely future developments. Using stoichiometric information, methods like elementary mode analysis permit direct genome scale studies providing, e.g. valuable information about potential maximal yields of overproduction also using mixed substrates. They also provide a certain guidance for the design of potentially useful mutants, e.g. by deletion of genes promoting by-product formation. We have applied this technique to analyze methionine production in C. glutamicum and E. coli [2]. On essentially the same basis genome wide metabolic flux analysis is possible delivering in vivo activities of a network at specific conditions. Combining flux balancing with, e.g. 13C-labelling techniques, a detailed picture can be routinely achieved for many bacterial systems and applied for designing mutants [3]. This requires, however, the combination of well defined cultivation, sampling, (bio)chemical analysis, modeling and parameter estimation techniques. Steadystate modelling of networks, particularly of atom transfer throughout a network, is less developed for eukaryotic systems, where the analysis is complicated by extensive compartmentation and related transport. In mammalian cells widespread reversible transport is further complicating the analysis. Relevant physiological information about transport is, however, rather incomplete. Due to the higher complexity significantly more experimental data is required to determine the larger number of unknown parameters of a network. We have started work on CHO-cultures, today most frequently used for the production of biopharmaceuticals. We studied transport of metabolites using special 13C experiments designed on the basis of network simulations. Several amino acids are exclusively consumed whereas others are consumed and secreted depending on the growth phase. 13C enrichment is anlysed in external metabolites as well as in macromolecular components of the cell, i.e. proteins, lipids, carbohydrates and nucleic acids using GC-MS techniques. For the quantification of metabolic activity of the production of secondary metabolites in potatoe tubers we used a dynamic labeling technique based on the HPLC-MS analysis of intracellular metabolites [4]. A dynamic model using power law kinetics was developed that allowed simulation of experimental data and the estimation of in vivo fluxes. On the basis of this model, flux control coefficients could be determined that provide guidance for the manipulation of genes to allow improved defense of e.g. microbial or viral attack.

A large number of matrix substances have been used for various applications in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The majority of matrices applied in ultraviolet-MALDI MS are crystalline, low molecular weight compounds. A problem encountered with many of these matrices is the formation of hot spots, which lead to inhomogeneous samples, thus leading to increased measurement times and hampering the application of MALDI MS for quantitative purposes. Recently, ionic (liquid) matrices (ILM or IM) have been introduced as a potential alternative to the classical crystalline matrices. ILM are equimolar mixtures of conventional MALDI matrix compounds such as 2,5-dihydroxybenzoic acid (DHB), alpha-cyano-4-hydroxycinnamic acid (CCA) or sinapinic acid (SA) together with organic bases [e.g., pyridine (Py), tributylamine (TBA) or N,N-dimethylethylenediamine (DMED)]. The present article presents a first overview of this new class of matrices. Characteristic properties of ILM, their influence on mass spectrometric parameters such as sensitivity, resolution and adduct formation and their application in the fields of proteome analysis, the measurement of low molecular weight compounds, the use of MALDI MS for quantitative purposes and in MALDI imaging will be presented. Scopes and limitations for the application of ILM are discussed.

A novel method for metabolic flux studies of central metabolism which is based on respirometric 13 C flux analysis, i.e., parallel 13 C tracer studies with online CO 2 labeling measurements is applied to flux quantification of a lysine-producing mutant of Corynebacterium glutamicum . For this purpose, 3 respirometric 13 C labeling experiments with [1- 13 C 1 ], [6- 13 C 1 ] and [1,6- 13 C 2 ] glucose were carried out in parallel. All fluxes comprising the reactions of glycolysis, of TCA cycle, of C3- and C4-metabolite interconversion and of lysine biosynthesis as well as the net reactions in the pentose phosphate pathway could be quantified solely using experimental data obtained from CO 2 labeling and extracellular rate measurements. At key branch points, 68±5% of glucose 6-phosphate were observed to be metabolized into pentose phosphate pathway and 48±1% of pyruvate into TCA cycle via pyruvate dehydrogenase. The results showed a good agreement with the previous studies using 13 C tracer cultivation and GC/MS analysis of proteinogenic amino acids. Also, respiratory quotient calculated from flux estimates using redox balance showed a high accordance with the value determined directly from the measured specific rates of O 2 consumption and CO 2 production. The results strongly support that the respirometric 13 C metabolic flux analysis is suited as an alternative to the conventional methods to study functional and regulatory activities of cells. The developed method is applicable to study growing or non-growing cells, primary and secondary metabolism and immobilized cells. Due to the non-accumulating nature of CO 2 labeling and instantaneous nature of the resulting fluxes, the method can also be used for dynamic profiling of metabolic activities. Therefore, it is complementary to conventional methods for metabolic flux analysis.

A novel method for (13)C flux analysis based on on-line CO(2) labeling measurements is presented. This so-called respirometric (13)C flux analysis requires multiple parallel (13)C labeling experiments using differently labeled tracer substrates. In Part I of the work, a membrane-inlet mass spectrometry-based measurement system with 6 parallel reactors with each 12 ml liquid volume and associated experimental and computational methods for the respirometric (13)C data acquisition and evaluation are described. Signal dynamics after switching between membrane probes follow exactly first-order allowing extrapolation to steady state. Each measurement cycle involving 3 reactors takes about 2 min. After development of a dynamic calibration method, the suitability and reliability of the analysis was examined with a lysine-producing mutant of Corynebacterium glutamicum using [1-(13)C(1)], [6-(13)C(1)], [1,6-(13)C(2)] glucose. Specific rates of oxygen uptake and CO(2) production were estimated with an error less than +/-0.3 mmol g(-1) h(-1) and had +/-3% to +/-10% deviations between parallel reactors which is primarily caused by inaccuracies in initial biomass concentration. The respiratory quotient could be determined with an uncertainty less than +/-0.02 and varied only +/-3% between reactors. Fractional labeling of CO(2) was estimated with much higher precision of about +/-0.001 to +/-0.005. The detailed statistical analysis suggested that these data should be of sufficient quality to allow physiological interpretation and metabolic flux estimation. The obtained data were applied for the respirometric (13)C metabolic flux analysis in Part II.

Matrix-assisted laser desorption/ionization mass spectrometry has become an indispensable tool for identification of proteins by peptide mass-fingerprint analysis. Selection of the matrix, addition of matrix additives, and sample-preparation techniques are known to affect the quality of the spectra and hence protein identification. We investigated the effect of pyridine as matrix additive for the commonly used crystalline matrix alpha-cyano-4-hydroxycinnamic acid (CCA), forming a pyridinium based ionic liquid matrix, on the mass spectra of synthetic peptides and tryptic protein digests. Beside the equimolar mixture of CCA and pyridine, the effect of addition of substoichiometric amounts of the base to the acid was tested. Optimum results in terms of signal-to-noise ratios, reduction of chemical noise, and reduced formation of alkali adducts and matrix clusters were observed for the matrix CCA-pyridine in the molar ratio 2:1. The optimized ionic liquid matrix was used for identification of tryptic digests of six model proteins and for identification of a protein extracted from a two-dimensional gel with the proteome of the bacterium Corynebacterium glutamicum, and shown to facilitate protein identification, yielding higher scores and increased sequence coverage compared with pure CCA. Thus CCA-Py 2:1 is a potential alternative for identification and characterization of proteins by peptide mass-fingerprint analysis.

Early process development is crucial for the economic and environmental performance of a final production process. A new process for the production of pyruvate is presented as a case study to show how process modeling and an analysis of the results regarding economic and environmental aspects improves the understanding of the process, its cost structure, and its environmental impact. It also enables the quantification of process improvements and the comparison of alternative designs. The model of the pyruvate production shows how strain and fermentation improvements propagate through the process and affect its economic and environmental performance. The comparison of two alternative purification concepts, liquid extraction and electrodialysis, show that electrodialysis is a promising approach for the purification of pyruvic acid.

Ionic liquids are interesting solvents for a number of applications in chemistry and biotechnology. We characterized five different ionic liquids by laser desorption/ionization (LDI) and by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and studied the analysis of amino acids, peptides and proteins dissolved in these solvents. Signals of both anions and cations of the ionic liquids could be observed both in LDI- and in MALDI-MS. In the latter case, adduct formation between anions and cations of the analytes was observed. Amino acids, peptides and proteins could be analyzed in ionic liquids after addition of matrix substances. Sodium and potassium adducts were not observed in any analysis involving ionic liquids. Low molecular mass compounds and peptides could be analyzed best in the presence of water-immiscible ionic liquids, whereas proteins gave the best results in water-miscible ionic liquids. Optimal analysis conditions such as molar matrix-to-analyte and ionic liquid-to-matrix ratios were determined. Homogeneity of samples in the presence of ionic liquids was reduced compared with classical MALDI preparations. Relative quantitation of amino acids was possible using isotope-labeled internal standards. MALDI-MS thus can be used for the analysis of chemical reactions and the screening of enzyme-catalyzed reactions in ionic liquids and for the analysis of the biocatalysts dissolved in these solvents. Theoretical aspects of ion formation in the presence of ionic liquids both in LDI and MALDI analysis are discussed.

A novel method to accomplish efficient numerical simulation of metabolic networks for flux analysis was developed. The only inputs required are the set of stoichiometric balances and the atom mapping matrices of all components of the reaction network. The latter are used to automatically calculate isotopomer mapping matrices. Using the symbolic toolbox of MATLAB the analytical solution of the stoichiometric balance equation system, isotopomer balances and the analytical Jacobian matrix of the total set of stoichiometric and isotopomer balances are created automatically. The number of variables in the isotopomer distribution equation system is significantly reduced applying modified isotopomer mapping matrices. These allow lumping of several consecutive isotopomer reactions into a single one. The solution of the complete system of equations is improved by implementing an iterative logical loop algorithm and using the analytical Jacobian matrix. This new method provided quick and robust convergence to the root of such equation systems in all cases tested. The method was applied to a network of lysine producing Corynebacterium glutamicum. The resulting equation system with the dimension of 546 x 546 was directly derived from 12 isotopomer balance equations. The results obtained yielded identical labeling patterns for metabolites as compared to the relaxation method.