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Clinical Proteomics

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https://www.readbyqxmd.com/read/29213220/the-proteins-cleaved-by-endogenous-tryptic-proteases-in-normal-edta-plasma-by-c18-collection-of-peptides-for-liquid-chromatography-micro-electrospray-ionization-and-tandem-mass-spectrometry
#1
Jaimie Dufresne, Angelique Florentinus-Mefailoski, Juliet Ajambo, Ammara Ferwa, Peter Bowden, John Marshall
The tryptic peptides from ice cold versus room temperature plasma were identified by C18 liquid chromatography and micro electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Samples collected on ice showed low levels of endogenous tryptic peptides compared to the same samples incubated at room temperature. Plasma on ice contained peptides from albumin, complement, and apolipoproteins and others that were observed by the X!TANDEM and SEQUEST algorithms. In contrast to ice cold samples, after incubation at room temperature, greater numbers of tryptic peptides from well characterized plasma proteins, and from cellular proteins were observed...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29209155/optimization-of-quantitative-proteomic-analysis-of-clots-generated-from-plasma-of-patients-with-venous-thromboembolism
#2
Aneta Stachowicz, Jakub Siudut, Maciej Suski, Rafał Olszanecki, Ryszard Korbut, Anetta Undas, Jacek R Wiśniewski
Background: It is well known that fibrin network binds a large variety of proteins, including inhibitors and activators of fibrinolysis, which may affect clot properties, such as stability and susceptibility to fibrinolysis. Specific plasma clot composition differs between individuals and may change in disease states. However, the plasma clot proteome has not yet been in-depth analyzed, mainly due to technical difficulty related to the presence of a highly abundant protein-fibrinogen and fibrin that forms a plasma clot...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29176938/a-proteomic-approach-to-understanding-the-pathogenesis-of-idiopathic-macular-hole-formation
#3
Pingbo Zhang, Min Zhu, Yuming Zhao, Jiang Qian, Craig Dufresne, Randi Turner, Richard D Semba, Sharon D Solomon
Idiopathic macular holes (IMH) are full-thickness defects of retinal tissue that cause severe vision loss due to disruption of the anatomic fovea. Abnormal vitreous traction is involved in the formation of macular holes. Both glial cells and hyalocytes contribute to epiretinal membrane formation in IMH. In order to gain further insight into the pathophysiology of IMH, we conducted a discovery phase investigation of the vitreous proteome in four patients with macular holes and six controls using one-dimensional gel fractionation and liquid chromatography-tandem mass spectrometry analyses on an Orbitrap Elite mass spectrometer...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29176937/proteomic-profiling-identifies-markers-for-inflammation-related-tumor-fibroblast-interaction
#4
Daniel Drev, Andrea Bileck, Zeynep N Erdem, Thomas Mohr, Gerald Timelthaler, Andrea Beer, Christopher Gerner, Brigitte Marian
Background: Cancer associated fibroblasts are activated in the tumor microenvironment and contribute to tumor progression, angiogenesis, extracellular matrix remodeling, and inflammation. Methods: To identify proteins characteristic for fibroblasts in colorectal cancer we used liquid chromatography-tandem mass spectrometry to derive protein abundance from whole-tissue homogenates of human colorectal cancer/normal mucosa pairs. Alterations of protein levels were determined by two-sided t test with greater than threefold difference and an FDR of < 0...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29142508/proteomic-characterisation-of-bovine-and-avian-purified-protein-derivatives-and-identification-of-specific-antigens-for-serodiagnosis-of-bovine-tuberculosis
#5
José Antonio Infantes-Lorenzo, Inmaculada Moreno, María de Los Ángeles Risalde, Álvaro Roy, Margarita Villar, Beatriz Romero, Nieves Ibarrola, José de la Fuente, Eugenia Puentes, Lucía de Juan, Christian Gortázar, Javier Bezos, Lucas Domínguez, Mercedes Domínguez
Background: Bovine purified protein derivative (bPPD) and avian purified protein derivative (aPPD) are widely used for bovine tuberculosis diagnosis. However, little is known about their qualitative and quantitative characteristics, which makes their standardisation difficult. In addition, bPPD can give false-positive tuberculosis results because of sequence homology between Mycobacterium bovis (M. bovis) and M. avium proteins. Thus, the objective of this study was to carry out a proteomic characterisation of bPPD, aPPD and an immunopurified subcomplex from bPPD called P22 in order to identify proteins contributing to cross-reactivity among these three products in tuberculosis diagnosis...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29093647/freeze-dried-plasma-proteins-are-stable-at-room-temperature-for-at-least-1-year
#6
Jaimie Dufresne, Trung Hoang, Juliet Ajambo, Angelique Florentinus-Mefailoski, Peter Bowden, John Marshall
Thirty human EDTA plasma samples from male and female subjects ranging in age from 24 to 74 years were collected on ice, processed ice cold and stored frozen at -80 °C, in liquid nitrogen (LN2), or freeze dried and stored at room temperature in a desiccator (FDRT) or freeze dried and stored at -20 °C for 1 year (FD-20). In a separate experiment, EDTA plasma samples were collected onto ice, processed ice cold and maintained on ice ± protease inhibitors versus incubated at room temperature for up to 96 h...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29051715/a-multiplex-platform-for-the-identification-of-ovarian-cancer-biomarkers
#7
Kristin L M Boylan, Kate Geschwind, Joseph S Koopmeiners, Melissa A Geller, Timothy K Starr, Amy P N Skubitz
BACKGROUND: Currently, there are no FDA approved screening tools for detecting early stage ovarian cancer in the general population. Development of a biomarker-based assay for early detection would significantly improve the survival of ovarian cancer patients. METHODS: We used a multiplex approach to identify protein biomarkers for detecting early stage ovarian cancer. This new technology (Proseek(®) Multiplex Oncology Plates) can simultaneously measure the expression of 92 proteins in serum based on a proximity extension assay...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/29026368/serum-protein-pattern-associated-with-organ-damage-and-lupus-nephritis-in-systemic-lupus-erythematosus-revealed-by-pea-immunoassay
#8
Anna Petrackova, Andrea Smrzova, Petr Gajdos, Marketa Schubertova, Petra Schneiderova, Pavel Kromer, Vaclav Snasel, Martina Skacelova, Frantisek Mrazek, Josef Zadrazil, Pavel Horak, Eva Kriegova
BACKGROUND: Systemic lupus erythematosus (SLE) is a remarkably heterogeneous autoimmune disease. Despite tremendous efforts, our knowledge of serum protein patterns in severe SLE phenotypes is still limited. We investigated the serum protein pattern of SLE, with special emphasis on irreversible organ damage and active lupus nephritis (LN) as assessed by renal Systemic Lupus Erythematosus Disease Activity Index. METHODS: We used proximity extension immunoassay (PEA, Proseek Multiplex, Olink) to assess the serum levels of ninety-two inflammation-related proteins in Czech patients with SLE (n = 75) and age-matched healthy control subjects (n = 23)...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28814946/protein-signatures-of-molecular-pathways-in-non-small-cell-lung-carcinoma-nsclc-comparison-of-glycoproteomics-and-global-proteomics
#9
Shuang Yang, Lijun Chen, Daniel W Chan, Qing Kay Li, Hui Zhang
BACKGROUND: Non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer deaths in the United States. More than half of NSCLC patients have clinical presentations with locally advanced or metastatic disease at the time of diagnosis. The large-scale genomic analysis of NSCLC has demonstrated that molecular alterations are substantially different between adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). However, a comprehensive analysis of proteins and glycoproteins in different subtypes of NSCLC using advanced proteomic approaches has not yet been conducted...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28814945/glomerular-abundance-of-complement-proteins-characterized-by-proteomic-analysis-of-laser-captured-microdissected-glomeruli-associates-with-progressive-disease-in-iga-nephropathy
#10
Teodora Ioana Flavia Paunas, Kenneth Finne, Sabine Leh, Hans-Peter Marti, Tom Eirik Mollnes, Frode Berven, Bjørn Egil Vikse
BACKGROUND: The clinical course of IgA nephropathy (IgAN) is variable and complement activation may predict prognosis. The present study investigated whether glomerular abundance of complement proteins associates with progression to end-stage renal disease (ESRD) in patients for whom prognosis could not be predicted based on clinical variables. METHODS: Based on data from the Norwegian Kidney Biopsy Registry and the Norwegian Renal Registry, three groups were included: IgAN patients with (n = 9) or without (n = 16) progression to ESRD during 10 years, and controls (n = 15) with a normal kidney biopsy...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28785178/down-regulation-of-metabolic-proteins-in-hepatocellular-carcinoma-with-portal-vein-thrombosis
#11
Wei-Chen Lee, Hong-Shiue Chou, Ting-Jung Wu, Chen-Fang Lee, Pao-Yueh Hsu, Hsiu-Ying Hsu, Tsung-Han Wu, Kun-Ming Chan
BACKGROUND: Hepatocellular carcinoma is an aggressive malignancy with poor prognosis and easy to recur even the tumor is totally removed by surgery. Portal vascular invasion is one of the major factors contributing to tumor recurrence and poor prognosis. However, why hepatocellular carcinoma is easy to grow into vessels is unclear. METHODS: Surgical specimens from seven hepatocellular carcinoma patients with portal vein thrombosis and seven patients without vascular invasion were utilized to analyze protein expression by proteomic technique...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28769740/discovery-and-validation-of-a-colorectal-cancer-classifier-in-a-new-blood-test-with-improved-performance-for-high-risk-subjects
#12
Lisa J Croner, Roslyn Dillon, Athit Kao, Stefanie N Kairs, Ryan Benz, Ib J Christensen, Hans J Nielsen, John E Blume, Bruce Wilcox
BACKGROUND: The aim was to improve upon an existing blood-based colorectal cancer (CRC) test directed to high-risk symptomatic patients, by developing a new CRC classifier to be used with a new test embodiment. The new test uses a robust assay format-electrochemiluminescence immunoassays-to quantify protein concentrations. The aim was achieved by building and validating a CRC classifier using concentration measures from a large sample set representing a true intent-to-test (ITT) symptomatic population...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28701906/proteomic-discovery-and-verification-of-serum-amyloid-a-as-a-predictor-marker-of-patients-at-risk-of-post-stroke-infection-a-pilot-study
#13
L Azurmendi, V Lapierre-Fetaud, J Schneider, J Montaner, M Katan, Jean-Charles Sanchez
BACKGROUND: Post-stroke infections occur in 20-36% of stroke patients and are associated with high morbidity and mortality rates. Early identification of patients at risk of developing an infection could improve care via an earlier treatment leading to a better outcome. We used proteomic tools in order to discover biomarkers able to stratify patients at risk of post-stroke infection. METHODS: The post hoc analysis of a prospective cohort study including 40 ischemic stroke patients included 21 infected and 19 non-infected participants...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28694743/interferon-%C3%AE-induced-compositional-changes-in-human-bone-marrow-derived-mesenchymal-stem-stromal-cells
#14
Qingdong Guan, Peyman Ezzati, Victor Spicer, Oleg Krokhin, Donna Wall, John A Wilkins
BACKGROUND: Mesenchymal stem/stromal cells (MSC) display a range of immunoregulatory properties which can be enhanced by the exposure to cytokines such interferon γ (IFN-γ). However the compositional changes associated with the 'licensing' of these cells have not been clearly defined. The present study was undertaken to provide a detailed comparative proteomic analysis of the compositional changes that occur in human bone marrow derived MSC following 20 h treatment with IFN-γ. METHODS: 2D LC MSMS analysis of control and IFN-γ treated cells from 5 different healthy donors provided confident identification of more than 8400 proteins...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28694742/clinical-validation-of-a-blood-based-classifier-for-diagnostic-evaluation-of-asymptomatic-individuals-with-pulmonary-nodules
#15
Charles E Birse, Jennifer L Tomic, Harvey I Pass, William N Rom, Robert J Lagier
BACKGROUND: The number of pulmonary nodules detected in the US is expected to increase substantially following recent recommendations for nationwide CT-based lung cancer screening. Given the low specificity of CT screening, non-invasive adjuvant methods are needed to differentiate cancerous lesions from benign nodules to help avoid unnecessary invasive procedures in the asymptomatic population. We have constructed a serum-based multi-biomarker panel and assessed its clinical accuracy in a retrospective analysis of samples collected from participants with suspicious radiographic findings in the Prostate, Lung, Chest and Ovarian (PLCO) cancer screening trial...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28670222/the-impact-of-growth-hormone-on-proteomic-profiles-a-review-of-mouse-and-adult-human-studies
#16
REVIEW
Silvana Duran-Ortiz, Alison L Brittain, John J Kopchick
Growth hormone (GH) is a protein that is known to stimulate postnatal growth, counter regulate insulin's action and induce expression of insulin-like growth factor-1. GH exerts anabolic or catabolic effects depending upon on the targeted tissue. For instance, GH increases skeletal muscle and decreases adipose tissue mass. Our laboratory has spent the past two decades studying these effects, including the effects of GH excess and depletion, on the proteome of several mouse and human tissues. This review first discusses proteomic techniques that are commonly used for these types of studies...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28649187/distinct-proteome-pathology-of-circulating-microparticles-in-systemic-lupus-erythematosus
#17
Ole Østergaard, Christoffer Tandrup Nielsen, Julia T Tanassi, Line V Iversen, Søren Jacobsen, Niels H H Heegaard
BACKGROUND: The pathogenesis of systemic lupus erythematosus (SLE) is poorly understood but has been linked to defective clearance of subcellular particulate material from the circulation. This study investigates the origin, formation, and specificity of circulating microparticles (MPs) in patients with SLE based on comprehensive MP proteome profiling using patients with systemic sclerosis (SSc) and healthy donors (HC) as controls. METHODS: We purified MPs from platelet-poor plasma using differential centrifugation of samples from SLE (n = 45), SSc (n = 38), and two sets of HC (n = 35, n = 25)...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28642677/a-novel-workflow-combining-plaque-imaging-plaque-and-plasma-proteomics-identifies-biomarkers-of-human-coronary-atherosclerotic-plaque-disruption
#18
Regent Lee, Roman Fischer, Philip D Charles, David Adlam, Alessandro Valli, Katalin Di Gleria, Rajesh K Kharbanda, Robin P Choudhury, Charalambos Antoniades, Benedikt M Kessler, Keith M Channon
BACKGROUND: Atherosclerotic plaque rupture is the culprit event which underpins most acute vascular syndromes such as acute myocardial infarction. Novel biomarkers of plaque rupture could improve biological understanding and clinical management of patients presenting with possible acute vascular syndromes but such biomarker(s) remain elusive. Investigation of biomarkers in the context of de novo plaque rupture in humans is confounded by the inability to attribute the plaque rupture as the source of biomarker release, as plaque ruptures are typically associated with prompt down-stream events of myocardial necrosis and systemic inflammation...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28592925/second-generation-multiple-reaction-monitoring-assays-for-enhanced-detection-of-ultra-low-abundance-mycobacterium-tuberculosis-peptides-in-human-serum
#19
Carolina Mehaffy, Karen M Dobos, Payam Nahid, Nicole A Kruh-Garcia
BACKGROUND: Mycobacterium tuberculosis (Mtb) is the causative agent of Tuberculosis (TB), the number one cause of death due to an infectious disease. TB diagnosis is performed by microscopy, culture or PCR amplification of bacterial DNA, all of which require patient sputum or the biopsy of infected tissue. Detection of mycobacterial products in serum, as biomarkers of diagnosis or disease status would provide an improvement over current methods. Due to the low-abundance of mycobacterial products in serum, we have explored exosome enrichment to improve sensitivity...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28546799/lectin-array-and-glycogene-expression-analyses-of-ovarian-cancer-cell-line-a2780-and-its-cisplatin-resistant-derivate-cell-line-a2780-cp
#20
Ran Zhao, Wenjun Qin, Ruihuan Qin, Jing Han, Can Li, Yisheng Wang, Congjian Xu
BACKGROUND: Ovarian cancer is one of the most lethal gynecological malignancies, in which platinum resistance is a common cause of its relapse and death. Glycosylation has been reported to be involved in drug resistance, and glycomic analyses of ovarian cancer may improve our understanding of the mechanisms underlying cancer cell drug resistance and provide potential biomarkers and therapeutic targets. METHODS: The serous ovarian cancer cell line A2780 and its platinum-resistant counterpart A2780-cp were used in this study...
2017: Clinical Proteomics
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