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Proteomics. Clinical Applications

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https://www.readbyqxmd.com/read/28895300/exsta-external-standard-addition-method-for-accurate-high-throughput-quantitation-in-targeted-proteomics-experiments
#1
Yassene Mohammed, Jingxi Pan, Suping Zhang, Jun Han, Christoph H Borchers
PURPOSE: Targeted proteomics using multiple reaction monitoring (MRM) with stable-isotope-labeled internal-standard (SIS) peptides is the current method of choice for protein quantitation in complex biological matrices. Better quantitation can be achieved with the internal standard-addition method, where successive increments of synthesized natural form (NAT) of the endogenous analyte are added to each sample, a response curve is generated, and the endogenous concentration is determined at the x-intercept...
September 11, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28887829/using-public-data-for-comparative-proteome-analysis-in-precision-medicine-programs
#2
Christopher S Hughes, Gregg B Morin
Maximizing the clinical utility of information obtained in longitudinal precision medicine programs would benefit from robust comparative analyses to known information to assess biological features of patient material, in the hopes of identifying the underlying features that drive their disease phenotype. In this study we investigate the potential for utilizing publically deposited mass spectrometry-based proteomics data to perform inter-study comparisons of cell line or tumour tissue materials. Using in-depth quantitative proteomics data acquired from analysis of ovarian cancer cell lines, we demonstrate the robust recapitulation of observable gene expression dynamics between individual studies carried out using significantly different methodologies...
September 9, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28856821/the-proteome-of-ulcerative-colitis-in-colon-biopsies-from-adults-optimized-sample-preparation-and-comparison-with-healthy-controls
#3
Armin Schniers, Endre Anderssen, Christopher Graham Fenton, Rasmus Goll, Yvonne Pasing, Ruth Hracky Paulssen, Jon Florholmen, Terkel Hansen
PURPOSE: The purpose of the study was to optimize the sample preparation and to further use an improved sample preparation to identify proteome differences between inflamed ulcerative colitis tissue from untreated adults and healthy controls. EXPERIMENTAL DESIGN: To optimize the sample preparation, we studied the effect of adding different detergents to a urea containing lysis buffer for a Lys-C/trypsin tandem digestion. With the optimized method, we prepared clinical samples from six ulcerative colitis patients and six healthy controls and analysed them by LC-MS/MS...
August 30, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28841253/identification-of-highly-expressed-plasmodium-vivax-proteins-from-clinical-isolates-using-proteomics
#4
Apoorva Venkatesh, Anwesha Lahiri, Panga Jaipal Reddy, Jayanthi Shastri, Sheetal Bankar, Swati Patankar, Sanjeeva Srivastava
PURPOSE: Plasmodium vivax is the most geographically widespread species responsible for malaria in humans. Our study focused on identifying highly expressed parasite proteins using a shotgun proteomics approach. EXPERIMENTAL DESIGN: Parasites (P. vivax) were isolated from 7 patient samples using saponin lysis. Protein extracts from these parasites were processed and subjected to LC-MS/MS analysis. RESULTS: An overall proteome coverage of 586 P...
August 25, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28816019/itraq-based-quantitative-proteomic-analyses-of-high-grade-esophageal-squamous-intraepithelial-neoplasia
#5
Jingjing Zhang, Chunchun Zhi, Fuxi Zhen, Xiaoqin Yuan, Chunhua Jiao, Hong Zhu, Hui Zhu, Yadong Feng
PURPOSE: Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and is the fourth most lethal cancer in China. Little is known about the proteome of high grade esophageal squamous intraepithelial neoplasia (HGN), which is a premalignant lesion of ESCC. EXPERIMENTAL DESIGN: A quantitative proteomic analysis using an Isobaric Tags for Relative and Absolute Quantification (iTRAQ) approach was used to characterize the protein expression profiles in HGN...
August 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28801933/maldi-imaging-guided-microproteomic-analyses-of-heterogeneous-breast-tumors-a-pilot-study
#6
Deborah Alberts, Charles Pottier, Nicolas Smargiasso, Dominique Baiwir, Gabriel Mazzucchelli, Philippe Delvenne, Mark Kriegsmann, Daniel Kazdal, Arne Warth, Edwin De Pauw, Rémi Longuespée
PURPOSE: Matrix-assisted laser desorption/ionization (MALDI) imaging is an ideal tool to study intratumor heterogeneity (ITH) and its implication in prognostic stratification of patients. However there are some drawbacks concerning protein identification. On the other hand, laser microdissection (LMD)-based microproteomics allows retrieving thousands of protein identifications from small tissue pieces. As a proof of concept, we combined these two complementary approaches to analyze heterogeneous regions in breast tumors...
August 11, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28799191/serum-proteome-in-a-sporadic-amyotrophic-lateral-sclerosis-geographical-cluster
#7
Stefano De Benedetti, Elisabetta Gianazza, Cristina Banfi, Alessandro Marocchi, Christian Lunetta, Silvana Penco, Francesco Bonomi, Stefania Iametti
PURPOSE: This study was meant to characterize the serum proteome in a small geographical cluster of sporadic ALS subjects originating from a restricted geographical area and sharing the same environmental exposure, in a broader context of evaluating the relevance of environmental factors to disease onset, status, and progression. EXPERIMENTAL DESIGN: An Artificial Neural Network based software was used to compare the relative abundance of proteins identified as different (by means of bi-dimensional electrophoresis and mass spectrometry) in the serum proteome of patients and age-matched healthy controls...
August 10, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28795537/proteomics-investigations-into-serum-proteins-adsorbed-by-high-flux-and-low-flux-dialysis-membranes
#8
Shuai Han, Kaiguang Yang, Jingdi Sun, Jianhui Liu, Lihua Zhang, Jiuyang Zhao
PURPOSE: Hemodialysis is one of the most important therapies for patients with uremia, and the dialysis membrane is the predominant factor that impacts the efficiency of dialysis. Here, we investigated protein adsorption on two different membranes to provide a basis for improving dialysis materials. METHODS: Two cases treated with the Polyflux 14L low-flux dialyzer and the Polyflux 140H high-flux dialyzers during two continuous therapies were selected. Four used dialyzers from selected patients were infused with C12Im-Cl to elute the adsorbed proteins...
August 10, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28731282/altered-signaling-associated-with-chronic-arsenic-exposure-in-human-skin-keratinocytes
#9
Sartaj Ahmad Mir, Santosh Renuse, Gajanan Sathe, Aafaque Ahmad Khan, Arun H Patil, Vishalakshi Nanjappa, Firdous Ahmad Bhat, T S Keshava Prasad, Ashok K Giri, Aditi Chatterjee, Harsha Gowda
Modulation of signaling pathways upon chronic arsenic exposure remains poorly studied. Here we carried out SILAC-based quantitative phosphoproteomics analysis to dissect the signaling induced upon chronic arsenic exposure in human skin keratinocyte cell line, HaCaT. We identified 4,171 unique phosphosites derived from 2,000 proteins. We observed differential phosphorylation of 406 phosphosites (2-fold) corresponding to 305 proteins. Several pathways involved in cytoskeleton maintenance and organization were found to be significantly enriched (p<0...
July 21, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28697276/comparative-proteomic-study-of-early-hypoxic-response-in-the-cerebral-cortex-of-rats-submitted-to-two-different-hypoxic-models
#10
David Ovelleiro, Santos Blanco, Raquel Hernández, María Ángeles Peinado
PURPOSE: The present study analyses and compares the cortical brain proteomic profiles of two different models of cerebral hypoxic insult in rats (HH: hypobaric hypoxia and HHI: ischemia followed by hypobaric hypoxia) in an attempt to describe the alterations of the early molecular hypoxic adaptive response underlying each one. EXPERIMENTAL DESIGN: A quantitative proteomic profile of left-brain cortices of rats under HH, HHI, and control conditions was determined using isobaric labeling (Tandem Mass Tag™) on the protein extracts from pools of five individuals...
July 11, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28697272/screening-of-antigenic-vesicular-fluid-proteins-of-echinococcus-multilocularis-as-potential-viability-biomarkers-to-monitor-drug-response-in-alveolar-echinococcosis-patients
#11
Benoît Valot, Bénédicte Rognon, Anais Prenel, Alice Baraquin, Jenny Knapp, Mathilde Anelli, Carine Richou, Solange Bresson-Hadni, Frederic Grenouillet, Junhua Wang, Dominique Angèle Vuitton, Bruno Gottstein, Laurence Millon
PURPOSE: The only drugs available to treat alveolar echinococcosis (AE) are mostly parasitostatic and in many cases prescribed for life. Decision criteria for discontinuation rely on the absence of parasitic viability. The aim of the present study was to search for candidate proteins that may exhibit good potential as biomarkers for viability. EXPERIMENTAL DESIGN: Sixteen serum samples (5 healthy controls,11 patients with AE), were used. AE-patients were classified into 3 groups 'Cured' (n = 2), 'ABZ-responders' (n = 4) and 'ABZ-non responders' (n = 5)...
July 11, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28688207/the-application-of-a-microfluidic-reactor-including-spontaneously-adsorbed-trypsin-for-rapid-protein-digestion-of-human-tear-samples
#12
Adam Kecskemeti, Cynthia Nora Nagy, Eva Csosz, Gergo Kallo, Attila Gaspar
In this study the application of a newly developed microfluidic immobilized enzymatic reactor (IMER) designed to accelerate protein digestion in clinical samples is presented. The IMER contains trypsin adsorbed on the porous surface of a PDMS microfluidic chip. Human tear with its relatively low volume and high protein content was collected and used for testing the digestion efficiency of the IMER. With the use of CZE peptide mapping, the efficiency and reproducibility of the reactor were investigated. No significant difference was observed in the CZE peptide profiles of the same tear sample digested in-solution or via microfluidic IMER...
July 8, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28679031/effect-of-social-interactions-on-hippocampal-protein-expression-in-animal-dominant-and-submissive-model-of-behavioral-disorders
#13
Natalia Borovok, Elimelech Nesher, Michal Reichenstein, Tatiana Tikhonova, Yishai Levin, Albert Pinhasov, Izhak Michaelevski
Psychiatric conditions often arise from social interactions, necessary for optimal mental functioning. Dominance and submissiveness are opposite poles of behavior, stemming from processes of social interactions between members inside one group or species. Extreme dominance/submissiveness expressions in humans is accompanied by mental impairments, mania or depression. Here, taking advantage of selectively bred dominant and submissive mice, we assessed protein expression profiles in the social interaction context...
July 5, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28679024/multi-pronged-proteomic-analysis-to-study-the-glioma-pathobiology-using-cerebrospinal-fluid-samples
#14
Nikita Gahoi, Darpan Malhotra, Aliasgar Moiyadi, Santosh G Varma, Mayuri N Gandhi, Sanjeeva Srivastava
PURPOSE: Gliomas are one of the most aggressive and lethal brain tumors arising from neoplastic transformation of astrocytes and oligodendrocytes. In this study, we have carried out a comprehensive quantitative analysis of proteome level differences in cerebrospinal fluid (CSF) across different grades of gliomas for a better understanding of glioma pathobiology. EXPERIMENTAL DESIGN: Glioma patients were diagnosed by radiology and histochemistry- based analyses. Differential proteomic analysis of high (n = 12) and low (n = 8) grade gliomas, and control (n = 3) samples was performed by using two complementary quantitative proteomic approaches; 2D-DIGE and iTRAQ...
July 5, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28734082/differential-protein-expression-in-exosomal-samples-taken-from-trauma-patients
#15
LETTER
Ron B Moyron, Nathan R Wall
No abstract text is available yet for this article.
September 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28726264/differential-protein-expression-in-exosomal-samples-taken-from-trauma-patients
#16
LETTER
Jia Wu, Ding Xu, Peng Luo
No abstract text is available yet for this article.
September 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28627779/new-horizon-for-breast-cancer-biomarker-discoveries-what-might-the-liquid-biopsy-of-nipple-aspirate-fluid-hold
#17
Ferdinando Mannello
The existence of cellular, molecular and biochemical heterogeneity of human breast cancers reveals the intricacy of biomarkers complexity, stimulating studies on new approaches (like "liquid biopsies") for the improvements in precision medicine. Breast cancer is recognized as a leading cause of morbidity and mortality worldwide with tumors significantly diverse and containing many types of cells showing different genetic and epigenetic profiles. In this field, the technology of liquid biopsy (applied to a fluid produced by breast gland, named nipple aspirate fluids, NAF) highlights the power of combining basic and clinical research...
September 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28627758/spectral-library-based-glycopeptide-analysis-detection-of-circulating-galectin-3-binding-protein-in-pancreatic-cancer
#18
Eslam N Nigjeh, Ru Chen, Yasuko Allen-Tamura, Randall E Brand, Teresa A Brentnall, Sheng Pan
PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease characterized by its late diagnosis, poor prognosis and rapid development of drug resistance. Using the data-independent acquisition (DIA) technique, the authors applied a spectral library-based proteomic approach to analyze N-glycosylated peptides in human plasma, in the context of pancreatic cancer study. EXPERIMENTAL DESIGN: The authors extended the application of DIA to the quantification of N-glycosylated peptides enriched from plasma specimens from a clinically well-defined cohort that consists of patients with early stage PDAC, chronic pancreatitis and healthy subjects...
September 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28561948/identification-of-fucosylated-fetuin-a-as-a-potential-biomarker-for-cholangiocarcinoma
#19
Lucy Betesh, Mary Ann Comunale, Mengjun Wang, Hongyan Liang, Julie Hafner, Aykan Karabudak, Nasra H Giama, Catherine D Moser, Eiji Miyoshi, Lewis R Roberts, Timothy M Block, Anand Mehta
PURPOSE: Cholangiocarcinoma (CCA) is a malignancy of the bile ducts. The purpose of this discovery study was to identify effective serum markers for surveillance of cholangiocarcinoma. EXPERIMENTAL DESIGN: Using a glycomic method, patients with CCA were determined to have increased levels of alpha-1,3 and alpha-1,6 linked fucosylated glycan. Proteomic analysis of the serum fucosylated proteome identified proteins such as alpha-2-macroglobulin, kininogen, hemopexin, fetuin-A, alpha-1 anti-trypsin, and ceruloplasmin as being hyperfucosylated in HCC...
September 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28544811/differential-protein-expression-in-exosomal-samples-taken-from-trauma-patients
#20
Ron B Moyron, Amber Gonda, Matthew J Selleck, Xian Luo-Owen, Richard D Catalano, Thomas O'Callahan, Carlos Garberoglio, David Turay, Nathan R Wall
Traumatic brain injuries (TBI) are among the most misdiagnosed and underreported types of head trauma. The potential long-term impact of undiagnosed or incorrectly identified concussions and other head injuries are potentially devastating, as evidenced by the increasing societal burden exhibited by soldiers returning from combat and athletes in contact sports. Concussions and TBI are notoriously difficult to correctly diagnose and prognosis for these injuries is poorly understood. In order to increase the likelihood of successful diagnosis, treatment, and prediction of outcomes, a definitive differential diagnosis will need to be established...
September 2017: Proteomics. Clinical Applications
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