Lactic acid production from lignocellulose-derived sugars using lactic acid bacteria: Overview and limits

Lactic acid is an industrially important product with a large and rapidly expanding market due to its attractive and valuable multi-function properties. The economics of lactic acid production by fermentation is dependent on many factors, of which the cost of the raw materials is very significant. It is very expensive when sugars, e.g., glucose, sucrose, starch, etc., are used as the feedstock for lactic acid production. Therefore, lignocellulosic biomass is a promising feedstock for lactic acid production considering its great availability, sustainability, and low cost compared to refined sugars. Despite these advantages, the commercial use of lignocellulose for lactic acid production is still problematic. This review describes the “conventional” processes for producing lactic acid from lignocellulosic materials with lactic acid bacteria. These processes include: pretreatment of the biomass, enzyme hydrolysis to obtain fermentable sugars, fermentation technologies, and separation and purification of lactic acid. In addition, the difficulties associated with using this biomass for lactic acid production are especially introduced and several key properties that should be targeted for low-cost and advanced fermentation processes are pointed out. We also discuss the metabolism of lignocellulose-derived sugars by lactic acid bacteria.     

The role of arginine 143 in the electrostatics and mechanism of Cu,Zn superoxide dismutase: Computational and experimental evaluation by mutational analysis

Cu, Zn superoxide dismutase protects cells from oxidative damage by removing superoxide radicals in one of the fastest enzyme reactions known. The redox reaction at the active-site Cu ion is rate-limited by diffusion and enhanced by electrostatic guidance. To quantitatively define the electrostatic and mechanistic contributions of sequence-invariant Arg-143 in human Cu, Zn superoxide dismutase, single-site mutants at this position were investigated experimentally and computationally. Rate constants for several Arg-143 mutants were determined at different pH and ionic strength conditions using pulse radiolytic methods and compared to results from Brownian dynamics simulations. At physiological pH, substitution of Arg-143 by Lys caused a 2-fold drop in rate, neutral substitutions (Ile, Ala) reduced the rate about 10-fold, while charge-reversing substitutions (Asp, Glu) caused a 100-fold decrease. Position 143 mutants showed pH dependencies not seen in other mutants. At low pH, the acidic residue mutations exhibited pro-tonation/deprotonation effects. At high pH, all enzymes showed typical decreases in rate except the Lys mutant in which the rate dropped off at an unusually low pH. Increasing ionic strength at acidic pH decreased the rates of the wild-type enzyme and Lys mutant, while the rate of the Glu mutant was unaffected. Increasing ionic strength at higher pH (>10) increased the rates of the Lys and Glu mutants while the rate of the wild-type enzyme was unaffected. Reaction simulations with Brownian dynamics incorporating electrostatic effects tested computational predictability of ionic strength dependencies of the wild-type enzyme and the Lys, Ile, and Glu mutants. The calculated and experimental ionic strength profiles gave similar slopes in all but the Glu mutant, indicating that the electrostatic attraction of the substrate is accurately modeled. Differences between the calculated and experimental rates for the Glu and Lys mutants reflect the mechanistic contribution of Arg-143. Results from this joint analysis establish that, aside from the Cu ligands, Arg-143 is the single most important residue in Cu, Zn superoxide dismutase both electrostatically and mechanistically, and provide an explanation for the evolutionary selection of arginine at position 143. © 1994 Wiley-Liss, Inc.     

Retinoic acid and hydrocortisone strengthen the barrier function of human RPMI 2650 cells, a model for nasal epithelial permeability

The nasal pathway represents an alternative route for non-invasive systemic administration of drugs. The main advantages of nasal drug delivery are the rapid onset of action, the avoidance of the first-pass metabolism in the liver and the easy applicability. In vitro cell culture systems offer an opportunity to model biological barriers. Our aim was to develop and characterize an in vitro model based on confluent layers of the human RPMI 2650 cell line. Retinoic acid, hydrocortisone and cyclic adenosine monophosphate, which influence cell attachment, growth and differentiation have been investigated on the barrier formation and function of the nasal epithelial cell layers. Real-time cell microelectronic sensing, a novel label-free technique was used for dynamic monitoring of cell growth and barrier properties of RPMI 2650 cells. Treatments enhanced the formation of adherens and tight intercellular junctions visualized by electron microscopy, the presence and localization of junctional proteins ZO-1 and β-catenin demonstrated by fluorescent immunohistochemistry, and the barrier function of nasal epithelial cell layers. The transepithelial resistance of the RPMI 2650 cell model reached 50 to 200 Ω × cm², the permeability coefficient for 4.4 kDa FITC-dextran was 9.3 to 17 × 10⁻⁶ cm/s, in agreement with values measured on nasal mucosa from in vivo and ex vivo experiments. Based on these results human RPMI 2650 cells seem to be a suitable nasal epithelial model to test different pharmaceutical excipients and various novel formulations, such as nanoparticles for toxicity and permeability.

Electronic supplementary material

The online version of this article (doi:10.1007/s10616-012-9493-7) contains supplementary material, which is available to authorized users.     

Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding

We have performed molecular dynamics (MD) simulations to study the dimerization, folding, and binding to a protein of peptides containing an unnatural amino acid. NMR studies have shown that the substitution of one residue in a tripeptide beta-strand by the unnatural amino acid Hao (5-HO2CCONH-2-MeO-C6H3-CO-NHNH2) modifies the conformational flexibility of the beta-strand and the hydrogen-bonding properties of its two edges: The number of hydrogen-bond donors and acceptors increases at one edge, whereas at the other, they are sterically hindered. In simulations in chloroform, the Hao-containing peptide 9 (i-PrCO-Phe-Hao-Val-NHBu) forms a beta-sheet-like hydrogen-bonded dimer, in good agreement with the available experimental data. Addition of methanol to the solution induces instability of this beta-sheet, as confirmed by the experiments. MD simulations also reproduce the folding of the synthetic peptide 1a (i-PrCO-Hao-Ut-Phe-Ile-Leu-NHMe) into a beta-hairpin-like structure in chloroform. Finally, the Hao-containing peptide, Ac-Ala-Hao-Ala-NHMe, is shown to form a stable complex with the Ras analogue, Rap1 A, in water at room temperature. Together with the available experimental data, these simulation studies indicate that Hao-containing peptides may serve as inhibitors of beta-sheet interactions between proteins.     

Two heterometal-organic coordination polymers with chelidamic acid: Syntheses, structures and optical properties

Two heterometal-organic coordination polymers with chelidamic acid ligands, [AgNd(C₇H₃NO₅)₂·3H₂O]_n (1) and 0.75H₃O·[K_0.25Nd(C₇H₃NO₅)₂·3H₂O]·1.75H₂O (2), have been synthesized and characterized by X-ray single-crystal diffraction. The crystal structure of 1 features that chelating units composed of one Nd(III) ion and two tridentate chelating chelidamic acid ligands are connected by the Ag(I) ions to form a one-dimensional chain, further linked by hydrogen bonds into a 3D network. As for 2, discrete independent molecules, made up of Nd(III) and K(I) ions and chelidamic acid ligands, are linked through the hydrogen bonds to form a 1D chain, which are further inter-linked through the complex hydrogen bonds to form a 3D network. The optical properties of 1 and 2 were investigated in terms of fluorescent spectra, which both exhibit good luminescence.     

Understanding the binding interaction between phenyl boronic acid P1 and sugars: determination of association and dissociation constants using S–V plots,steady‐state spectroscopic methods and molecular docking

Continuous monitoring of glucose and sugar sensing plays a vital role in diabetes control. The drawbacks of the present enzyme‐based sugar sensors have encouraged the investigation into alternate approaches to design new sensors. The popularity of fluorescence sensors is due to their ability to bind reversibly to compounds containing diol. In this study we investigated the binding ability of phenyl boronic acid P1 for monosaccharides and disaccharides (sugars) in aqueous medium at physiological pH 7.4 using steady‐state fluorescence and absorbance. P1 fluorescence was quenched due to formation of esters with sugars. Absorbance and fluorescence measurements led to results that indicated that the sugars studied could be ordered in terms of their affinity to P1, as stated: sucrose > lactose > galactose > xylose > ribose > arabinose. In each case, the slope of modified Stern–Volmer plots was nearly 1, indicating the presence of only a single binding site in boronic acids for sugars. Docking studies were carried out using Schrodinger Maestro v.11.2 software. The binding affinity of phenyl boronic acid P1 with periplasmic protein (PDB ID 2IPM and 2IPL) was estimated using GlideScore.     

A comprehensive model for the diffusion and hybridization processes of nucleic acid probes in fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) has been extensively used in the past decades for the detection and localization of microorganisms. However, a mechanistic approach of the whole FISH process is still missing, and the main limiting steps for the hybridization to occur remain unclear. In here, FISH is approached as a particular case of a diffusion-reaction kinetics, where molecular probes (MPs) move from the hybridization solution to the target RNA site within the cells. Based on literature models, the characteristic times taken by different MPs to diffuse across multiple cellular barriers, as well as the reaction time associated with the formation of the duplex molecular probe-RNA, were estimated. Structural and size differences at the membrane level of bacterial and animal cells were considered. For bacterial cells, the limiting step for diffusion is likely to be the peptidoglycan layer (characteristic time of 7.94 × 10² – 4.39 × 10³ s), whereas for animal cells, the limiting step should be the diffusion of the probe through the bulk (1.8–5.0 s) followed by the diffusion through the lipid membrane (1 s). The information provided here may serve as a basis for a more rational development of FISH protocols in the future.     

Molecular imprinting of nitrophenol and hydroxybenzoic acid isomers: effect of molecular structure and acidity on imprinting

Three nitrophenol isomer-imprinted polymers were prepared under the same conditions using 4-vinylpyridine as a functional monomer. Different recognition capacities for template molecules were observed for the three polymers. Another imprinting system with stronger acidity than nitrophenol isomers, 2-hydroxybenzoic acid (salicylic acid) and 4-hydroxybenzoic acid, was imprinted using 4-vinylpyridine or acrylamide as functional monomer respectively. Both 4-hydroxybenzoic acid-imprinted polymers using the two monomers showed recognition ability for the template molecule. However, when acrylamide was chosen as functional monomer, the salicylic acid-imprinted polymer showed very weak recognition for the template molecule, whereas strong recognition ability of the resultant polymer for salicylic acid was observed with 4-vinylpyridine as functional monomer. It seems that the structure and acidity of template molecules is responsible for the difference in recognition, by influencing the formation and strength of interaction between template molecule and functional monomer during the imprinting process. An understanding of the mechanism of molecular imprinting and molecular recognition of MIPs will help to predict the selectivity of MIPs on the basis of template molecule properties.     

Five-, seven-, and eight-coordinate Cd(II) coordination polymers built by anthranilic acid derivatives: Synthesis, structures and photoluminescence

Two novel Cd(II) coordination polymers, [(CH₃)₂NH₂]₂[Cd(cma)₂](H₂O) (1) and [Cd₃(bcma)₂(H₂O)](H₂O) (2) (H₂cma = N-(carboxymethyl)-anthranilic acid, H₃bcma = N,N′-bis-(carboxymethyl)-anthranilic acid), have been synthesized under hydrothermal conditions and characterized by X-ray single crystal analysis, IR spectra and TGA. Compound 1 possesses 1D double-stranded chain, which further packs into square channels. Compound 2 consists of a novel 3D framework, which not only possesses unique meniscus-like channels but also contains infinite helical chains. Compound 2 is the first example of Cd(II)-aminopolycarboxylate coordination polymers containing three crystallographically independent Cd(II) centres, in which Cd(1), Cd(2), and Cd(3) present distorted pentagonal bipyramidal, tetragonal antiprismatic, and trigonal bipyramidal coordination geometry, respectively. Both compounds display intense room temperature photoluminescence in the solid state.     

Chitosan gels for the vaginal delivery of lactic acid: Relevance of formulation parameters to mucoadhesion and release mechanisms

The aim of this work was to assess the effect of formulation parameters of a mucoadhesive vaginal gel based on chitosan and lactic acid, and to highlight its release mechanisms. Two molecular weight chitosans were used to prepare gels with 2 lactic acid concentrations. Both chitosan molecular weight and lactic acid concentration had a significant and mutually dependent influence on mucoadhesion, measured on pig vaginal mucosa. Similarly, the lactate release profiles were found to be dependent on lactic acid content and polymer molecular weight. One gel formulation based on the stoichiometric lactate to chitosan ratio was subjected to release test in media with 2 different counterions and increasing ionic strength. This test demonstrated that the lactate release is mainly due to ionic displacement.     

Moleclar imprinting by noncovalent interactions: Tailor-made chiral stationary phases of high selectivity and sample load capacity

A moleclar imprinting technique based on electrostatic and hydrogen bonding interactions was used to prepare polymers of high selectvity for the original print molecule (D or L form of an amino acid derivative). In the chromatographic mode ig enantioselectivity was observed, in particular for amino acid amides and basic amino acid esters. As indicated y he broad peaks obtained, the mass transfer, including the kinetics of the binding and dissociation process, was slow and appeared to be slower in systems where a higher number of interactions between the solute and the stationary phase could be expected. In such systems enhanced selectivity was observed. For polymers prepared at a lower temperature the mass transfer was more rapid and a higher selectivity was observed, wich allowed the separations to be performed at room temperature. A more rapid mass transfer and a higher selectivity could also be achieved by increasing the column temperature. Furthermore the polymers showed a high sample load capacity and a high stability, and the can easily be prepared.     

杀虫剂胁迫下褐飞虱迁飞虫和本地虫后代体内粗脂肪、可溶性糖及氨基酸含量的比较

为了解迁飞种群与居留种群后代发生再猖獗的生理生化差异,探讨再猖獗的机制,比较研究了在两个水稻品种（TN1和协优963）上施用杀虫剂后褐飞虱Nilaparvata lugens (Stål)迁飞虫和本地虫后代3龄、5龄若虫和成虫体内可溶性糖和粗脂肪含量以及迁飞成虫与其后代成虫体内游离氨基酸含量的变化。结果表明： 施药以及未施药处理(对照)TN1水稻品种上的迁飞后代3龄、5龄若虫和成虫体内的可溶性糖含量均显著高于本地虫。与可溶性糖含量相比,施药以及对照TN1水稻品种上的迁飞后代3龄、5龄若虫和成虫体内的粗脂肪含量均显著低于本地虫。协优963上3龄、5龄若虫体内可溶性糖含量的变化趋势与TN1上相同。对照水稻上迁飞成虫的粗脂肪含量显著高于本地种群,迁飞与本地3龄、5龄若虫间粗脂肪含量没有显著差异。杀虫剂处理后的水稻上迁飞后代5龄若虫和成虫体内粗脂肪含量显著高于本地虫。方差分析结果也显示,可溶性糖和粗脂肪含量的变化在虫源和杀虫剂,虫源和杀虫剂浓度以及杀虫剂类型和浓度方面有显著交互作用。两种水稻品种上,迁飞当代成虫体内的游离氨基酸含量显著低于其后代成虫。在经3种杀虫剂处理后,TN1上施用三唑磷后成虫体内的氨基酸含量显著高于施用溴氰菊酯和吡虫啉的处理,而协优963上施用溴氰菊酯和吡虫啉显著高于施用三唑磷的处理。本研究结果对深入阐明农药诱导褐飞虱再猖獗的机制具有参考价值。     

Kinetics of Organic Transformations under Mild Aqueous Conditions: Implications for the Origin of Life and its Metabolism

The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates.     

16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine

Lactic acid bacteria (LAB) are found in a great variety of habitats, including grape must and wines. There is a close relationship between the species of LAB which develop during fermentation and the eventual quality of the wine. For these reasons analytical techniques allowing fast and reliable identification of wine LAB are needed. In this work a simple and accurate protocol for identifying species of LAB isolated from grape must and wine is presented. This protocol is based on the amplification, directly from colony, of 16S rDNA and later digestion with one of the following restriction enzymes BfaI, MseI and AluI. A sequential use of the three enzymes is proposed to simplify LAB wine identification, first MseI, then BfaI and finally, if necessary, AluI digestion. The technique was able to discriminate 32 of the 36 LAB reference species tested and allowed the identification of 342 isolates from musts and wines. The isolates belonged to the species: Lactobacillus brevis, L. collinoides, L. coryniformis, L. bilgardii, L. mali, L. paracasei, Leuconostoc mesenteroides, Oenococcus oeni, Pediococcus parvulus and P. pentosaceus.     

Preparation, circular dichroism induced helical conformation and optical property of chitosan acid salt complexes for biomedical applications

The efficient procedure for preparation of chitosan acid complexes containing aspartic acid, benzilic acid and terephthalic acid moieties in isopropyl alcohol under mild condition has been demonstrated. The ionic complexation between chitosan and the acid is confirmed by FTIR and ¹H NMR spectroscopy. The circular dichroism (CD) spectra of chitosan/aspartic acid complex showed negative (at λ = 312) band, chitosan/benzilic acid and chitosan/terephthalic complexes showed positive (at λ = 286 and 315 nm) band in DMSO, indicating that the polymers adopted helical (left-handed and last two right-handed) secondary structure. The inversion of the CD pattern in chitosan acid salt complexes suggests that there is a change in the chiral structure of the polymer system. Some physical properties and surface morphology were analyzed by X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetry (TG) and scanning electron microscopy (SEM). Optical properties of chitosan derivatives are evaluated by photoluminescence (PL) spectroscopy which showed red shift. The introduction of acid moieties into chitosan increases the solubility in most of the organic solvents, which opens new perspectives for the employment of chitosan-based biohybrid in biomedical applications.     

Comparative acid stress response of Listeria monocytogenes, Escherichia coli O157:H7 and Salmonella Typhimurium after habituation at different pH conditions

AIMS: The aim of the study was to evaluate the effect of habituation at different pH conditions on the acid resistance of Listeria monocytogenes, Escherichia coli O157:H7 and Salmonella enterica serotype Typhimurium, and to identify potential differences between the adaptive responses of the three pathogens. METHODS: Stationary phase cells of L. monocytogenes, E. coli O157:H7 and S. Typhimurium, grown in glucose-free media, were exposed to pH 3.5 broth directly or after habituation for 90 min at various pH conditions from 4.0 to 6.0. Survivors at pH 3.5 were determined by plating on tryptic soy agar and incubating at 30 degrees C for 48 h. The kinetics (death rate) of the pathogens at pH 3.5 was calculated by fitting the data to an exponential model. RESULTS: Habituation to acidic environments provided protection of the pathogens against lethal acid conditions. This acid protection, however, was found to be pH dependent. For example, for E. coli O157:H7 an increased acid resistance was observed after habituation at a pH range from 4.0 to 5.5, while the maximum acid tolerance was induced at pH 5.0. Furthermore, the effect of low pH habituation was different among pathogens. For L. monocytogenes, E. coli O157:H7 and S. Typhimurium, the pH range within which habituation resulted to increased acid resistance was 5.0-6.0, 4.0-5.5 and 4.0-5.0, respectively, while the maximum acid tolerance was induced after habituation at pH 5.5, 5.0 and 4.5, respectively. SIGNIFICANCE: Acid stress conditions are common within current food processing technologies. The information on adaptive responses of L. monocytogenes, E. coli O157:H7 and S. Typhimurium after habituation to different pH environments provided in the present study, could lead to a more realistic evaluation of food safety concerns and to a better selection of processes in order to avoid adaptation phenomena and to minimize the potential for food safety risks.     

Production of spent mushroom substrate hydrolysates useful for cultivation of Lactococcus lactis by dilute sulfuric acid, cellulase and xylanase treatment

Spent mushroom substrate (SMS) was treated with dilute sulfuric acid followed by cellulase and xylanase treatment to produce hydrolysates that could be used as the basis for media for the production of value added products. A L9 (3⁴) orthogonal experiment was performed to optimize the acid treatment process. Pretreatment with 6% (w/w) dilute sulfuric acid at 120 °C for 120 min provided the highest reducing sugar yield of 267.57 g/kg SMS. No furfural was detected in the hydrolysates. Exposure to 20 PFU of cellulase and 200 XU of xylanase per gram of pretreated SMS at 40 °C resulted in the release of 79.85 g/kg or reducing sugars per kg acid pretreated SMS. The dilute sulfuric acid could be recycled to process fresh SMS four times. SMS hydrolysates neutralized with ammonium hydroxide, sodium hydroxide, or calcium hydroxide could be used as the carbon source for cultivation of Lactococcus lactis subsp. lactis W28 and a cell density of 2.9 × 10¹¹ CFU/mL could be obtained. The results provide a foundation for the development of value-added products based on SMS.     

干旱半干旱地区生物结皮层藓类植物氨基酸和营养物质组成特征及适应性分析

通过对生长在干旱-半干旱地区的藓类体内的氨基酸组成及含量变化、营养元素含量变化和可溶性糖含量变化及藓类结皮土壤相应营养元素含量变化的分析,以揭示藓类的营养组成特征及对环境的适应性机制。研究样地选择在内蒙古鄂尔多斯高原的典型草原区和宁夏腾格里沙漠南缘的草原化荒漠区。通过实验,从藓类植物体内检测出17种氨基酸,表明其体内的氨基酸组成大部分与高等植物相同,其中天门冬氨酸、谷氨酸、丙氨酸、亮氨酸和精氨酸的含量最高,约占总氨基酸的50%。脯氨酸含量在所有氨基酸中处于较低水平,平均只占氨基酸总量的3.12%。草原化荒漠区与典型草原区分布真藓平均总氨基酸含量均大于土生对齿藓,两地区间真藓有10种氨基酸(包括脯氨酸)含量有显著性均数差异(p<0.05),而土生对齿藓只有脯氨酸有显著性差异(p<0.05)。赖氨酸、精氨酸含量在两个地区各种藓类体内有相对稳定的含量,没有显著差异,而脯氨酸的含量在同一地区没有显著的差异,但在不同地区却有显著性差异。藓类体内营养元素显著高于结皮层土壤,表明苔藓植物有很强的元素富集能力,其中N含量最高,P含量最低。不同种类植物体内营养元素Ca、Mg、K的含量存在差异,表明藓类植物对金属营养元素有很强的选择吸收能力。元素相对利用能力(植物/土壤),K最大,P最小,Ca、Mg因种类不同存在差异。N/P比率在草原化荒漠区分别为真藓10.25,刺叶赤藓13.59,土生对齿藓15.78;在典型草原区分别为真藓11.91,土生对齿藓10.55,盐土藓11.37,可知N、P在干旱区不是藓类植物生长的限制因子。元素之间的相关分析表明N和P,Ca和Mg明显相关(p<0.05),而K和Ca、Mg之间则显著负相关(p<0.01),表明K和Ca、Mg之间存在制约关系。可溶性糖和脯氨酸含量分析表明,随降雨量增加二者含量明显呈现递减趋势,说明脯氨酸、可溶性糖的含量与苔藓植物的抗旱性有一定的关系。     

Utility of mass spectrometry for proteome analysis: part II. Ion-activation methods,statistics, bioinformatics and annotation

This is the second article in a series, intended as a tutorial to provide the interested reader with an overview of the concepts not covered in part I, such as: the principles of ion-activation methods, the ability of mass-spectrometric methods to interface with various proteomic strategies, analysis techniques, bioinformatics and data interpretation and annotation. Although these are different topics, it is important that a reader has a basic and collective understanding of all of them for an overall appreciation of how to carry out and analyze a proteomic experiment. Different ion-activation methods for MS/MS, such as collision-induced dissociation (including postsource decay) and surface-induced dissociation, electron capture and electron-transfer dissociation, infrared multiphoton and blackbody infrared radiative dissociation have been discussed since they are used in proteomic research. The high dimensionality of data generated from proteomic studies requires an understanding of the underlying analytical procedures used to obtain these data, as well as the development of improved bioinformatics tools and data-mining approaches for efficient and accurate statistical analyses of biological samples from healthy and diseased individuals, in addition to determining the utility of the interpreted data. Currently available strategies for the analysis of the proteome by mass spectrometry, such as those employed for the analysis of substantially purified proteins and complex peptide mixtures, as well as hypothesis-driven strategies, have been elaborated upon. Processing steps prior to the analysis of mass spectrometry data, statistics and the several informatics steps currently used for the analysis of shotgun proteomic experiments, as well as proteomics ontology, are also discussed.