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Showing papers in "Electrophoresis in 1999"


Journal ArticleDOI
TL;DR: A new computer program, Mascot, is presented, which integrates all three types of search for protein identification by searching a sequence database using mass spectrometry data, and the scoring algorithm is probability based.
Abstract: Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be compared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.

8,195 citations


Journal ArticleDOI
TL;DR: By using the destaining method, the sensitivity and quality of mass spectra is increased for matrix‐assisted laser desorption ionization‐time of flight (MALDI‐TOF) mass spectrometric analysis, permitting more proteins to be identified by peptide mass database analysis.
Abstract: Mass spectrometry is a powerful technique for the identification of proteins at nanogram quantities. However, some degree of sample preparation prior to mass spectrometry is required, and silver-stained protein gel samples are most problematic. Here we report our strategy to obtain peptide mass profiles from silver-stained protein gel samples from one- or two-dimensional gels by destaining prior to enzymatic digestion. This study demonstrates that by using the destaining method, the sensitivity and quality of mass spectra is increased for matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometric analysis, permitting more proteins to be identified by peptide mass database analysis.

909 citations


Journal ArticleDOI
TL;DR: The structure of the catalytic subunit with the fixed positioning of the activation segment in the active conformation through its own aminoterminal region suggests a regulation at the transcriptional level making a regulation by second messengers unlikely.
Abstract: Protein kinase CK2 is a pleiotropic, ubiquitous and constitutively active protein kinase that can use both ATP and GTP as phosphoryl donors with specificity for serine/threonine residues in the vicinity of acidic amino acids. Recent results show that the enzyme is involved in transcription, signaling, proliferation and in various steps of development. The tetrameric holoenzyme (alpha2beta2) consists of two catalytic alpha-subunits and two regulatory beta-subunits. The structure of the catalytic subunit with the fixed positioning of the activation segment in the active conformation through its own aminoterminal region suggests a regulation at the transcriptional level making a regulation by second messengers unlikely. The high conservation of the catalytic subunit from yeast to man and its role in the tetrameric complex supports this notion. The regulatory beta-subunit has been far less conserved throughout evolution. Furthermore the existence of different CK2beta-related proteins together with the observation of deregulated CK2beta levels in tumor cells and the reported association of CK2beta protein with key proteins in signal transduction, e.g. A-Raf, Mos, pg90rsk etc. are suggestive for an additional physiological role of CK2beta protein beside being the regulatory compound in the tetrameric holoenzyme.

389 citations


Journal ArticleDOI
TL;DR: Five approaches presented here resulted in the detection of disease‐associated proteins, including Calgranulin B was upregulated in colorectal cancer, and hepatoma‐derived aldose reductase‐like protein was reexpressed in a rat model during hepatocarcinogenesis.
Abstract: In recent years, genomics has increased the understanding of many diseases Proteomics is a rapidly growing research area that encompasses both genetic and environmental factors The protein composition represents the functional status of a biological compartment The five approaches presented here resulted in the detection of disease-associated proteins Calgranulin B was upregulated in colorectal cancer, and hepatoma-derived aldose reductase-like protein was reexpressed in a rat model during hepatocarcinogenesis In these two investigations, attention was focused on one protein, obviously differing in amount, directly after two-dimensional electrophoresis (2-DE) Additional methods, such as enzyme activity measurements and immunohistochemistry, confirmed the disease association of the two candidates resulting from 2-DE subtractive analysis The following three investigations take advantage of the holistic potential of the 2-DE approach The comparison of 2-DE patterns from dilated cardiomyopathy patients with those of controls revealed 25 statistically significant intensity differences, from which 12 were identified by amino acid analysis, Edman degradation or matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) A human myocardial 2-DE database was constructed, containing 3300 protein spots and 150 identified protein species The number of identified proteins was limited by the capacity of our group, rather than by the principle of feasibility Another field where proteomics proves to be a valuable tool in identifying proteins of importance for diagnosis is proteome analysis of pathogenic microorganisms such as Borrelia burgdorferi (Lyme disease) and Toxoplasma gondii (toxoplasmosis) Sera from patients with early or late symptoms of Lyme borreliosis contained antibodies of various classes against about 80 antigens each, containing the already described antigens OspA, B and C, flagellin, p83/100, and p39 Similarly, antibody reactivity to seven different marker antigens of T gondii allowed differentiation between acute and latent toxoplasmosis, an important diagnostic tool in both pregnancy and immunosuppressed patients

293 citations


Journal ArticleDOI
TL;DR: Proteomics‐based studies offer a powerful complementary approach to DNA/RNA‐based investigations and are now being applied to investigate aspects of many diseases including cancer, but the heterogeneous nature of tissue samples often makes interpretation difficult.
Abstract: Proteomics-based studies offer a powerful complementary approach to DNA/RNA-based investigations and are now being applied to investigate aspects of many diseases including cancer. However, the heterogeneous nature of tissue samples often makes interpretation difficult. We have undertaken a study into the potential use of a novel laser capture microdissection (LCM) system to isolate cells of interest for subsequent proteomic analysis. Retrieval of selected cells is achieved by activation of a transfer film placed in contact with a tissue section, by a laser beam (30 or 60 microm diameter) which is focused on a selected area of tissue using an inverted microscope. The precise area of film targeted by the laser bonds to the tissue beneath it and these cells are then lifted free of surrounding tissue. Although the technique has been shown to be readily compatible with subsequent analysis of nucleic acids, little information is yet available regarding the application of protein-based analyses to the captured tissue. We report here preliminary data regarding the potential use of the LCM system in combination with two-dimensional electrophoresis to examine protein profiles of selected tissue areas. Electrophoretic profiles of proteins from normal and malignant renal tissue samples showed little change following LCM, nine selected proteins showed identical mass spectrometric sequencing profiles, and two selected proteins retained antigenicity. Dissection of epithelial tissue from a sample of normal human cervix resulted in enrichment of some proteins compared with analysis of the whole tissue. LCM will be a valuable adjunct to proteomic studies although further detailed validation is necessary.

292 citations


Journal ArticleDOI
TL;DR: To determine the effect of environmental factors on the preservation of DNA, archeological teeth of approximately similar age but greatly differing site milieu were examined for DNA content.
Abstract: To determine the effect of environmental factors on the preservation of DNA, archeological teeth of approximately similar age but greatly differing site milieu were examined for DNA content. The complex relational system of locational milieu of the samples was reduced to its essential and, at the same time, easily measurable factors. These are temperature, humidity, pH value, the geochemical properties of the soil, the amount of postmortal organic substances and the general degree of microbial infestation in the respective soil. The relative DNA content in the samples was established by determining the rate of successful polymerase chain reaction (PCR) amplifications. Differences in quantity and quality of the results are attributed to the respective prevailing environmental factor or to the respective storage conditions. Dryness, low temperature and absence of microorganisms favors the preservation of DNA. The bioapatite of bones and teeth, like the DNA, are preserved under neutral or slightly alkaline conditions. Brief storage at room temperature does not affect the amount of amplifiable DNA but does affect the reproducibility of the results. Long storage outside a lab freezer reduces the amount and the reproducibility of DNA amplifications in ancient specimens.

265 citations


Journal ArticleDOI
TL;DR: The theory and practice of SSCP and HA are reviewed, including the factors contributing to the sensitivity of mutation detection, including choice of gel matrix, electrophoretic conditions, presence of neutral additives, fragment size, and G+C content.
Abstract: Single-strand conformation polymorphism (SSCP) and heteroduplex analysis (HA) are popular electrophoretic methods for the identification of sequences. The principle reasons for the popularity of these two methods are their technical simplicity and their relatively high sensitivity for the detection of mutations. Here we review the theory and practice of SSCP and HA, including the factors contributing to the sensitivity of mutation detection. For SSCP analysis, these factors include: choice of gel matrix, electrophoretic conditions, presence of neutral additives, fragment size, and G+C content For HA, the principle factors influencing sensitivity are the gel matrix and the identity of the base mismatch.

255 citations


Journal ArticleDOI
TL;DR: Two‐dimensional (2‐D) electrophoresis remains the highest resolution technique for protein separation and is the method of choice when complex samples need to be arrayed for characterisation, as in proteomics.
Abstract: Two-dimensional (2-D) electrophoresis remains the highest resolution technique for protein separation and is the method of choice when complex samples need to be arrayed for characterisation, as in proteomics. However, in current proteome projects the total number of proteins identified from 2-D gels is often only a small percentage of the predicted proteome. In addition, there is an almost complete lack of hydrophobic proteins on 2-D gels, especially those using immobilised pH gradients. Recently there have been a number of publications reporting reagents which improve protein solubilisation prior to isoelectric focusing. The improved solubilization possible with these reagents has increased the total number of proteins able to be visualised on 2-D gels and also allowed the separation of hydrophobic proteins, such as integral membrane proteins.

251 citations


Journal ArticleDOI
TL;DR: It is shown here that simply selecting from the sequence database the protein that has the most matching fragment masses often leads to false‐positive results, which is a significant bottleneck for the proteomics work flow.
Abstract: Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of protein samples from two-dimensional (2-D) gels in conjunction with protein sequence database searches is frequently used to identify proteins. Moreover, the automatic analysis of complete 2-D gels with hundreds and even thousands of protein spots ("proteome analysis") is possible, without human intervention, with the availability of highly accurate mass spectrometry instruments, and high-throughput facilities for preparation and handling of protein samples from 2-D gels. However, the lack of software for precise automatic analysis and annotation of mass spectra, as well as software for in-batch sequence database queries, is increasingly becoming a significant bottleneck for the proteomics work flow. In the present paper we outline an algorithm for reliable, accurate, and automatic evaluation of mass spectrometric data and database searches. We show here that simply selecting from the sequence database the protein that has the most matching fragment masses often leads to false-positive results. Reliable protein identification is dependent on several parameters: the accuracy of fragment mass determination, the number of masses submitted for query, the mass distribution of query masses, the number of masses matching between sample and database protein, the size of the sequence database, and the kind and number of modifications considered. Using these parameters, we derive a simple statistical estimation that can be used to calculate the probability of true-positive protein identification.

246 citations


Journal ArticleDOI
TL;DR: Because a strong water transport from cathode to anode (reverse electroendosmotic flow) inherent to narrow immobilized pH gradients (IPGs) exceeding pH 11, such as IPG 10—12, was negligible, the wide‐range IPGs 3—12 and 6—12 proved to be perfectly suited for an overview separation of total cell extracts.
Abstract: Wide-range immobilized pH 3—12 and 6—12 gradients were generated. Depending on the extraction method of sample preparation, proteins with pIs up to pH 11.7 were resolved. Highly reproducible protein patterns, focused to the steady-state with round-shaped spots up to the basic end were obtained. Moreover, because a strong water transport from cathode to anode (reverse electroendosmotic flow) inherent to narrow immobilized pH gradients (IPGs) exceeding pH 11, such as IPG 10—12, was negligible, the wide-range IPGs 3—12 and 6—12 could be run under standard conditions as originally described by Gorg et al. (Electrophoresis 1988, 9, 531—546). The wide-range immobilized pH gradient 3—12 proved to be perfectly suited for an overview separation of total cell extracts. Resolution could be increased by extending the separation distance from 18 to 24 cm. Furthermore, two-dimensional gel electrophoresis with IPGs (IPG-Dalt) was simplified by the use of an integrated system (IPGphor) where sample application by in-gel rehydration and isoelectric focusing (IEF) are performed automatically in a one-step procedure, overnight, without human assistance.

244 citations


Journal ArticleDOI
TL;DR: It is concluded that the current set of STR loci is adequate for addressing most problems of human identification (including interpretations of DNA mixtures), however, if suitable number of SNPs are used that would match the power of this set of short tandem repeat (STR) loci, they alone cannot resolve more complex cases unless they are supplemented by the validatedSTR loci.
Abstract: Since the first characterization of the population genetic properties of repeat polymorphisms, the number of short tandem repeat (STR) loci validated for forensic use has now grown to at least 13. Worldwide variations of allele frequencies at these loci have been studied, showing that variations of interpopulation diversity at these loci do not compromise the power of identification of individuals. However, data collected for validation of these loci for forensic use has utility beyond human identification; the origin and past migration history of modern humans can be reconstructed from worldwide variations at these loci. Furthermore, complex forensic cases previously unresolvable can now be investigated with the help of the validated STR loci. Here, we provide the absolute power of the validated set of 13 STR loci for addressing these issues using multilocus genotype data on 1,401 individuals belonging to seven populations (US European-American, US African-American, Jamaican, Italian, Swiss, Chinese and Apache Native-American). Genomic research is discovering new classes of polymorphic loci (such as the single nucleotide polymorphisms, SNPs) and lineage markers (such as the mitochondrial DNA and Y-chromosome markers); our aim, therefore, was to determine how many SNP loci are needed to match the power of this set of 13 STR loci. We conclude that the current set of STR loci is adequate for addressing most problems of human identification (including interpretations of DNA mixtures). However, if suitable number of SNPs are used that would match the power of the STR loci, they alone cannot resolve more complex cases unless they are supplemented by the validated STR loci.

Journal ArticleDOI
TL;DR: All US isolates could be differentiated by a unique, strain‐specific PCR fingerprint or RAPD pattern in contrast to most of the non‐US isolates, which showed a substantially higher degree of genetic homogeneity, with some clonality, in different parts of the world.
Abstract: A total of 356 clinical isolates of the encapsulated basidiomycetous fungus Cryptococcus neoformans var. neoformans, obtained from Australia, Argentina, Brazil, India, Italy, New Zealand, Papua New Guinea, South Africa, Thailand and the USA, were analyzed to lay the basis for a comprehensive evaluation of the global genetic structure of C. neoformans. Two polymerase chain reaction (PCR)-based typing techniques were standardized: PCR fingerprinting using a single primer specific to minisatellite or microsatellite DNA, and randomly amplified polymorphic DNA (RAPD) analysis using two combinations of three 20- to 22-mer random primers. Previous studies showed that the resultant profiles are reproducible and stable over time. Identical results were obtained in two different laboratories and by different scientists in the same laboratory. Both typing techniques separated the isolates into four major groups (VNI and VNII, serotype A; VNIII, serotype A/D; and VNIV, serotype D). The majority (78%) of isolates belonged to VNI, compared with 18% VNII, 1% VNIII and 3% VNIV. All US isolates could be differentiated by a unique, strain-specific PCR fingerprint or RAPD pattern in contrast to most of the non-US isolates, which showed a substantially higher degree of genetic homogeneity, with some clonality, in different parts of the world. Isolates obtained from the same patient at different times and from different body sites, had identical banding patterns. Both typing techniques should provide powerful tools for epidemiological studies of medically important fungi.

Journal ArticleDOI
TL;DR: This review focuses on the various, mainly genetic, applications of the proteomic tools that have been developed in recent years: characterization of individuals or lines, estimation of genetic variability within and between populations, establishment of genetic distances that can be used in phylogenetic studies, characterization of mutants and localization of the genes encoding the revealed proteins.
Abstract: Proteomics is becoming a necessity in plant biology, as it is in medicine, zoology and microbiology, for deciphering the function and role of the genes that are or will be sequenced. In this review we focus on the various, mainly genetic, applications of the proteomic tools that have been developed in recent years: characterization of individuals or lines, estimation of genetic variability within and between populations, establishment of genetic distances that can be used in phylogenetic studies, characterization of mutants and localization of the genes encoding the revealed proteins. Improvements in specifically devoted software have permitted precise quantification of the variation in amounts of proteins, leading to the concept of "protein quantity loci" which, combined with the "quantitative trait loci" approach, results in testable hypotheses regarding the role of "candidate proteins" in the metabolism or phenotype under study. This new development is exemplified by the reaction of plants to drought, a trait of major agronomic interest. The accumulation of data regarding genomic and cDNA sequencing will be connected to the protein databases currently developed in plants.

Journal ArticleDOI
TL;DR: In this review, the weak points in the chain of analysis are highlighted and recent trends toward automation in instrumentation and software are summarized and the author's own personal view of future developments in the field is offered.
Abstract: Proteome analysis is concerned with the global changes in protein expression as visualized most commonly by two-dimensional gel electrophoresis and analyzed by mass spectrometry. A drastic increase in the rapidity and reproducibility of protein isolation and identification is needed for proteome analysis to become a useful complement to global mRNA analysis. Simplification and standardization, based on innovation in both hard- and software, are prerequisites to the creation of automated proteomics platforms that are both robust and user-friendly, and will allow many more laboratories access to this technique. In this review we highlight the weak points in the chain of analysis (such as sample handling, protein separation and digestion) and summarize recent trends toward automation in instrumentation and software and offer our own personal view of future developments in the field.

Journal ArticleDOI
TL;DR: It is demonstrated that minor mismatches in the primer or the probe region, decrease overall PCR efficiency but do not abolish the quantification, in contrast to major mismatches of three or four nucleotides, which lead to complete inhibition of the real‐time PCR detection.
Abstract: Lentiviruses are associated not only with immunodeficiency but also with malignancies. The mechanisms involved in tumorigenesis are still not fully understood. Cats infected with feline immunodeficiency virus (FIV) in the wild represent one model in which the role of viral load in the pathogenesis can be studied, since tumors, especially lymphomas, are quite often observed in cats infected with FIV. To be able to compare the viral load data among cats infected with different FIV isolates, the method used to obtain the viral load has to be unaffected by isolate-specific differences. This is especially true for the real-time polymerase chain reaction (PCR), a new method for viral load determination, since nucleotide sequence mismatches have been used for allelic discrimination with this method. To investigate the influence of these mismatches on PCR efficiency, we have used an FIV-specific real-time PCR and determined the influence of nucleotide sequence variation in several characterized FIV isolates as well as unknown isolates from naturally infected cats. We could demonstrate that minor mismatches, such as point mutations in the primer or the probe region, decrease overall PCR efficiency but do not abolish the quantification, in contrast to major mismatches of three or four nucleotides, which lead to complete inhibition of the real-time PCR detection. Based on these results, it will be possible to design real-time PCR systems allowing the quantification of a broad range of isolates, which is a prerequisite for the investigation of the impact of viral load in tumorigenesis.

Journal ArticleDOI
TL;DR: This review summarizes the different changes of O‐ and N‐linked glycoproteins observed in cancer cells, the impact of the tumor‐related carbohydrate phenotypes on the clinical outcome of the cancer disease, and the various ways in which carbohydrate structures can interact with different carbohydrate‐detecting adhesion molecules, selectins, and sialoadhesins.
Abstract: Alteration of the expression of carbohydrate structures is frequently observed in tumor cells. This review summarizes the different changes of O- and N-linked glycoproteins observed in cancer cells, the impact of the tumor-related carbohydrate phenotypes on the clinical outcome of the cancer disease, and the various ways in which carbohydrate structures can interact with different carbohydrate-detecting adhesion molecules, selectins, and sialoadhesins. Various ways of inhibiting the formation of cell adhesion-engaged carbohydrates on the cell surface, or inhibiting the binding are discussed. Carbohydrate structures which are in clinical use as circulating tumor markers and the effect of genotypes on tumor marker concentrations are reviewed.

Journal ArticleDOI
TL;DR: The principles of the microarray technology as applied to cancer research are described, the literature on its use so far is summarized, and speculate on the future application of this powerful technique are speculated on.
Abstract: Currently there are over 1,000,000 human expressed sequence tag (EST) sequences available on the public database, representing perhaps 50-90% of all human genes The cDNA microarray technique is a recently developed tool that exploits this wealth of information for the analysis of gene expression In this method, DNA probes representing cDNA clones are arrayed onto a glass slide and interrogated with fluorescently labeled cDNA targets The power of the technology is the ability to perform a genome-wide expression profile of thousands of genes in one experiment In our review we describe the principles of the microarray technology as applied to cancer research, summarize the literature on its use so far, and speculate on the future application of this powerful technique

Journal ArticleDOI
TL;DR: Two‐dimensional (2‐D) polyacrylamide gel electrophoresis has much to contribute to experimental analysis of the proteomes of microbial organisms, since this method separates most cellular proteins and allows synthesis rates to be determined quantitatively.
Abstract: Two-dimensional (2-D) polyacrylamide gel electrophoresis has much to contribute to experimental analysis of the proteomes of microbial organisms, since this method separates most cellular proteins and allows synthesis rates to be determined quantitatively. Databases generated using 2-D gels can grow to be very large from even just a few experiments, since each sample provides the data for a field (or column) in the database for several hundreds to even thousands of records (or rows), each of which represents a single polypeptide species. The value of such databases for generating an encyclopedia of how each of the cell's proteins behave in different conditions (protein phenotypes) has been recognized for some time. The potential exists, however, to glean even more valuable information from such databases. Because the measurements of each protein are made in the context of all other proteins, a comprehensive glimpse of the cell's physiological state is theoretically achievable with each 2-D gel. By examining enough conditions (and 2-D gels), expression patterns of subsets of proteins (proteomic signatures) can be found that correlate with the cell's state. This type of information can provide a unique contribution to proteomic analysis, and should be a major focus of such analyses.

Journal ArticleDOI
TL;DR: Three different procedures for the solubilization of yeast (S. cerevisiae) cell proteins were compared on the basis of the obtained two‐dimensional (2‐D) polypeptide patterns and major emphasis was laid on minimizing handling steps, protein modification or degradation, and quantitative loss of high molecular mass proteins.
Abstract: Three different procedures for the solubilization of yeast (S. cerevisiae) cell proteins were compared on the basis of the obtained two-dimensional (2-D) polypeptide patterns. Major emphasis was laid on minimizing handling steps, protein modification or degradation, and quantitative loss of high molecular mass proteins. The procedures employed were sonication, followed by (i) protein solubilization with “standard” lysis buffer (9 M urea, 2% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS)), 1% dithiothreitol (DTT), 2% v/v carrier ampholytes, (ii) presolubilization of proteins with sodium dodecyl sulfate (SDS) buffer, consisting of 1% SDS and 100 mM tris(hydroxymethyl)aminomethane (Tris)-HCl, pH 7.0, followed by dilution with “standard” lysis buffer, and (iii) boiling the sample with SDS during cell lysis, followed by dilution with thiourea/urea lysis buffer (2 M thiourea / 7 M urea, 4% w/v CHAPS, 1% w/v DTT, 2% v/v carrier ampholytes). All procedures tested were rapid and simple. However, with the first procedure (i), considerable degradation of high Mr proteins occurred. In contrast, protein degradation was minimized by boiling the sample in SDS buffer immediately after sonication (method ii). Protein disaggregation and solubilization of high Mr proteins were further improved by pre-boiling with SDS and using thiourea/urea lysis buffer instead of “standard” lysis buffer (procedure iii).

Journal ArticleDOI
TL;DR: A new algorithm to identify proteins by means of peptide mass fingerprinting using matrix‐assisted laser desorption/ionization‐time‐of‐flight spectra and environmental data, as well as chemical modifications or number of missed cleavages of a protein.
Abstract: We have developed a new algorithm to identify proteins by means of peptide mass fingerprinting. Starting from the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra and environmental data such as species, isoelectric point and molecular weight, as well as chemical modifications or number of missed cleavages of a protein, the program performs a fully automated identification of the protein. The first step is a peak detection algorithm, which allows precise and fast determination of peptide masses, even if the peaks are of low intensity or they overlap. In the second step the masses and environmental data are used by the identification algorithm to search in protein sequence databases (SWISS-PROT and/or TrEMBL) for protein entries that match the input data. Consequently, a list of candidate proteins is selected from the database, and a score calculation provides a ranking according to the quality of the match. To define the most discriminating scoring calculation we analyzed the respective role of each parameter in two directions. The first one is based on filtering and exploratory effects, while the second direction focuses on the levels where the parameters intervene in the identification process. Thus, according to our analysis, all input parameters contribute to the score, however with different weights. Since it is difficult to estimate the weights in advance, they have been computed with a generic algorithm, using a training set of 91 protein spectra with their environmental data. We tested the resulting scoring calculation on a test set of ten proteins and compared the identification results with those of other peptide mass fingerprinting programs.

Journal ArticleDOI
TL;DR: It is demonstrated here that analysis of these genetic markers can now be performed routinely in a rapid, automated, and high‐throughput fashion using time‐of‐flight mass spectrometry and a primer extension assay with a novel cleavable primer.
Abstract: The high frequency of single nucleotide polymorphisms (SNPs) in the human genome makes them a valuable source of genetic markers for identity testing, genome mapping, and medical diagnostics. Conventional technologies for detecting SNPs are laborious and time-consuming, often prohibiting large-scale analysis. A rapid, accurate, and cost-effective method is needed to meet the demands of a high-throughput DNA assay. We demonstrate here that analysis of these genetic markers can now be performed routinely in a rapid, automated, and high-throughput fashion using time-of-flight mass spectrometry and a primer extension assay with a novel cleavable primer. SNP genotyping by mass spectrometry involves detection of single-base extension products of a primer immediately adjacent to the SNP site. Measurement of the mass difference between the SNP primer and the extension peak reveals which nucleotide is present at the polymorphic site. The primer is designed such that its extension products can be purified and chemically released from the primer in an automated format. The reduction in size of the products as a result of this chemical cleavage allows more accurate identification of the polymorphic base, especially in samples from a heterozygotic population. All six possible heterozygotes are resolved unambiguously, including an A/T heterozygote with extension products differing by only 9 Da. Multiplex SNP determination is demonstrated by simultaneously probing multiple SNP sites from a single polymerase chain reaction (PCR) product as well as from multiplexed PCR amplicons. Samples are processed in parallel on a robotic workstation, and analyzed serially in an automated mass spectrometer with analysis times of only a few seconds per sample, making it possible to process thousands of samples per day.

Journal ArticleDOI
TL;DR: Three proteins, E‐FABP, cofilin, and 14-3‐3‐σ (stratifin) was found to be overexpressed only in the mitoxantrone‐selected atypical multidrug‐resistant cell line, and the possible significance of these findings is discussed.
Abstract: In order to study possible mechanisms leading to chemoresistance in pancreatic adenocarcinoma we examined the global protein expression of pancreatic cancer cells in vitro. We used a cell culture model derived from the adenocarcinoma of the pancreas (EPP85-181P). A classical multidrug-resistant subline, EPP85-181RDB, selected in presence of daunorubicin, and an atypical multidrug-resistant cell variant, EPP85-181RNOV, selected in presence of mitoxantrone, were analyzed using two-dimensional electrophoresis. After staining and image analysis, spots of interest were isolated using preparative two-dimensional electrophoresis and subjected to mass spectrometry and microsequencing. Three proteins, E-FABP, cofilin, and 14-3-3-sigma (stratifin), were overexpressed in chemoresistant cell lines. Cofilin was present in both multidrug in chemoresistant cell lines. Cofilin was present in both multidrug-resistant cell lines. E-FABP and 14-3-3-sigma (stratifin) was found to be overexpressed only in the mitoxantrone-selected atypical multidrug-resistant cell line. The possible significance of these findings is discussed.

Journal ArticleDOI
TL;DR: The dual‐channel image analysis is described that offers the opportunity to visualize the content and synthesis rate of a whole set of bacterial proteins on a single electropherogram and is useful for the rapid search for proteins that belong to different stimulons or regulons.
Abstract: The allocation of proteins to stimulons and regulons is an essential step towards the understanding of the global regulation of the expression of entire genomes. The computer-aided evaluation and matching of two-dimensional protein gels loaded with radioactively labeled proteins from exponentially growing or stressed cells is a useful but time-consuming procedure for the description of stimulons and regulons. This paper describes the dual-channel image analysis that offers the opportunity to visualize the content and synthesis rate of a whole set of bacterial proteins on a single electropherogram. By pulse-labeling with L-[35S]methionine, the protein synthesis pattern (red color) can be directly compared with the protein level pattern (green color). Because matching of other gels can be avoided, this new technique is useful for the rapid search for proteins that belong to different stimulons or regulons. This approach was tested for the identification of proteins of heat stress or oxidative stress stimulons. Proteins that were induced by heat or oxidative stress colored red while proteins whose synthesis was switched off by the stress factor colored green. Proteins that were continuously synthesized before and after the imposition of stress retained their yellow color. The advantages and possible pitfalls of the technique are discussed.

Journal ArticleDOI
TL;DR: The conditions required for optimal extraction and separation of normal red blood cell ghost proteins by two‐dimensional gel electrophoresis were defined and several protein spots were found only in infected ghosts and are expected to represent parasite‐encoded proteins.
Abstract: Parasite-encoded membrane proteins translocated to the surface of infected erythrocytes or in specialized vesicles underneath (Maurer's clefts) play a key role in the asexual life cycle of Plasmodium falciparum (a malaria-causing protozoan), by mediating key steps such as red blood cell invasion, sequestration of infected cells in microcapillaries, and red blood cell rupture. A large-scale analysis of these membrane proteins would therefore be of great help to gain knowledge of the different stages of the Plasmodium falciparum life cycle. In order to be able to detect and identify parasite-encoded proteins directed to the red blood cell membrane, we first defined the conditions required for optimal extraction and separation of normal red blood cell ghost proteins by two-dimensional gel electrophoresis. These conditions included the use of urea, thiourea and new zwitterionic detergents in the extraction and isoelectric focusing media. The optimized conditions were then applied to analyze normal and P. falciparum-infected red blood cell ghosts. Several protein spots were found only in infected ghosts and are expected to represent parasite-encoded proteins. These proteins are currently under investigation.

Journal ArticleDOI
TL;DR: Columns packed with reverse‐phase material subjected to silicate entrapment demonstrated faster separations of retained analytes and increased efficiencies compared with nonentrapped columns.
Abstract: Designed especially for capillary electrochromatography (CEC), silicate-entrapped columns are made by trapping particles of chromatographic packing material in a network of silica. Once entrapped, the capillary no longer requires frits. This renders a more homogeneous and stable packed bed. Accidental breakage of the fragile frits is not an issue with these robust columns. Columns packed with reverse-phase material subjected to silicate entrapment demonstrated faster separations of retained analytes and increased efficiencies compared with nonentrapped columns. The method was also used to prepare chiral CEC columns by entrapping a molecular imprinted polymeric (MIP) packing having minimal surface charge density, thus being unable alone to support sufficient electroosmotic flow for CEC.

Journal ArticleDOI
TL;DR: Two methods were employed for the purification of hydrophobic proteins from Arabidopsis thaliana leaf plasma membrane (PM) model plants, prior to analysis on 2‐DE immobilized pH gradient (IPG) gels, resulting in the resolution of several integral proteins and the disappearance of peripheral proteins.
Abstract: An extensive proteomic approach relies on the possibility to visualize and analyze various types of proteins, including hydrophobic proteins which are rarely detectable on two-dimensional electrophoresis (2-DE) gels. In this study, two methods were employed for the purification of hydrophobic proteins from Arabidopsis thaliana leaf plasma membrane (PM) model plants, prior to analysis on 2-DE immobilized pH gradient (IPG) gels. Solubilization efficiency of two detergents, (3-[(3-cholomidopropyl)-1-propanesulfonic acid] (CHAPS)) and C8∅, were tested for the recovery of hydrophobic proteins. An immunological approach was used to determine the efficiency of the above methods. Fractionation of proteins by Triton X-114 combined with solubilization with CHAPS resulted in the inability to detect hydrophobic proteins on 2-DE gels. The use of C8∅ for protein solubilization did not improve this result. On the contrary, after treatment of membranes with alkaline buffer, the solubilization of PM proteins with detergent C8∅ permitted the recovery of such proteins on 2-DE gels. The combination of membrane washing and the use of zwitterionic detergent resulted in the resolution of several integral proteins and the disappearance of peripheral proteins. In the resolution of expressed genome proteins, both large pH gradients in the first dimension and various acrylamide concentrations in the second dimension must be used. Notwithstanding, it is important to combine various sample treatments and different detergents in order to resolve soluble and hydrophobic proteins.

Journal ArticleDOI
TL;DR: The two‐dimensional map may be useful as a reference database to study changes in the protein level caused by various disorders, such as Alzheimer's disease, major depression and schizophrenia.
Abstract: Samples of human brain from the parietal cortex lobe were analyzed by two-dimensional gel electrophoresis, using immobilized pH gradient strips covering the various pH regions. The protein spots were visualized with colloidal Coomassie blue stain and identified by matrix-assisted laser desorption/ionization mass spectrometry. Approximately 400 spots were identified, corresponding to 180 different brain proteins. The list of identified proteins includes a large number of structural proteins and of enzymes or enzyme subunits with various catalytic activities. The majority of proteins are localized in the cytoplasma and in mitochondria. The two-dimensional map may be useful as a reference database to study changes in the protein level caused by various disorders, such as Alzheimer's disease, major depression and schizophrenia.

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TL;DR: The performance of standard and modified techniques with a variety of DNA‐damaging agents are compared and possible explanations for the differences in behaviour of DNA under alternative electrophoretic conditions are offered.
Abstract: Single cell gel electrophoresis, also known as the comet assay, is widely used for the detection and measurement of DNA strand breaks With the addition of a step in which DNA is incubated with specific endonucleases recognising damaged bases, these lesions can be measured, too In the standard protocol, electrophoresis is carried out at high pH If, instead, electrophoresis is in neutral buffer, the effect of DNA damage seems to be much reduced--either because alkaline conditions are needed to reveal certain lesions, or because the effect of the same number of breaks on DNA migration is greater at high pH A lower sensitivity can be useful in some circumstances, as it extends the range of DNA damage levels over which the assay can be used Here we compare the performance of standard and modified techniques with a variety of DNA-damaging agents and offer possible explanations for the differences in behaviour of DNA under alternative electrophoretic conditions

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TL;DR: The number N, the equivalent number of maximally informative SNPs, is suggested as a measure of marker informativity in the context of kinship testing because Linear regression analysis of a large number of simulated SNP sets reveals that only a minor linear correction of N is required for large n.
Abstract: Common single nucleotide polymorphisms (SNPs) have the potential to provide a widely used means of simple and robust kinship testing. Suitable measures of polymorphism informativity are therefore required in order to guide the search for the most efficient combinations of SNPs. In the context of kinship testing, such measures should preferably be related to Z, the power of excluding false paternity in trios comprising mother, child and alleged father. Since the bulk of SNPs is expected to be biallelic, a Z-related measure of informativity can be defined for SNPs in a particularly elegant manner: allele frequency vectors of sets of n biallelic SNPs that give rise to the same Z value approximate to an n-dimensional sphere around (1/2,…,1/2). Owing to this relationship, it can be shown that the number N of maximally informative SNPs (i.e., of SNPs with allele frequencies 1/2), providing the same Z value as a given set of n SNPs, approximates to 2n times the average gene diversity of the latter. Linear regression analysis of a large number of simulated SNP sets reveals that only a minor linear correction of N is required for large n. Since Z = 1—(13/16)N, N can also be calculated easily for multiallelic markers with known Z. The “equivalent number of maximally informative SNPs”, N, is therefore suggested as a measure of marker informativity in the context of kinship testing.

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TL;DR: Two proteins that are differentially expressed in genotypically diseased but phenotypically normal animals are detected, identifying a possible mechanism for the onset of the disease and the possibility that inappropriate ubiquination of proteins plays an important role in the disease is discussed.
Abstract: Bovine hereditary dilated cardiomyopathy (bCMP) is endemic in Switzerland and hearts from diseased animals display important clinical and biochemical similarities to human DCM. Recent research has identified at least one protein (myoglobin) to be significantly reduced in bovine DCM. Using a proteomic approach, we have separated over 1125 protein species from bovine ventricular tissue. Gel analysis and protein characterisation have identified a number of proteins whose abundance is significantly altered in bovine DCM. Twenty-four proteins are of decreased abundance in diseased tissue, whilst 11 proteins are of increased abundance in the diseased state. A combination of amino acid compositional analysis, peptide mass profiling, N-terminal microsequencing and MultiIdent (http://www.expasy.ch/sprot/multiident. html) has been employed in order to elucidate the identities of the differentially expressed proteins. Using these techniques we have currently determined the identity of 12 of the 35 altered proteins. We have also detected three proteins that are differentially expressed in genotypically diseased but phenotypically normal animals, identifying a possible mechanism for the onset of the disease. The possibility that inappropriate ubiquination of proteins plays an important role in the disease is discussed. A database of bovine proteins is currently being established. The identity of the proteins affected, together with a comparison of the human and bovine expression patterns, is displayed.