pinecone/core-2020-05-10-deduplication huggingface dataset:
Chip electrospray mass spectrometry for carbohydrate analysis

Currently two types of chip systems are used in conjunction with MS: out-of-plane devices, where hundreds of nozzles, nanospray emitters are integrated onto a single silicon substrate from which electrospray is established perpendicular to the substrate, and planar microchips, embedding a microchannel at the end of which electrospray is generated in-plane, on the edge of the microchip. In the last two years, carbohydrate research greatly benefited from the introduction and implementation of the chip-based MS. In two laboratories the advantages of the chip electrospray in terms of ionization efficiency, sensitivity, reproducibility, quality of data in combination with high mass accuracy, and resolution of detection were systematically explored for several carbohydrate classes: O- and N-glycopeptides, oligosaccharides, gangliosides and glycoprotein-derived O- and N-glycans, and glycopeptides. The current state-of-the-art in interfacing the chip electrospray devices to high-performance MS for carbohydrate analysis, and the particular requirements for method optimization in both positive and negative ion modes are reviewed here. The recent applications of these miniaturized devices and their general potential for glycomic-based surveys are highlighted
Capillary electrophoresis-mass spectrometry of Spirulina platensis proteins obtained by pressurized liquid extraction

In this work, the usefulness of CE-MS to monitor and optimize the pressurized liquid\ud
extraction (PLE) of proteins from Spirulina platensis microalga is demonstrated. Crude\ud
and purified PLE extracts from microalga were analyzed by CE-MS. It was observed\ud
that the use of purification protocols of phycobiliproteins (namely, ultrafiltration or precipitation-\ud
dialysis-freeze drying) resulted in better CE resolution and MS signals,\ud
demonstrating that sample matrix plays an important role in CE-MS of proteins in real\ud
samples. Ultrafiltration was found less laborious and much faster than precipitationdialysis-\ud
freeze drying (1 vs. 48 h). Direct analysis of crude extracts was demonstrated\ud
to be also possible by CE-MS, providing less-quality information but enough to characterize\ud
PLE extracts in a much faster way. Therefore, the latter protocol was selected\ud
to monitor and optimize the extraction process of phycobiliproteins from S. platensis.\ud
To do that, different extraction conditions were tested, including time, temperature and\ud
pressure of extraction, nature of pressurized liquid, distribution of microalga inside the\ud
extraction cell, type of packing, etc. It is demonstrated that the combined use of PLE\ud
and CE-MS allows the attainment of extracts rich in phycobiliproteins in short extraction\ud
times (namely, yields of 20% can be obtained in less than 2 h under the optimum\ud
PLE process in an automatic way). To our knowledge, this work shows for the first time\ud
the usefulness of CE-MS for monitoring and optimizing a PLE process.Financial support from AGL2002–04621-C02–02 project\ud
(CICYT, Ministerio de Ciencia y Tecnlogía) is acknowledged.\ud
M.H. thanks MCYT for an FPI grant. C.S. thanks\ud
Consejería de Educación y Cultura (Comunidad de\ud
Madrid) for a fellowship.Peer reviewe
Development of a capillary electrophoresis method for the determination of soybean proteins in soybean-rice gluten-free dietary products. Research Article

CE has been applied for the first time to the simultaneous separation of soybean and\ud
rice proteins. Treated and untreated capillaries with different effective lengths as well\ud
as separation media at different pHs were tested. For that purpose, samples and\ud
standard solutions were prepared in 25:75 ACN–water media containing 0.3% v/v\ud
acetic acid. The use of an untreated capillary of 50 cm effective length together with an\ud
80 mM borate buffer (pH 8.5) modified with 20% v/v ACN and UV detection at 254 nm\ud
were the conditions working the best. These conditions enabled the determination of\ud
soybean proteins in gluten-free dietary commercial products elaborated with soybean\ud
protein and/or soybean flour and rice flour using the standard additions calibration\ud
method. The method was linear up to 26 mg/mL of soybean proteins, the precision\ud
(expressed as RSD) was always better than 6%, and recoveries obtained for soybean\ud
proteins when spiking commercial products were very close to 100%The authors thank the Ministry of Science and Technology\ud
(Spain) for the research project BQU2002–01199 and F. J.\ud
Cabello-Murillo for technical assistance. C.G.-R. also\ud
thanks the Ministry of Science and Technology for the\ud
Ramón y Cajal program (RYC-2003–001)
Recent advances in the analysis of antibiotics by capillary electrophoresis

In this review, the main aspects related to the separation of different groups of antibiotics by CE as well as the different applications reported in the literature from the beginning 2003 till May 2005 will be provided to the readers. Firstly, the experimental conditions employed to achieve the analysis of antibiotics by CE are given. Then, the main applications performed in the pharmaceutical, clinical, food, and environmental\ud
fields have been reviewed making emphasis on sample preparation requirements needed in each case. Finally, the main conclusions and future prospects in this field are presented
RECENT ADVANCES IN THE APPLICATION OF CAPILLARY ELECTROMIGRATION METHODS FOR FOOD ANALYSIS

This article reviews the latest developments in the application of capillary electromigration methods for the analysis of foods and food components. Nowadays, methods based on capillary electrophoresis (CE) techniques are becoming widely used in food analytical and research laboratories. This review covers the application of CE to analyze amino acids, biogenic amines, peptides, proteins, DNAs, carbohydrates, phenols, polyphenols, pigments, toxins, pesticides, vitamins, additives, small organic and inorganic ions, chiral compounds, and other compounds in foods, as well as to investigate food interactions and food processing. The use of microchips as well as other foreseen trends in CE analysis of foods are discussed. Papers that were published during the period June 2002-June 2005 are included following the previous review by Frazier and Papadopoulou (Electrophoresis 2003, 24, 4095–4105).Projects AGL2002-04621-C02-02  (CICYT) and 2004IT0037 (CSIC-CNR)Peer reviewe
CAPILLARY ELECTROPHORESIS USING COPOLYMERS OF DIFFERENT COMPOSITION AS PHYSICAL COATINGS. A COMPARATIVE STUDY.

In this work, a comparative study on the use of different polymers as physically adsorbed coatings for Capillary Electrophoresis (CE) is presented. It is demonstrated that the use of ad hoc synthesized polymers as coatings allows tailoring the electroosmotic flow (EOF) in CE increasing the flexibility of this analytical technique. Namely, different polymers were synthesized at our laboratory using different percentages of ethylpyrrolidine methacrylate (EpyM) and N,N-dimethylacrylamide (DMA). Thus, by modifying the percentage of EpyM and DMA monomers it is possible to manipulate the positive charge of the copolymer, varying the global electrical charge on the capillary wall and with that the EOF. These coated capillaries are obtained by simply flushing a given EpyM-DMA aqueous solution into bare silica capillaries. It is shown that by using these coated capillaries at adequate pHs, faster or more resolved CE separations can be achieved depending on the requirements of each analysis. Moreover, it is demonstrated that these coated capillaries reduce the electrostatic adsorption of basic proteins onto the capillary wall. Furthermore, EpyM-DMA coatings allow the reproducible chiral separation of enantiomers through the partial filling technique. The EpyM-DMA coated capillaries are demonstrated to provide reproducible EOF values independently of the pH and polymer composition with % RSD values lower than 2 % for the same day. It is also demonstrated that the coating procedure is reproducible between capillaries. The compatibility of this coating protocol with CE in microchips is discussed.Peer reviewe
Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view.

website publisher: http://www3.interscience.wiley.com/International audienceThe proper functioning of mitochondria requires that both the mitochondrial and the nuclear genome are functional. To investigate the importance of the mitochondrial genome, which encodes only 13 subunits of the respiratory complexes, the mitochondrial rRNAs and a few tRNAs, we performed a comparative study on the 143B cell line and on its Rho-0 counterpart, i.e., devoid of mitochondrial DNA. Quantitative differences were found, of course in the respiratory complexes subunits, but also in the mitochondrial translation apparatus, mainly mitochondrial ribosomal proteins, and in the ion and protein import system, i.e., including membrane proteins. Various mitochondrial metabolic processes were also altered, especially electron transfer proteins and some dehydrogenases, but quite often on a few proteins for each pathway. This study also showed variations in some hypothetical or poorly characterized proteins, suggesting a mitochondrial localization for these proteins. Examples include a stomatin-like protein and a protein sharing homologies with bacterial proteins implicated in tyrosine catabolism. Proteins involved in apoptosis control are also found modulated in Rho-0 mitochondria
Expression of high-abundance proteins in sera of patients with endometrial and cervical cancers: analysis using 2-DE with silver staining and lectin detection methods

The expression of high-abundance serum proteins in newly diagnosed patients with endometrial adenocarcinoma (EACa), squarnous cell cervical carcinoma (SCCa) and cervical adenocarcinorna (ACCa), relative to control female subjects, was analyzed by subjecting serum samples to 2-DE followed by image analysis of the silver-stained protein profiles. The three cohorts of cancer patients demonstrated different altered expression of serum high-abundance proteins compared to negative control women. Tl-ie expression of alpha(1)-antitrypsin, alpha(1)-B glycoprotein, cleaved high-molecular-weight kininogen (light chain) and antithrombin III were consistently altered in all the patients. However, clusterin was upregulated only in the patients with EACa, while those with SCCa and ACCa were typically characterized by the upregulated expression of zinc alpha-2-glycoprotein. The aberrant expression of selective serum proteins in the various cohorts of cancer patients was validated by competitive ELISA as well as by lectin detection. Analysis by using the charnpedak galactose binding lectin further highlighted an unidentified protein that may be differently glycosylated in the sera of the EACa patients that were studied
CE methods for the determination of non-protein amino acids in foods: Review

In addition to the 20 amino acids universally distributed as protein constituents in living organisms, there are other amino acids of non-protein origin that can be found in foods. The determination of these non-protein amino acids is interesting since they can be indicative of the quality and safety of foods. This work presents for the first time an updated and comprehensive review devoted to show the possibilities of capillary electrophoresis for the determination of non-protein amino acids in food samples. The results reported have been classified according to the chemical structure of the non-protein amino acid studied. Separation conditions as well as detection systems used have been detailed since most of these amino acidic compounds do not possess chromophore groups detectable by conventional UV-Vis detection, being in this case necessary a previous derivatization step. Finally, the application of microchip electrophoresis to the determination of non-protein amino acids in foodstuffs is also included in this revie
Detection of microbial food contaminants and their products by capillary electromigration techniques

This work reviews the different analytical strategies based on capillary electromigration techniques developed for detecting microbial contaminants and their products in food matrices. Namely, this work presents an exhaustive and critical review, including works published till March 2007, on CE methods developed to detect and identify contaminants of microbial origin that represent a hazard to humans in foods. First, an overview on the strategies adopted for the analysis of intact microorganisms is presented. Next, CE methodologies based on the analysis of microbial constituents, including those based on genomics and proteomics approaches, are described. Finally, CE methods developed for detecting microbial toxins are discussed.Peer reviewe
Capillary electrophoresis-electrospraymass spectrometry in peptide analysis and peptidomics

In the present work, an exhaustive review of the main developments and applications of CEMS\ud
for peptide analysis is given. This review includes the use of different CE separation\ud
modes, MS analyzers, capillary coatings, preconcentration techniques, on-chip applications\ud
as well as other different multidimensional strategies for peptide analysis. Key applications\ud
are critically discussed and relevant works published from January 2000 to May 2007 are\ud
summarized including information concerning the type of sample, CE-MS parameters as\ud
well as some figures of merit of the different CE-MS procedures developed for peptide\ud
analysis and peptidomics.This study was supported by ProjectsAGL2005-05320-C02-01\ud
Ciencia) and S-505/AGR-0153 (ALIBIRD, Comunidad de\ud
Madrid). M. H. would like to thank the Spanish Education and\ud
Science Ministry (MEC) for a post-doctoral fellowship.Peer reviewe
Recent advances in the application of capillary electromigration methods for food analysis

This review covers the application of capillary electromigration methods to analyze foods and food components, including amino acids, biogenic amines, peptides, proteins, DNAs, carbohydrates, phenols, polyphenols, pigments, toxins, pesticides, vitamins, additives, small organic and inorganic ions, chiral compounds, and other compounds in foods, as well as those applications of CE for monitoring food interactions and food processing. The use of microchips as well as other foreseen trends in food analysis by CE are discussed. Papers that were published during the period June 2005-March 2007 are included following the previous review by Cifuentes (Electrophoresis 2006, 27, 283-303).Peer reviewe
Development of an in-capillary derivatization method by CE for the determination of chiral amino acids in dietary supplements and wines

A fast in-capillary derivatization method by CE with 6-aminoquinolyl-N-hydroxysuccinimidyl\ud
carbamate was developed for the first time for the determination of\ud
amino acid enantiomers (arginine, lysine, and ornithine) in dietary supplements and\ud
wines. Because of the initial current problems due to the formation of precipitates into\ud
the capillary during the derivatization reaction, a washing step with an organic solvent as\ud
DMSO between injections was necessary. Different approaches were also investigated to\ud
enhance the sensitivity of detection. A derivatization procedure, where plugs of ACN,\ud
derivatizing agent (10mM 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate), and\ud
sample in borate (1:1 v/v) were injected in tandem (2, 3, and 6 s, respectively, at 50 mbar),\ud
was selected because it enabled to obtain the most sensitive and reproducible results.\ud
Appropriate analytical characteristics (linearity, LOD and LOQ, precision, absence of\ud
matrix interferences, and accuracy) were obtained for this method. Finally, the optimized\ud
method was successfully applied to the determination of the enantiomers of arginine,\ud
lysine, and ornithine in food samples of different complexities (dietary supplements and\ud
wines).The authors thank the Ministry of Education and Science (Spain) and the Comunidad Autónoma de Madrid (Spain) for research projects CTQ2006-03849/BQU and S-0505/AGR- 0312, respectively. Carmen Garcı´a-Ruiz thanks the Ministry of Science and Technology (Spain) for the Ramon y Cajal program (RYC-2003-001). A.B.M.-G. thanks the University of Alcala for her pre-doctoral contract
Cyclodextrin-modified capillary electrophoresis for achiral and chiral separation of ergostane and lanostane compounds extracted from the fruiting body of Antrodia camphorata

A CD-modified capillary electrophoretic method has been developed for achiral and chiral analysis of seven bioactive compounds isolated from the fruiting body of Antrodia camphorata. Such important target analytes exhibit similar chemical structures and are known for their diverse properties including antioxidant and anticancer effects. The analytes were separated in 25 min using a pH 9.3, 20mM sodium borate buffer containing 20mM methyl-\u3b2-CD and 30mM sulfobutylether-\u3b2-CD. With the exception of the optical isomer pairs (antcin B or zhankuic acid A, zhankuic acid C, and antcin A), the remaining bioactive compounds including the chiral pair antcin C were baseline-separated. Analysis time was noticeably longer to baseline separate all of the above chiral pairs (~38 min) by adding 5% DMF to the running buffer. The migration order was reversed compared with the HPLC elution. More hydrophobic compounds complexed favorably with methyl-\u3b2-CD and emerged earlier in the electropherogram than their more hydrophilic counterparts which were strongly associated with sulfobutylether-\u3b2- CD. The simple capillary electrophoretic method developed was applicable for rapid separation and characterization of several important bioactive compounds isolated from the fruiting body of A. camphorata.NRC publication: Ye
Membrane proteins and proteomics: Love is possible, but so difficult.

International audienceDespite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum varies with different proteins, while most protein chemistry methods work mainly, if not only, in water-based media. Taking this review [Santoni, Molloy and Rabilloud, Membrane proteins and proteomics: un amour impossible? Electrophoresis 2000, 21, 1054-1070] as a pivotal paper, the current paper analyzes how the field of membrane proteomics exacerbated the trend in proteomics, i.e. developing alternate methods to the historical two-dimensional electrophoresis, and thus putting more and more pressure on the mass spectrometry side. However, in the case of membrane proteins, the incentive in doing so is due to the poor solubility of membrane proteins. This review also shows that in some situations, where this solubility problem is less acute, two-dimensional electrophoresis remains a method of choice. Last but not least, this review also critically examines the alternate approaches that have been used for the proteomic analysis of membrane proteins
CE-TOF MS analysis of complex protein hydrolyzates from genetically modified soybeans – A tool for foodomics

9 páginas, 7 figuras.-- El pdf del artículo es la versión de autor.-- et al.A CE-TOF MS proteomic approach was applied for the analysis of hydrolyzates from complex soybean protein mixtures. After CE-TOF MS method development, the new approach provided the simultaneous analysis of more than 150 peptides from the soybean protein fraction soluble in ACN-water (80/20 v/v). The method is fast (about 30 min of analysis per sample) and is characterized by a relatively low running cost. The approach was used to study the substantial equivalence between a genetically modified variety of soybean compared with its traditional counterpart. No significant differences were found between the two studied soybeans based on the protein fraction studied. The capacity of the CE-TOF MS method to analyze complex mixtures of peptides in short times opens interesting possibilities in the growing Foodomics area.This work was supported by AGL2008-05108-C03-01 and\ud
CTQ2006-03849/BQU projects (Ministerio de Educacion y\ud
Ciencia, Spain) and CSD2007-00063 FUN-C-FOOD\ud
(Programa CONSOLIDER, Ministerio de Educacion y Ciencia,\ud
Spain) projects. E.D.-V. thanks the University of Alcala for her\ud
pre-doctoral grant.Peer reviewe
Microfluidic preparative free-flow isoelectric focusing in a triangular channel: System development and characterization

A preparative scale free-flow IEF device is developed and characterized with the aim of addressing needs of molecular biologists working with protein samples on the milligrams and milliliters scale. A triangular-shape separation channel facilitates the establishment of the pH gradient with a corresponding increase in separation efficiency and decrease in focusing time compared with that in a regular rectangular channel. Functionalized, ion-permeable poly(acrylamide) gel membranes are sandwiched between PDMS and glass layers to both isolate the electrode buffers from the central separation channel and also to selectively adjust the voltage efficiency across the separation channel to achieve high electric field separation. The 50×70 mm device is fabricated by soft lithography and has 24 outlets evenly spaced across a pH gradient between pH 4 and 10. This preparative free-flow IEF system is investigated and optimized for both aqueous and denaturing conditions with respect to the electric field and potential efficiency and with consideration of Joule-heating removal. Energy distribution across the functionalized polyacrylamide gel is investigated and controlled to adjust the potential efficiency between 15 and 80% across the triangular separation channel. The device is able to achieve constant electric fields high as 370±20 V/cm through the entire triangular channel given the separation voltage of 1800 V, enabling separation of five fluorescent pI markers as a demonstration example.United States. Army Research Office (Grant Number: W911NF-07-D-0004)National Institutes of Health (U.S.) (Grant Number: GM68762
Simultaneous analysis of multiple PCR amplicons enhances capillary SSCP discrimination of MHC alleles

Major histocompatibility complex (MHC) genotyping still remains one of the most challenging issues for evolutionary ecologists. To date, none of the proposed methods have proven to be perfect, and all provide both important pros and cons. Although denaturing capillary electrophoresis has become a popular alternative, allele identification commonly relies upon conformational polymorphisms of two single-stranded DNA molecules at the most. Using the MHC class II (β chain, exon 2) of the black kite (Aves: Accipitridae) as our model system, we show that the simultaneous analysis of overlapping PCR amplicons from the same target region subshttps://digital.csic.es/listadoMetadatos.jsp?ID=autores&vocabulary=autores&plataforma=pasarelatantially enhances allele discrimination. To cover this aim, we designed a multiplex PCR capable to generate four differentially sized and labeled amplicons from the same allele. Informative peaks to assist allele calling then fourfold those generated by the analysis of single PCR amplicons. Our approach proved successful to differentiate all the alleles (N = 13) isolated from eight unrelated birds at a single optimal run temperature and electrophoretic conditions. In particular, we emphasize that this approach may constitute a straight-forward and cost-effective alternative for the genotyping of single or duplicated MHC genes displaying low to moderate sets of divergent alleles. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.Peer Reviewe