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Abstracts from the 4th ImmunoTherapy of Cancer Conference. J Immunother Cancer 2017. [PMCID: PMC5374589 DOI: 10.1186/s40425-017-0219-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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2
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Smartphone-based colorimetric analysis for detection of saliva alcohol concentration. APPLIED OPTICS 2015; 54:9183-9. [PMID: 26560572 DOI: 10.1364/ao.54.009183] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A simple device and associated analytical methods are reported. We provide objective and accurate determination of saliva alcohol concentrations using smartphone-based colorimetric imaging. The device utilizes any smartphone with a miniature attachment that positions the sample and provides constant illumination for sample imaging. Analyses of histograms based on channel imaging of red-green-blue (RGB) and hue-saturation-value (HSV) color space provide unambiguous determination of blood alcohol concentration from color changes on sample pads. A smartphone-based sample analysis by colorimetry was developed and tested with blind samples that matched with the training sets. This technology can be adapted to any smartphone and used to conduct color change assays.
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[Catch-up vaccination of worldwide newcoming (adopted, refugee or migrant) children in France]. Arch Pediatr 2014; 21:329-34. [PMID: 24512806 DOI: 10.1016/j.arcped.2013.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 11/16/2022]
Abstract
In France, international adoption includes around to 90,000 children since 1980 and near 300,000 immigrant children were counted in 2008. This population is heterogeneous, according to age and country of origin, and its large number. It is not easy to completely and surely assess the vaccine status of the child. Due to a great variability of individual situations, it is not possible to have systematic and unchangeable rules. This article aims to give an update of catch-up vaccination of internationally adopted or refugee or migrant children in France. The vaccination status of a child who recently arrived in France is complex and has to be adapted to his country of origin. Some of them were never vaccinated whereas the vaccine status of others is uncertain or unknown. Three parameters have to be considered: the age of the child, the country of origin, and sometimes serology in the case of doubts of his vaccine status. Catch-up vaccination of foreign children has to be adapted to French vaccine recommendations, as a reference, and to vaccines already administered to the child.
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Integrated Sample Preparation Methodology for Proteomics: Analysis of Native Proteins. Anal Chem 2013; 85:8039-45. [PMID: 23937592 DOI: 10.1021/ac401477w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics 2013; 12:2623-39. [PMID: 23689285 DOI: 10.1074/mcp.m112.027078] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.
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Intrinsic subtype-associated changes in the plasma proteome in breast cancer. Proteomics Clin Appl 2012; 3:1305-13. [PMID: 21136952 DOI: 10.1002/prca.200900040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Breast cancers are classified into five intrinsic subtypes: Luminal subtype A, Luminal subtype B, HER2+, Basal, and Normal-like. In this study, we compared the plasma proteome of patients with Luminal A, Luminal B, HER2+, and Basal subtype with plasma from healthy individuals. Protein changes were considered significant if q-value (false discovery rate) was less than 5%. The highest number of changes in the plasma proteome was observed in patients with Luminal type B followed by Basal type breast cancers. The plasma proteome of Luminal A and HER2+ breast cancer patients did not differ significantly from healthy individuals. In Basal breast cancer, a significant number of plasma proteins were downregulated compared with healthy individuals. Acute phase-response proteins α-glycoprotein orosomucoid 1 and serum amyloid protein P were specifically upregulated in the plasma of Luminal B breast cancer patients, suggesting prevalence of low-grade inflammation. Proteins involved in immune response and free radical scavenging were downregulated in the plasma of Luminal B patients, which is in agreement with defective immune system observed in cancer patients. These results reveal intrinsic subtype specific changes in the plasma proteome that may influence tumor progression as well as the systemic effects of cancer.
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Towards a Metadata Model for Mass-Spectrometry Based Clinical Proteomics. Curr Bioinform 2012. [DOI: 10.2174/157489312802460785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers. J Proteome Res 2012; 11:2508-20. [PMID: 22309216 DOI: 10.1021/pr201206w] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We used a lectin chromatography/MS-based approach to screen conditioned medium from a panel of luminal (less aggressive) and triple negative (more aggressive) breast cancer cell lines (n=5/subtype). The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which recognize fucose and sialic acid, respectively. The bound fractions were enzymatically N-deglycosylated and analyzed by LC-MS/MS. In total, we identified 533 glycoproteins, ∼90% of which were components of the cell surface or extracellular matrix. We observed 1011 glycosites, 100 of which were solely detected in ≥3 triple negative lines. Statistical analyses suggested that a number of these glycosites were triple negative-specific and thus potential biomarkers for this tumor subtype. An analysis of RNaseq data revealed that approximately half of the mRNAs encoding the protein scaffolds that carried potential biomarker glycosites were up-regulated in triple negative vs luminal cell lines, and that a number of genes encoding fucosyl- or sialyltransferases were differentially expressed between the two subtypes, suggesting that alterations in glycosylation may also drive candidate identification. Notably, the glycoproteins from which these putative biomarker candidates were derived are involved in cancer-related processes. Thus, they may represent novel therapeutic targets for this aggressive tumor subtype.
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[Current events in vaccination]. Arch Pediatr 2011; 18:1234-46. [PMID: 22019286 DOI: 10.1016/j.arcped.2011.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The annual meeting of the Infectious Disease Society of America (IDSA) ; which brought together nearly 5000 participants from over 80 countries in Vancouver, Canada, October 21 to 24, 2010 ; provided a review of the influenza (H1N1) 2009 pandemic, evaluated vaccination programmes and presented new vaccines under development. With 12,500 deaths in the United States in 2009-2010, the influenza (H1N1) 2009 pandemic was actually less deadly than the seasonal flu. But it essentially hit the young, and the toll calculated in years of life lost is high. The monovalent vaccines, whether live attenuated or inactivated with or without adjuvants, were well tolerated in toddlers, children, adults and pregnant women. In order to protect infants against pertussis, family members are urged to get their booster shots. The introduction of the 13-valent Pneumococcal conjugated vaccine in the beginning of 2010 may solve - but for how long ? - the problem of serotype replacement, responsible for the re-increasing incidence of invasive Pneumococcal infections observed in countries that had introduced the 7-valent vaccine. The efficacy of a rotavirus vaccine has been confirmed, with a reduction in hospitalization in the United States and a reduction in gastroenteritis-related deaths in Mexico. In the United States, vaccination of pre-adolescents against human papillomavirus (HPV) has not resulted in any specific undesirable effects. Routine vaccination against chicken pox, recommended since 1995, has not had an impact on the evolution of the incidence of shingles. Vaccination against shingles, recommended in the United States for subjects 60 years and over, shows an effectiveness of 55 %, according to a cohort study (Kaiser Permanente, Southern California). Although some propose the development of personalized vaccines according to individual genetic characteristics, the priority remains with increasing vaccine coverage, not only in infants but also in adults and the elderly. Vaccine calendars that cover a whole lifetime should be promoted, since the vaccination of adults and seniors is a determining factor of good health at all ages.
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Abstract
Cyclin dependent kinase-5 (Cdk5) activity is deregulated in Alzheimer's disease (AD) and contributes to all three hallmarks: neurotoxic β-amyloid formation, neurofibrillary tangles, and neuronal death. However, the mechanism leading to Cdk5 deregulation remains controversial. Cdk5 deregulation in AD is usually linked to the formation of p25, a proteolysis product of Cdk5 activator p35, which leads to Cdk5 mislocalization and hyperactivation. A few studies have indeed shown increased p25 levels in AD brains; however, others have refuted this observation. These contradictory findings suggest that additional factors contribute to Cdk5 deregulation. This study identified glutathione-S-transferase pi 1 (GSTP1) as a novel Cdk5 regulatory protein. We demonstrate that it is a critical determinant of Cdk5 activity in human AD brains and various cancer and neuronal cells. Increased GSTP1 levels were consistently associated with reduced Cdk5 activity. GSTP1 directly inhibits Cdk5 by dislodging p25/p35, and indirectly by eliminating oxidative stress. Cdk5 promotes and is activated by oxidative stress, thereby engaging a feedback loop which ultimately leads to cell death. Not surprisingly, GSTP1 transduction conferred a high degree of neuroprotection under neurotoxic conditions. Given the critical role of oxidative stress in AD pathogenesis, an increase in GSTP1 level may be an alternative way to modulate Cdk5 signaling, eliminate oxidative stress, and prevent neurodegeneration.
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11
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Effect of different green tea formulations on diabetes in the Zucker Diabetic Rat. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.729.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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GAPDH is conformationally and functionally altered in association with oxidative stress in mouse models of amyotrophic lateral sclerosis. J Mol Biol 2008; 382:1195-210. [PMID: 18706911 DOI: 10.1016/j.jmb.2008.07.088] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 07/15/2008] [Accepted: 07/30/2008] [Indexed: 11/26/2022]
Abstract
It is proposed that conformational changes induced in proteins by oxidation can lead to loss of activity or protein aggregation through exposure of hydrophobic residues and alteration in surface hydrophobicity. Because increased oxidative stress and protein aggregation are consistently observed in amyotrophic lateral sclerosis (ALS), we used a 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (BisANS) photolabeling approach to monitor changes in protein unfolding in vivo in skeletal muscle proteins in ALS mice. We find two major proteins, creatine kinase (CK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), conformationally affected in the ALS G93A mouse model concordant with a 43% and 41% reduction in enzyme activity, respectively. This correlated with changes in conformation and activity that were detected in CK and GAPDH with in vitro oxidation. Interestingly, we found that GAPDH, but not CK, is conformationally and functionally affected in a longer-lived ALS model (H46R/H48Q), exhibiting a 22% reduction in enzyme activity. We proposed a reaction mechanism for BisANS with nucleophilic amino acids such as lysine, serine, threonine, and tyrosine, and BisANS was found to be primarily incorporated to lysine residues in GAPDH. We identified the specific BisANS incorporation sites on GAPDH in nontransgenic (NTg), G93A, and H46R/H48Q mice using liquid chromatography-tandem mass spectrometry analysis. Four BisANS-containing sites (K52, K104, K212, and K248) were found in NTg GAPDH, while three out of four of these sites were lost in either G93A or H46R/H48Q GAPDH. Conversely, eight new sites (K2, K63, K69, K114, K183, K251, S330, and K331) were found on GAPDH for G93A, including one common site (K114) for H46R/H48Q, which is not found on GAPDH from NTg mice. These data show that GAPDH is differentially affected structurally and functionally in vivo in accordance with the degree of oxidative stress associated with these two models of ALS.
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Identification of oxidized proteins in rat plasma using avidin chromatography and tandem mass spectrometry. Proteomics 2008. [DOI: 10.1002/pmic.200890044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Protein:protein aggregation induced by protein oxidation. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 873:8-14. [PMID: 18760979 DOI: 10.1016/j.jchromb.2008.04.025] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 04/01/2008] [Accepted: 04/13/2008] [Indexed: 10/22/2022]
Abstract
When the level of reactive oxygen species (ROS) in cells exceeds a genetically coded defense capacity, the cells experience damage to vital components such as DNA, proteins and lipids that leads to non-specific interactions and the production of a series of high molecular weight protein aggregates. The dynamics of oxidative stress induced aggregation were studied here using model proteins and yeast. Model proteins were oxidized at increasing ROS concentrations and analyzed using size exclusion chromatography (SEC). Changes in the SEC elution profile showed that aggregation happens in stages and protein fragments produced as a result of oxidation also give rise to aggregates. Yeast cells were stressed with hydrogen peroxide to investigate in vivo aggregation. Equal amounts from control and oxidized lysates were chromatographed on a size exclusion column and proteins of molecular weight exceeding 700 kDa were collected from both samples which were then differentially labeled using light and heavy isotope coded N-acetoxysuccinamide and mixed in a 1:1 ratio. The coded mixture was analyzed using LC/MS and peptides that appeared as singlets representing the proteins that aggregated with higher molecular mass protein complexes were identified. Twenty-five proteins were identified to be of this type. Fifteen members in this group were found to have been carbonylated. These proteins are part of the proteome known as the aggresome. The protein content of the aggresome may provide vital information for mechanistic studies targeting disease and aging.
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Identification of oxidized proteins in rat plasma using avidin chromatography and tandem mass spectrometry. Proteomics 2008; 8:1516-27. [DOI: 10.1002/pmic.200700363] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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16
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Abstract
Common-path differential phase-contrast interferometry measures the spatial gradient of surface dipole density on a bio-optical compact disk (BioCD) and is sensitive to small changes in dipole density following molecular binding of target molecules out of solution. The recognition molecules are antibody IgG proteins that are deposited in periodic patterns on the BioCD using soft lithography or photolithography on the silanized silica surfaces of dielectric mirrors. Spatial carrier-wave sideband demodulation extracts the slowly varying protein envelope that modulates the protein carrier frequency. The experimental interferometric profilometry has surface height sensitivity down to 20 pm averaged over a lateral scale of 70 microm with a corresponding scaling mass sensitivity limit of 1.5 pg/mm. Under the conditions of an IgG immunoassay with background changes caused during incubation, the scaling mass sensitivity is approximately 7 pg/mm. A saturated reverse immunoassay performed with IgG at 100 ng/ml showed false positive and false negative rates of 0.2%.
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Abstract
Living systems have efficient degradative pathways for dealing with the fact that reactive oxygen species (ROS) derived from cellular metabolism and the environment oxidatively damage proteins and DNA. But aggregation and cross-linking can occur as well, leading to a series of problems including disruption of cellular regulation, mutations, and even cell death. The mechanism(s) by which protein aggregation occurs and the macromolecular species involved are poorly understood. In the study reported here, evidence is provided for a new type of aggregate between proteins and RNA in ribosomes. While studying the effect of oxidative stress induced in the yeast proteome it was noted that ribosomal proteins were widely oxidized. Eighty six percent of the proteins in yeast ribosomes were found to be carbonylated after stressing yeast cell cultures with hydrogen peroxide. Moreover, many of these proteins appeared to be cross-linked based on their coelution patterns during RPC separation. Since they were not in direct contact, it was not clear how this could occur unless it was through the RNA separating them in the ribosome. This was confirmed in a multiple-step process, the first being derivatization of all carbonylated proteins in cell lysates with biotin hydrazide through Schiff base formation. Following reduction of Schiff bases with sodium cyanoborohydride, biotinylated proteins were selected from cell lysates with avidin affinity chromatography. Oxidized proteins thus captured were then selected again using boronate affinity chromatography to capture vicinal diol-containing proteins. This would include proteins cross-linked to an RNA fragment containing a ribose residue with 2',3'-hydroxyl groups. Some glycoproteins would also be selected by this process. LC/MS/MS analyses of tryptic peptides derived from proteins captured by this process along with MASCOT searches resulted in the identification of 37 ribosomal proteins that appear to be cross-linked to RNA. Aggregation of proteins with ribosomal RNA has not been previously reported. The probable impact of this phenomenon cells is to diminish the protein synthesis capacity.
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Identification of yeast oxidized proteins: chromatographic top-down approach for identification of carbonylated, fragmented and cross-linked proteins in yeast. J Chromatogr A 2006; 1141:22-31. [PMID: 17188699 DOI: 10.1016/j.chroma.2006.11.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 11/01/2006] [Accepted: 11/02/2006] [Indexed: 11/29/2022]
Abstract
The effects of oxidative stress on the yeast proteome were studied using hydrogen peroxide as the stress agent. Oxidized proteins were isolated by (1) biotinylation of oxidized proteins with biotin hydrazide, (2) affinity selection using monomeric avidin affinity chromatography, and (3) further fractionated by reversed-phase liquid chromatography (RPLC) on a C(8) column. Oxidized protein fractions from RPLC were then trypsin digested and the peptide cleavage fragments identified by tandem mass spectrometry (MS/MS). Slightly over 400 proteins were identified. Sites of carbonyl formation were found in roughly one fourth of these proteins. Oxidation on other amino acids in carbonylated peptides was seen in 32 cases while carbonylation was absent in 96 of the oxidized proteins observed. Although there are large numbers of potential oxidation sites, oxidation seemed to be restricted to a small area in most of the proteins identified. Sometimes multiple amino acids in the same tryptic peptide were oxidized. A second trend was that more than 8% of the proteins identified appeared in more than one of the RPLC fractions. Based on the position of the peptides identified in the primary structure of protein candidates derived from databases it was concluded that this occurred by fragmentation of a parent protein. It is not clear from the data whether the fragmentation process was of enzymatic or oxidative origin. Finally, peptides from two or more proteins occurred together in more than one reversed phase fraction with 2% of the proteins identified. This data was interpreted to mean that this was the result of protein cross-linking.
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Abstract
Abstract
Background: We describe a direct-detection immunoassay that uses high-speed optical interferometry on a biological compact disc (BioCD).
Methods: We fabricated phase-contrast BioCDs from 100-mm diameter 1.1-mm thick borosilicate glass disks coated with a 10-layer dielectric stack of Ta2O5/SiO2 that serves as a mirror with a center wavelength at 635 nm. The final layer is a λ/4 layer of SiO2 onto which protein patterns are immobilized through several different chemical approaches. Protein on the disc is scanned by a focused laser spot as the disc spins. Interaction of the light with the protein provides both a phase-modulated signal and a local reference that are combined interferometrically to convert phase into intensity. A periodic pattern of protein on the spinning disc produces an intensity modulation as a function of time that is proportional to the surface-bound mass. The binding of antigen or antibodies is detected directly, without labels, by a change in the interferometric intensity. The technique is demonstrated with a reverse assay of immobilized rabbit and mouse IgG antigen incubated against anti-IgG antibody in a casein buffer.
Results: The signal increased with increased concentration of analyte. The current embodiment detected a concentration of 100 ng/L when averaged over ∼3000 100-micron-diameter protein spots.
Conclusions: High-speed interferometric detection of label-free protein assays on a rapidly spinning BioCD is a high-sensitivity approach that is amenable to scaling up to many analytes.
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Identification and quantification of protein carbonylation using light and heavy isotope labeled Girard's P reagent. J Chromatogr A 2006; 1134:122-33. [PMID: 16996067 DOI: 10.1016/j.chroma.2006.08.096] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2006] [Revised: 08/21/2006] [Accepted: 08/30/2006] [Indexed: 11/22/2022]
Abstract
Protein carbonyls are one of the most widely studied markers of oxidative stress. Determining increases in the concentration of protein carbonyls known to be associated with neurodegenerative diseases, heart disease, cancer and ageing. Identification of carbonylation sites in oxidized proteins has been a challenge. Even though recent advances in proteomics has facilitate the identification of carbonylation sites in oxidized proteins, confident identification remains a challenge due to the complicated nature of oxidative damage and the wide range of oxidative modifications. Here, we report the development of a multiplexing strategy that facilitates confident carbonylated peptide identification through a combination of heavy and light isotope coding and a multi-step filtering process. This procedure involves (1) labeling aliquots of oxidized proteins with heavy and light forms of Girard's reagent P (GPR) and combining them in a 1:1 ratio along with (2) LC/MS and MALDI-MS/MS analysis. The filtering process uses LC/MS and MALDI-MS/MS data to rule out false positives by rejecting peptide doublets that do not appear with the correct concentration ratio, retention time, tag number, or resolution. This strategy was used for the identification of heavily oxidized transferrin peptides and resulted in identification 13 distinct peptides. The competency of the method was validated in a complex mixture using oxidized transferrin in a yeast lysate as well as oxidized yeast. Twenty-five percent of the peptides identified in a pure oxidized sample of transferrin were successfully identified from the complex mixture. Analysis of yeast proteome stressed with hydrogen peroxide using this multiplexing strategy resulted in identification of 41 carbonylated peptides from 36 distinct proteins. Differential isotope coding of model peptides at different concentrations followed by mixing at different ratios was used to establish the linear dynamic range for quantification of carbonylated peptides using light and heavy forms of GPR.
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Abstract
Oxidative stress is a factor in a series of diseases and aging, primarily through irreversible oxidative modification of proteins. A major question is how nonenzymatic oxidation has the specificity to impact cellular regulation. Here, we report the degree to which in vivo protein oxidation to the ketone and aldehyde level is random using yeast as a simple model system and hydrogen peroxide as an environmental oxidative stress agent. Among 415 affinity-selected proteins identified throughout the matrix of stressed cells, oxidation sites were found in 87, predominantly on lysine, arginine, proline, histidine, threonine, and methionine residues. In almost all cases, one to two specific oxidation sites on the exterior of proteins were identified using MS-derived sequence and publicly available 3-D structural data. This suggests that, when regulation or disease progression is mediated by protein oxidation, specific new "allotypic active sites" are being created in proteins that trigger the process.
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Abstract
With the advent of electrospray ionization mass spectrometry, the world was given a new way to look at complex peptide mixtures. Identification of proteins via their signature peptides requires ionization of a representative portion of the peptides derived from proteins by proteolysis. Unfortunately, matrix effects prohibited electrospray ionization of many peptides. This paper describes the development of a new labeling reagent that simultaneously adds a permanent positive charge to peptides and increases their hydrophobicity to enhance their ionization efficiency. The labeling agent is preactivated with N-hydroxysuccinimide to react with primary amines to form a peptide bond. In the most dramatic case, ionization efficiency of the peptide ADRDQYELLCLDNTRKPVDEYK increased 500-fold after derivatization as opposed to other peptides where ionization efficiency was impacted little. Ionization efficiency of peptides was enhanced roughly 10-fold in general by derivatization. Peptides of less than 500 Da experienced the greatest increase in ionization efficiency by derivatization. Poor ionization efficiency of native peptides was found to be due more to their inherent structural properties than the matrix in which ionization occurs.
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Identification of Rotenone-Induced Modifications in α-Synuclein Using Affinity Pull-Down and Tandem Mass Spectrometry. Anal Chem 2006; 78:2422-31. [PMID: 16579629 DOI: 10.1021/ac051978n] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Parkinson's disease is a movement disorder that results from a loss of dopaminergic neurons in the substantia nigra. The disease is characterized by mitochondrial dysfunction, oxidative stress, and the presence of "Lewy body" inclusions enriched with aggregated forms of alpha-synuclein, a presynaptic protein. Although alpha-synuclein is modified at various sites in Lewy bodies, it is unclear how sequence-specific posttranslational modifications modulate the aggregation of the protein in oxidatively stressed neurons. To begin to address this problem, we developed an affinity pull-down/mass spectrometry method to characterize the primary structure of histidine-tagged alpha-synuclein isolated from catecholaminergic neurons. Using this method, we mapped posttranslational modifications of alpha-synuclein from untreated neurons and neurons exposed to rotenone, an inhibitor of mitochondrial complex I. Various posttranslational modifications suggestive of oxidative damage or repair were identified in a region comprising a 20-residue stretch in the C-terminal part of the protein. The results indicate that alpha-synuclein is subject to discrete posttranslational modifications in neurons with impaired mitochondrial function. Our affinity pull-down/mass spectrometry method is a useful tool to examine how specific modifications of alpha-synuclein contribute to neurologic disorders such as Parkinson's disease.
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Enrichment of Carbonylated Peptides Using Girard P Reagent and Strong Cation Exchange Chromatography. Anal Chem 2005; 78:770-8. [PMID: 16448050 DOI: 10.1021/ac0514220] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has been shown that oxidatively modified forms of proteins accumulate during oxidative stress, aging, and in some age-related diseases. One of the unique features of protein oxidation by a wide variety of routes is the generation of carbonyl groups. Of major interest in the study of oxidative stress diseases is which proteins in a proteome are being oxidized and the site(s) of oxidation. Based on the fact that proteins are generally characterized through tryptic peptide fragments, this paper reports a method for the isolation of oxidized peptides, which involves (1) derivatization of oxidized proteins with Girard P reagent (GRP; 1-(2-hydrazino-2-oxoethyl)pyridinium chloride), (2) following proteolysis enrichment of the derivatized peptide using strong cation exchange (SCX) chromatography, and (3) identification of oxidation sites using tandem mass spectrometry. Derivatization of aldehydes and ketones in oxidized proteins was accomplished by reacting protein carbonyls with the hydrazide of GRP. The resulting hydrazone bond was reduced by sodium cyanoborohydride to further stabilize the labeling. Derivatization time and concentrations of the derivatizing agent were optimized with model peptides. Oxidized transferrin was used as model protein to study derivatization efficiency at the protein level. Following metal-catalyzed oxidation of transferrin, the protein was derivatized with GRP and trypsin digested. Positively charged peptides were then selected from the digest with SCX chromatography at pH 6.0. Seven GRP-derivatized peptides were found to be selected from transferrin by MALDI-TOF-TOF analysis. Fourteen underivatized native peptides were also captured by the SCX column at pH 6.0. Mapping of the derivatized peptides onto the primary structure of transferrin indicated that the oxidation sites were all on solvent-accessible regions at the protein surface. Efficiency of the method was further demonstrated in the identification of oxidized proteins from yeast.
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Affinity Chromatographic Selection of Carbonylated Proteins Followed by Identification of Oxidation Sites Using Tandem Mass Spectrometry. Anal Chem 2005; 77:2386-92. [PMID: 15828771 DOI: 10.1021/ac0484373] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It has been shown that oxidatively modified forms of proteins accumulate during oxidative stress, aging, and in some age-related diseases. One of the unique features of a wide variety of routes by which proteins are oxidized is the generation of carbonyl groups. This paper reports a method for the isolation of oxidized proteins, which involves (1) biotinylation of oxidized proteins with biotin hydrazide and (2) affinity enrichment using monomeric avidin affinity chromatography columns. The selectivity of the method was validated by adding in vitro oxidized biotinylated BSA to a yeast lysate and showing that the predominant protein recovered was BSA. This method was applied to the question of whether large doses of 2-nitropropane produce oxidized proteins. A study of rat liver homogenates showed that animals dosed with 2-nitropropane produced 17 times more oxidized protein than controls in 6 h. Tryptic digestion of these oxidized proteins followed by reversed-phase chromatography and tandem mass spectrometry led to the identification of 14 peptides and their parent proteins. Nine of the 14 identified peptides were found to carry 1 or 2 oxidation sites and 5 of the 9 peptides were biotinylated. The significance of this affinity method is that it allows the isolation of oxidized proteins from the rest of the proteome and facilitates their identification. In some cases, it is even possible to identify the site of oxidation.
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Structure specific chromatographic selection in targeted proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 817:23-34. [PMID: 15680786 DOI: 10.1016/j.jchromb.2004.08.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 08/18/2004] [Indexed: 11/21/2022]
Abstract
The whole proteome of any organism is too complicated to be analyzed in a simple one-step process and direct attempts for the entire proteome analysis normally lead to considerable loss of information. A practical approach is the targeting of the specific structural feature of interest using chromatography. This approach simplifies the proteome while preserving most of the vital information necessary for analysis. Selection of peptides with specific amino acids (cysteine, histidine and methionine) or N- or C-terminal peptides is an accepted procedure for proteome simplification when general analysis is desired. While selection of enzymatically and non-enzymatically modified proteins and peptides is used when post-translational modifications are targeted. Protein interaction with small molecules as well as other proteins also has been studied using chromatographic selection methods.
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Abstract
INTRODUCTION In order to evaluate the efficacy of 131 Iodine on goitre volume and on thyroid function, we studied a cohort of patients exhibiting a multinodular and toxic or non toxic goitre. METHODS This retrospective study was conducted at the Marc Linquette clinic in Lille, in collaboration with the department of nuclear medicine. Thirty-eight patients treated with 131 Iodine were included from 1995 to 2001. Clinical examination and serum analyses including TSH, free T4 and T3, anti-thyroid peroxidase and anti-thyroglobulin antibodies and TSH-receptor antibodies measurements were conducted on inclusion and then at 3, 6, 12 and 72 months. The activity of 131 Iodine corresponded to a standard dose or was calculated according to Marinelli's method. We excluded patients who had not undergone assessment at the above-mentioned time schedules. RESULTS The treatment was indicated in 30 patients presenting with a non compressive but toxic goitre, in 5 patients with a toxic compressive goitre and in 3 patients with a compressive but non-toxic goitre. Surgery had been excluded for all these patients because of their age, their cardiac status or because they had refused surgery after failure with prior partial thyroidectomy or medical treatment. Among the toxic goitres, TSH levels were low and T3 and T4 increased in 17 patients. In the 18 others, hyperthyroidism was manifested by an isolated decrease of TSH. The thyroid volume before treatment, assessed in 20 patients, was of 18 to 135 cm3 (mean: 53 cm3). Treatment consisted in administration of radioactivity of 3 to 30 mCi in 30 patients and standard activity of 20 to 25 mCi in 8. Functional efficacy with reduction in hyperthyroidism was noted after 3 months, and corrected in nearly all patients after 1 year, and morphological efficacy, with a mean decrease of 33.5% in the size of the goitres. No supplementary surgery was required, notably for the initially compressed goitres. Immediate and long term tolerance was satisfactory. CONCLUSION Metabolic 131Iodine radiotherapy is effective for the functional and morphological treatment of goitres with good tolerance and few side effects. 131 Iodine is a reasonable alternative in cases with absolute or relative contraindication for surgery.
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Abstract
Lectins have been widely used in glycan structure analysis. The studies described here exploit this fact to select glycopeptides carrying disease-associated modifications in their oligosaccharides. Coupling lectin affinity selection with recent advances in stable isotope coding for quantitative proteomics allowed a comparative proteomics method to be developed for examining aberrant glycosylation in cancer. Control and experimental samples were individually tryptic digested and differentially coded with stable isotope coding agents before they were mixed and affinity selected with a lectin affinity chromatography column. Glycopeptides carrying an alpha-L-fucose residue were selected with Lotus tetragonolobus agglutinin (LTA) immobilized on a chromatography matrix. Because the oligosaccharides of glycoproteins are generally heterogeneous and often of unknown structure, it was necessary to deglycosylate the selected peptides with PNGase F before they could be compared to sequences in DNA and protein databases. After deglycosylated peptides were transferred to a reversed phase chromatography (RPC) column and fractionated by gradient elution with increasing amounts of acetonitrile. The RPC fractions were then analyzed by both matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS). When this method was applied to a study of lymphosarcoma in canines, it was found that during chemotherapy, a series of fucosylated proteins in the blood of patients decreased in concentration more than 2-fold. Two of the proteins identified, CD44 and E-selectin, are known to be involved in cell adhesion and cancer cell migration. The observed aberrant fucosylation of these proteins is consistent with the hypothesis that CD44 and E-selectin play a key role in metastasis and the spread of cancer cells to remote sites.
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Abstract
This review focuses on techniques for quantification and identification in proteomics by stable isotope coding. Methods are examined for analyzing expression, post-translational modifications, protein:protein interactions, single amino acid polymorphism, and absolute quantification. The bulk of the quantification literature in proteomics focuses on expression analysis, where a wide variety of methods targeting different features of proteins are described. Methods for the analysis of post-translational modification (PTM) focus primarily on phosphorylation and glycosylation, where quantification is achieved in two ways, either by substitution or tagging of the PTM with an isotopically coded derivatizing agent in a single process or by coding and selecting PTM modified peptides in separate operations. Absolute quantification has been achieved by age-old internal standard methods, in which an isotopically labeled isoform of an analyte is synthesized and added to a mixture at a known concentration. One of the surprises is that isotope coding can be a valuable aid in the examination of intermolecular association of proteins through stimulus:response studies. Preliminary efforts to recognize single amino acid polymorphism are also described. The review ends with the conclusion that (1) isotope ratio analysis of protein concentration between samples does not necessarily relate directly to protein expression and rate of PTM and (2) that multiple new methods must be developed and applied simultaneously to make existing stable isotope quantification methods more meaningful. Although stable isotope coding is a powerful, wonderful new technique, multiple analytical issues must be solved for the technique to reach its full potential as a tool to study biological systems.
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Integrative Biological Analysis of the APOE*3-Leiden Transgenic Mouse. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2004; 8:3-13. [PMID: 15107233 DOI: 10.1089/153623104773547453] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Integrative (or systems biology) is a new approach to analyzing biological entities as integrated systems of genetic, genomic, protein, metabolite, cellular, and pathway events that are in flux and interdependent. Here, we demonstrate the application of intregrative biological analysis to a mammalian disease model, the apolipoprotein E3-Leiden (APO*E3) transgenic mouse. Mice selected for the study were fed a normal chow diet and sacrificed at 9 weeks of age-conditions under which they develop only mild type I and II atherosclerotic lesions. Hepatic mRNA expression analysis showed a 25% decrease in APO A1 and a 43% increase in liver fatty acid binding protein expression between transgenic and wild type control mice, while there was no change in PPAR-alpha expression. On-line high performance liquid chromatography-mass spectrometry quantitative profiling of tryptic digests of soluble liver proteins and liver lipids, coupled with principle component analysis, enabled rapid identification of early protein and metabolite markers of disease pathology. These included a 44% increase in L-FABP in transgenic animals compared to controls, as well as an increase in triglycerides and select bioactive lysophosphatidylcholine species. A correlation analysis of identified genes, proteins, and lipids was used to construct an interaction network. Taken together, these results indicate that integrative biology is a powerful tool for rapid identification of early markers and key components of pathophysiologic processes, and constitute the first application of this approach to a mammalian system.
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Evaluating immobilized metal affinity chromatography for the selection of histidine-containing peptides in comparative proteomics. J Proteome Res 2003. [PMID: 12814271 DOI: 10.1021/pr034006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Agarose based immobilized metal affinity chromatography (IMAC) columns loaded with copper (II) were evaluated for the selection of histidine-containing peptides in comparative proteomics. Recovery, binding specificity, and reproducibility were investigated with model proteins. Cu(II)-IMAC was found to be highly selective for histidine containing peptides; moreover, a low degree of nonspecific selection was observed. Acylation of the amino-terminus of peptides with either succinic anhydride, N-acetoxysuccinamide, or [3-(2,5)-dioxopyrrolidin-1-yloxycarbonyl)-propyl]-trimethylammonium (quaternary amine) reduced the number of histidine-containing peptides bound by the Cu(II)-IMAC columns. This provides an additional possibility for sample simplification in proteomic applications. The number of acylated peptides selected decreased in the order of quaternary amine > N-acetoxysuccinamide > succinic anhydride derivatization. Although the selection of N-terminally derivatized peptides is biased toward peptides that contain more than one histidine, it is not yet possible to predict selectivity.
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Evaluating immobilized metal affinity chromatography for the selection of histidine-containing peptides in comparative proteomics. J Proteome Res 2003; 2:321-9. [PMID: 12814271 DOI: 10.1021/pr034006+] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Agarose based immobilized metal affinity chromatography (IMAC) columns loaded with copper (II) were evaluated for the selection of histidine-containing peptides in comparative proteomics. Recovery, binding specificity, and reproducibility were investigated with model proteins. Cu(II)-IMAC was found to be highly selective for histidine containing peptides; moreover, a low degree of nonspecific selection was observed. Acylation of the amino-terminus of peptides with either succinic anhydride, N-acetoxysuccinamide, or [3-(2,5)-dioxopyrrolidin-1-yloxycarbonyl)-propyl]-trimethylammonium (quaternary amine) reduced the number of histidine-containing peptides bound by the Cu(II)-IMAC columns. This provides an additional possibility for sample simplification in proteomic applications. The number of acylated peptides selected decreased in the order of quaternary amine > N-acetoxysuccinamide > succinic anhydride derivatization. Although the selection of N-terminally derivatized peptides is biased toward peptides that contain more than one histidine, it is not yet possible to predict selectivity.
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Abstract
The commonly used gated injection scheme was examined and found to suffer from multiple levels of electrokinetic sampling bias, including a new type based on transradial electrokinetic selection (TREKS). TREKS occurs as analytes of differing electrophoretic mobilities migrate around the corner at a channel junction in a microchip. The overall sample bias in gated injection was shown to be time-dependent and resulted in a larger sample bias against components of negative electrophoretic mobility. A new injection procedure for microchip devices based on interstream diffusion at zero potential is proposed. Diffusion of molecules into the separation channel is the main driving force for this type of injection. The new scheme is shown to be useful for injection of complex samples with multiply charged components, such as peptide mixtures. This procedure allows sampling of volumes from 12 to 45 pL, reproducible retention times (RSD < 1.5%), and reproducible peak areas (RSD < 2.3%).
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Nanoliter capillary electrochromatography columns based on collocated monolithic support structures molded in poly(dimethyl siloxane). Electrophoresis 2001; 22:3736-43. [PMID: 11699912 DOI: 10.1002/1522-2683(200109)22:17<3736::aid-elps3736>3.0.co;2-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Following current trends in miniaturization of analytical chemistry, an inexpensive disposable analytical tool in the form of a liquid chromatography column fabricated on a poly(dimethyl siloxane) (PDMS) chip was created. Ease of fabricating the chromatography column was demonstrated by molding collocated monolithic support structures (COMOSS) directly in the column. Positive photo-resist, SPR 220, was used to create column structures on a negative relief master providing final channel dimensions of 2.7-5.2 microm wide by 10.0 microm deep, while monolithic dimensions were 9.8 x 9.8 x 10.0 microm - 12.3 x 12.3 x 10.0 microm. The ability to separate biological samples such as peptides from a tryptic digest of fluorescein isothiocyanate labeled bovine serum albumin (FITC-BSA) was shown. Separations in capillary electrochromatographic (CEC) mode were performed yielding column efficiencies of 4.0 x 10(5) plates/m.
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Proteomics of glycoproteins based on affinity selection of glycopeptides from tryptic digests. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 752:293-306. [PMID: 11270868 DOI: 10.1016/s0378-4347(00)00550-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Identification of glycoproteins in complex mixtures derived from either human blood serum or a cancer cell line was achieved in a process involving the steps of (1) reduction and alkylation, (2) proteolysis of all proteins in the mixture with trypsin, (3) affinity chromatographic selection of the glycopeptides with an immobilized lectin, (4) direct transfer of the glycopeptide fraction to a reversed-phase liquid chromatography (RPLC) column and further fractionation by gradient elution, (5) matrix-assisted laser desorption ionization mass spectrometry of individual fractions collected from the RPLC column, and (6) peptide identification based on a database search. The types of glycoproteins analyzed were; (1) N-type glycoproteins of known primary structure, (2) N-type glycoproteins of unknown structure, and (3) O-type glycoproteins glycosylated with a single N-acetylglucosamine. Identification of peptides from complex mixtures was greatly facilitated by either C-terminal sequencing with a carboxypeptidase mixture or by comparing chromatographic behavior and mass to standards, as in the case of a known protein. In addition, deglycosylation of peptides with N glycosidase F was necessary to identify N-type glycoproteins of unknown structure. The strength of this approach is that it is fast and targets specific molecular species or classes of glycoproteins for identification. The weakness is that it does not discriminate between glycoforms.
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Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2000; 745:197-210. [PMID: 10997715 DOI: 10.1016/s0378-4347(00)00192-4] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper describes a new analytical strategy for identifying proteins in concentration flux based on isotopic labeling peptides in tryptic digests. Primary amino groups in peptides from control and experimental samples were derivatized with acetate and trideuteroacetate, respectively. After mixing samples thus labeled from these two sources, the relative concentration of peptides was determined by isotope ratio analysis with MALDI and ESI mass spectrometry. More than a 100-fold difference in relative concentration could be detected. Simplification of complex tryptic digests prior to mass spectral analysis was achieved by selection of histidine-containing peptides with immobilized metal affinity sorbents or of glycopeptides by lectin columns. Because most of these peptides have sequences that are unique to a single protein, they are a signature of the protein from which they were derived; providing a facile route to protein analysis.
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Abstract
Solvent and reagent filters were micromachined into quartz wafers using deep reactive ion etching to create a network of intersecting 1.5 x 10 microns channels. When placed at the bottom of reservoirs with a side exit, this channel network behaved as a lateral percolation filter composed of an array of cubelike structures one layer deep. Flow through these filters was driven by electroosmotic flow (EOF). Silanol groups at the walls of channels in the network provided the requisite charge to trigger EOF when voltage was applied laterally to the filter. Adsorption of cationic proteins in this silanol-rich matrix was controlled by the application of a polyacrylamide coating prepared by bonding N-hydroxysuccinimide (NHS)-activated poly(acrylic acid) to (gamma-aminopropyl)silane-derivatized filters. Subsequent reaction of residual NHS groups in the coating with 2-(2-aminoethoxy)ethanol provided channels of low charge density and adsorptivity. These lateral percolation filters were shown to be efficacious in filtering solvents containing a variety of particulate materials, ranging from dust to cells.
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Characterization of peroxidase:anti-peroxidase immune complexes by capillary zone electrophoresis and high-performance size-exclusion chromatography. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 724:275-80. [PMID: 10219668 DOI: 10.1016/s0378-4347(98)00575-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determination of the molecular constituents of commercial peroxidase:anti-peroxidase (PAP) preparations is necessary for the proper interpretation of PAP applications based on competitive binding assay. Capillary zone electrophoresis with field 300 V/cm, 40 cm capillary length (20 cm effective length), and high-performance size exclusion chromatography equipped with Superose 12 HR10/30 column revealed that a PAP preparation used for Fc gamma receptor studies contained multiple sizes of immune complexes, an excess amount of free peroxidase, and little or no free anti-peroxidase antibody. The antibody:antigen ratios of the three major immune complex components were 2:2, 1:2, and 1:1. These techniques provide useful methods of qualitative, as well as quantitative analysis of PAP preparations.
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Abstract
This paper shows that in situ micromachining can be used to simultaneously position and define (i) support particles, (ii) convective transport channels, (iii) an inlet distribution network of channels, and (iv) outlet channels in multiple chromatography columns on a single quartz wafer to the level of a few tenths of a micrometer. Stationary phases were bonded to 5 x 5 x 10 microns collocated monolith support structures separated by rectangular channels 1.5 microns wide and 10 microns deep with a low degree of deviation of channel width between the top and bottom of channels. High aspect ratio microfabrication can only be achieved with deep reactive ion etching. The volume of a 150 microns x 4.5 cm column was 18 nL. Column efficiency was evaluated in the capillary electrochromatography (CEC) mode using rhodamine 123 and a hydrocarbon stationary phase. Plate heights in these columns were typically 0.6 micron in the nonretained and 1.3 microns in the retained modes of operation. Columns were designed to have identical mobile-phase velocity in all channels in an effort to minimize outgassing during operation. When the total lateral cross-sectional area of channels at all points along the separation axis is identical, linear velocity of the mobile phase in a CEC column should be the same. Columns were operated at atmospheric pressure.
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Abstract
There is great interest today in massively parallel analytical strategies as a way to accelerate the rate of discovery in biological research; among them being 'biochips' and 'laboratories-on-a-chip'. The concept in the 'chip' approach is that minaturization will allow large numbers of operations to be performed in parallel in a small space, as in electronics. Proceeding with the semiconductor analogy, this paper demonstrates that in situ micromachining can be used to simultaneously fabricate millions of micrometer size, particle like structures in multiple liquid chromatography columns on a single wafer. Reduction of this widely used bioanalytical tool to the nanoliter volume, parallel processing, chip format is a significant step toward laboratories-on-a-chip.
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Monoclonal antibody production with on-line harvesting and process monitoring. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1998; 707:257-65. [PMID: 9613958 DOI: 10.1016/s0378-4347(97)00472-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A semi-automated system has been designed for on-line harvesting and monitoring of monoclonal antibody (mAb) production. [The antibody was directed against the peptide AGPAGTGKTTKDL.] Analytical and purification units were interfaced to the fermenter via a hollow fiber cartridge in which fermentation broth was continuously circulated through the lumen of the hollow fiber system. Permeate from the hollow fiber cartridge was pumped through either an analytical sampling loop or a preparative Protein G column where antibody species were captured. Switching between monitoring and harvesting was achieved by two 3-way toggle valves. Samples from the analytical sampling loop were transported to an analytical Protein G chromatography column for quantitation of all immunoglobulin G species in the fermenter. Data acquisition and processing was performed by the data system of the liquid chromatograph. All valves in the system except the two toggle valves were controlled by the liquid chromatograph. Antibody biosynthesis was monitored for the first 60 h of fermentation. Harvesting was initiated when mAb accumulated in the fermenter. Complete harvesting took approximately 90 h.
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Abstract
The synthesis of structural analogs and the process of drug discovery have evolved dramatically through recent advances in solid-phase synthesis reagents and automated screening systems. As molecular diversity strategies emerge, the need for automated target-based selection of lead candidates becomes equally important. Multidimensional automated chromatographic techniques coupled to electrospray ionization mass spectrometry facilitate the selection process and provide maximum characterization information in a single screening run. The capture of tightly bound affinity leads by target biomolecules, followed by subsequent release and high-resolution separation with sensitive detection, significantly reduces the time required to identify and characterize lead compounds. This automated multidimensional chromatographic approach coupled with mass spectrometry, Selectronics, was used with several organic and natural libraries to demonstrate an automated target-based screening technique to select for high-affinity binders as potential lead compounds.
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Future potential of targeted component analysis by multidimensional liquid chromatography-mass spectrometry. J Chromatogr A 1996; 750:3-10. [PMID: 8938379 DOI: 10.1016/0021-9673(96)00638-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Multidimensional liquid chromatography (MDLC) may be used in either (i) the profiling mode where it is the objective to fractionate all components in a mixture or (ii) the targeted component mode in which it is the objective to determine specific analytes. This paper focuses on targeted component analysis from complex mixtures, addressing the critical operations of analyte selection and transport from the first to the second dimension. Although the physical operation of switching a component into the second dimension with computer controlled valving is simple, it is shown that changes in analyte retention time and peak width with column age and fouling are a serious problem. The analyte moves out of the preselected time window for valve switching and quantitation is compromised in the second dimension. It is proposed that a solution to the "drifting peak" phenomenon in targeted component analysis is to use binary mobility elution in the first dimension. Binary mobility refers to those systems, such as affinity chromatography, in which analyte mobility is generally either 0 or 1 relative to mobile phase velocity. Coupling these binary changes in analyte mobility in the first dimension with valve switching eliminates the "drifting peak" phenomenon. In addition, it is shown that a wide time window may be used in affinity separations without compromising the separation or accumulating contaminants. Several cases are described in which immunosorbents were used with reversed phase columns to provide quantitative targeted component analyses from complex mixtures.
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Abstract
The tetrapeptide GPRP was previously shown to be an effective affinity ligand for fibrinogen when immobilized to Fractogel (Kuyas et al., 1990). The authors synthesized the GPRP peptide directly onto an aminefunctionalized POROS chromatographic resin to demonstrate the effectiveness of this approach for generating perfusive affinity media. Fibrinogen from plasma bound to an NH2-GPRP-POROS column under 50 mM phosphate buffer, 0.15 M NaCl, pH 7 at 15 ml/min flow rate. The bound fibrinogen showed weak clotting activity when eluted with 20 mM acetate buffer, pH 4. The peptide column did not bind denatured fibrinogen. The dynamic binding capacity of the column by frontal analysis was 10.2 mg/ml column volume. The total analysis time was under 5 min. Similarly, the CAQCHTVEK peptide of cytochrome c with heme group covalently attached to the SH groups of the two cysteines is known to bind to albumins (Adams et al., 1989). A simplified peptide analogue, GAQGHTVEK, was synthesized directlyon POROS resin. Under 20 mM MES, pH 6, albumin from human serum bound specifically to this peptide column and eluted with a salt gradient at 0.2 M NaCl, 20 mM MES (2-[N-Morpholino]ethane sulfonic acid), pH 6. The dynamic binding capacity of human serum albumin by frontal analysis was 19 mg/ml column volume. Thus, this column can purify albumin from human serum under non-denaturing conditions.
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Affinity-based screening of combinatorial libraries using automated, serial-column chromatography. Nat Biotechnol 1996; 14:504-7. [PMID: 9630929 DOI: 10.1038/nbt0496-504] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have developed an automated serial chromatographic technique for screening a library of compounds based upon their relative affinity for a target molecule. A "target" column containing the immobilized target molecule is set in tandem with a reversed-phase column. A combinatorial peptide library is injected onto the target column. The target-bound peptides are eluted from the first column and transferred automatically to the reversed-phase column. The target-specific peptide peaks from the reversed-phase column are identified and sequenced. Using a monoclonal antibody (3E-7) against beta-endorphin as a target, we selected a single peptide with sequence YGGFL from approximately 5800 peptides present in a combinatorial library. We demonstrated the applicability of the technology towards selection of peptides with predetermined affinity for bacterial lipopolysaccharide (LPS, endotoxin). We expect that this technology will have broad applications for high throughout screening of chemical libraries or natural product extracts.
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Abstract
This paper describes an automated analytical system for the examination of protein primary structure in which (i) the target protein is first purified by immunoaffinity chromatography, (ii) subsequent chromatographic and chemical reaction steps in the sequencing process are directly coupled, (iii) buffer exchange between these unit operations is achieved while the protein is absorbed on a mixed bed of strong ion exchange sorbents, (iv) proteolysis occurs in an immobilized trypsin column having a 10-1000 fold-excess of enzyme, (v) the tryptic digest is directly transferred to a perfusion dilute capture column where it is concentrated and rapidly desalted, and (vi) peptides eluted from the dilute capture column and analytical microbore and capillary perfusion reversed-phase chromatography columns are analyzed by either single-stage mass spectrometry (MS) or tandem MS/MS. Protein structure variants were easily recognized, and in the case of hemoglobin (Hb) S, the site of variation from Hb A0 was verified.
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Abstract
UNLABELLED In this study, 144 consecutive percutaneous liver biopsies performed with a 1.6 mm Menghini needle, during a 2-year period were reviewed. All the children were aged under 15 years, 57 patients less than 1 year and 87 more than 1 year. All biopsies were adequate and the mean number of portal tracts examined was 17.6 per biopsy (14.3 in patients weighing less than 10 kg and 19.1 in the others). There were no deaths and we observed only bleeding complications. In patients with normal coagulation (128 cases), 1 bleeding requiring transfusion occurred; and in patients with abnormal coagulation (16 cases), we observed 2 bleeding cases requiring transfusion. CONCLUSION Percutaneous liver biopsy can be performed with 1.6 mm needles in children. For increased safety, ultrasound-guided biopsies are recommended.
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Purification of antibody Fab fragments by cation-exchange chromatography and pH gradient elution. J Chromatogr A 1995. [DOI: 10.1016/0021-9673(95)00319-i] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
BACKGROUND The diagnosis of Tangier disease in childhood is based on the specific aspect of tonsils or by screening relatives of affected subjects. CASE REPORT A moderately enlarged liver associated with splenomegaly was found upon routine physical examination of a 3 month-old breast-fed boy, born in Turkey from consanguineous parents. Laboratory studies disclosed moderate increase in serum alanine aminotransferase activity (ALAT 52 UI/l, N < 30). The diagnosis of Tangier disease was confirmed by studies of plasma cholesterol and apolipoprotein A. By 8 months of age, the patient had enlarged orange tonsils. Small cervical, axillary and inguinal lymphadenopathies were present. The tonsilar and adenoidal tissues were removed at 18 months of age because the patient suffered from chronic airway obstruction. Colonoscopic examination revealed tiny flat orange spots, 1 to 2 mm in diameter, scattered throughout the rectosigmoidal and colonic mucosa. Survey of the family led to the discovery of one sister, with asymptomatic apolipoprotein Al deficiency and a normal sister, while the parents were heterozygotes for Tangier disease. CONCLUSION Enlarged liver associated with a moderate level in serum aminotransferase may be an early manifestation of Tangier disease in infants. Rectosigmoidal and colonic lesions may be convenient for biopsy when tonsillectomy is not indicated.
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