scholarly journals Comparative analysis of post-translational modifications in plasma proteome of patients with cerebral ischemia based on HPLC-MS/MS method

2019 ◽  
Vol 65 (3) ◽  
pp. 251-258
Author(s):  
Y.S. Kisrieva ◽  
N.A. Petushkova ◽  
N.F. Samenkova ◽  
G.P. Kuznetsova ◽  
O.B. Larina ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Cerebral Ischemia ◽  
Plasma Samples ◽  
Plasma Proteome ◽  
Label Free ◽  
Post Translational Modifications ◽  
Comparative Proteomic Analysis ◽  
Clinically Significant ◽  
Relative Differences ◽  
Ms Search

The relative differences between post-translational modifications (PTM) of proteins in blood plasma samples of patients with cerebral ischemia (CI) and healthy people were investigated using of the method of label-free comparative proteomic analysis based on the technology of tandem HPLC-MS/MS. For PTM detection we used multiple MS/MS search in the database Mascot for variable PTM and Progenesis LS-MS software. In the CI plasma samples, we observed an increase in the proportion of peptides with such PTM as phosphorylation of serine, threonine, and tyrosine, acetylation of lysine and protein N-term, ubiquitination of lysine and deamidation of glutamine related to clinically significant processes were revealed.

A Comparative Analysis of D-Dimer Assays in Patients with Clinically Suspected Pulmonary Embolism

1993 ◽  
Vol 70 (03) ◽  
pp. 408-413 ◽  
Author(s):  
Edwin J R van Beek ◽  
Bram van den Ende ◽  
René J Berckmans ◽  
Yvonne T van der Heide ◽  
Dees P M Brandjes ◽  
...  
Keyword(s):  
Pulmonary Embolism ◽  
Comparative Analysis ◽  
High Probability ◽  
Pulmonary Emboli ◽  
Plasma Samples ◽  
Suspected Pulmonary Embolism ◽  
Lung Scan ◽  
D Dimer

SummaryTo avoid angiography in patients with clinically suspected pulmonary embolism and non-diagnostic lung scan results, the use of D-dimer has been advocated. We assessed plasma samples of 151 consecutive patients with clinically suspected pulmonary embolism. Lung scan results were: normal (43), high probability (48) and non-diagnostic (60; angiography performed in 43; 12 pulmonary emboli). Reproducibility, cut-off values, specificity, and percentage of patients in whom angiography could be avoided (with sensitivity 100%) were determined for two latex and four ELISA assays.The latex methods (cut-off 500 μg/1) agreed with corresponding ELISA tests in 83% (15% normal latex, abnormal ELISA) and 81% (7% normal latex, abnormal ELISA). ELISA methods showed considerable within- (2–17%) and between-assay Variation (12–26%). Cut-off values were 25 μg/l (Behring), 50 μg/l (Agen), 300 μg/l (Stago) and 550 μg/l (Organon). Specificity was 14–38%; in 4–15% of patients angiography could be avoided.We conclude that latex D-dimer assays appear not useful, whereas ELISA methods may be of limited value in the exclusion of pulmonary embolism.

Label-Free Mass Spectrometry-Based Plasma Proteomics Identified LY6D, DSC3, CDSN, SERPINB12, and SLURP1,as Novel Protein Biomarkers For Pulmonary Tuberculosis

2019 ◽  
Vol 17 ◽  
Author(s):  
Xiaoli Yu ◽  
Lu Zhang ◽  
Na Li ◽  
Peng Hu ◽  
Zhaoqin Zhu ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Search Algorithm ◽  
Differentially Expressed ◽  
P Value ◽  
Plasma Samples ◽  
Label Free ◽  
Protein Biomarkers ◽  
Protein Database ◽  
Leave One Out ◽  
Potential Biomarkers

Aim: We aimed to identify new plasma biomarkers for the diagnosis of Pulmonary tuberculosis. Background: Tuberculosis is an ancient infectious disease that remains one of the major global health problems. Until now, effective, convenient, and affordable methods for diagnosis of Pulmonary tuberculosis were still lacked. Objective: This study focused on construct a label-free LC-MS/MS based comparative proteomics between six tuberculosis patients and six healthy controls to identify differentially expressed proteins (DEPs) in plasma. Method: To reduce the influences of high-abundant proteins, albumin and globulin were removed from plasma samples using affinity gels. Then DEPs from the plasma samples were identified using a label-free Quadrupole-Orbitrap LC-MS/MS system. The results were analyzed by the protein database search algorithm SEQUEST-HT to identify mass spectra to peptides. The predictive abilities of combinations of host markers were investigated by general discriminant analysis (GDA), with leave-one-out cross-validation. Results: A total of 572 proteins were identified and 549 proteins were quantified. The threshold for differentially expressed protein was set as adjusted p-value < 0.05 and fold change ≥1.5 or ≤0.6667, 32 DEPs were found. ClusterVis, TBtools, and STRING were used to find new potential biomarkers of PTB. Six proteins, LY6D, DSC3, CDSN, FABP5, SERPINB12, and SLURP1, which performed well in the LOOCV method validation, were termed as potential biomarkers. The percentage of cross-validated grouped cases correctly classified and original grouped cases correctly classified is greater than or equal to 91.7%. Conclusion: We successfully identified five candidate biomarkers for immunodiagnosis of PTB in plasma, LY6D, DSC3, CDSN, SERPINB12, and SLURP1. Our work supported this group of proteins as potential biomarkers for pulmonary tuberculosis, and be worthy of further validation.

Label-free based comparative proteomic analysis of whey proteins between different milk yields of Dezhou donkey

2019 ◽  
Vol 508 (1) ◽  
pp. 237-242 ◽  
Author(s):  
Xinhao Zhang ◽  
Haijing Li ◽  
Jie Yu ◽  
Xiangshan Zhou ◽  
Chuanliang Ji ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Whey Proteins ◽  
Label Free ◽  
Comparative Proteomic Analysis

scholarly journals The phosphoproteome of rice leaves responds to water and nitrogen supply

2021 ◽  
Author(s):  
Sara Hamzelou ◽  
Vanessa J. Melino ◽  
Darren C. Plett ◽  
Karthik Shantharam Kamath ◽  
Arkadiusz Nawrocki ◽  
...  
Keyword(s):  
Prolonged Exposure ◽  
Water Channel ◽  
Nitrogen Supply ◽  
Nitrogen Fertilizers ◽  
Label Free ◽  
Limited Information ◽  
Irrigated Rice ◽  
Post Translational Modifications ◽  
Growth Adaptation

The scarcity of freshwater is an increasing concern in flood-irrigated rice, whilst excessive use of nitrogen fertilizers is both costly and contributes to environmental pollution. To co-ordinate growth adaptation under prolonged exposure to limited water or excess nitrogen supply, plants have processes for signalling and regulation of metabolic processes. There is limited information on the involvement of one of the most important post-translational modifications (PTMs), protein phosphorylation, on plant adaptation to long-term changes in resource supply. Oryza sativa cv. Nipponbare was grown under two regimes of nitrogen from the time of germination to final harvest. Twenty-five days after germination, water was withheld from half the pots in each nitrogen treatment and low water supply continued for an additional 26 days, while the remaining pots were well watered. Leaves from all four groups of plants were harvested after 51 days in order to test whether phosphorylation of leaf proteins responded to prior abiotic events. The dominant impact of these resources is exerted in leaves, where PTMs have been predicted to occur. Proteins were extracted and phosphopeptides were analysed by nanoLC-MS/MS analysis, coupled with label-free quantitation. Water and nitrogen regimes triggered extensive changes in phosphorylation of proteins involved in membrane transport, such as the aquaporin OsPIP2-6, a water channel protein. Our study reveals phosphorylation of several peptides belonging to proteins involved in RNA-processing and carbohydrate metabolism, suggesting that phosphorylation events regulate the signalling cascades that are required to optimize plant response to resource supply.

scholarly journals Comparative analysis of clinical and neurological manifestations in patients with chronic cerebral ischemia and chronic heart failure with stored and reduced release fraction

2017 ◽  
pp. 43-52
Author(s):  
N. Zhhilova
Keyword(s):  
Heart Failure ◽  
Nervous System ◽  
Comparative Analysis ◽  
Cerebral Ischemia ◽  
Chronic Heart Failure ◽  
Left Ventricular ◽  
Left Ventricular Ejection ◽  
Neurological Manifestations ◽  
Chronic Cerebral Ischemia ◽  
Ventricular Ejection Fraction

The activation of the sympathetic nervous system plays an important pathophysiological role in the development of heart failure, in particular, in the development of left ventricular insufficiency. Although high blood pressure is considered as the main determinant of structural changes in the left ventricle, sex, salt intake, obesity, diabetes, as well as neurohumoral and genetic factors can affect the mass and left ventricular geometry. The usual concept of hypertonic re-modeling. In the comparative analysis of clinical and neurological manifestations in patients with chronic cerebral ischemia and chronic heart failure with a preserved and reduced release fraction, changes in the nervous system that showed a tendency to increase the disturbances and deviations from the norm with increasing heart failure, the fraction of release and the presence of hypertensive encephalopathy In the correlation analysis, a direct correlation between the quality of life indicator and the degree of heart failure (r = 0.56), the presence of myocardial infarction in the history (r = 0.42), arterial hypertension (r = 0.33) and the presence of valvular pathology the heart (r = 0.31) and the inverse correlation dependence on the indicator of the left ventricular ejection fraction (r = -0.69). A comparative analysis of correlation relationships indicates a reliable clinical and social significance of the left ventricular ejection fraction in patients with chronic cerebral ischemia and chronic heart failure.

scholarly journals Subcellular orchestration of alpha-synuclein variants in Parkinson’s disease brains revealed by 3D multicolor STED microscopy

2018 ◽  
Author(s):  
Tim E. Moors ◽  
Christina A. Maat ◽  
Daniel Niedieker ◽  
Daniel Mona ◽  
Dennis Petersen ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Lewy Bodies ◽  
Distribution Patterns ◽  
Alpha Synuclein ◽  
Label Free ◽  
Post Translational Modifications ◽  
Sted Microscopy ◽  
C Terminus

AbstractPost-translational modifications of alpha-synuclein (aSyn), particularly phosphorylation at Serine 129 (Ser129-p) and truncation of its C-terminus (CTT), have been implicated in Parkinson’s disease (PD) pathology. To gain more insight in the relevance of Ser129-p and CTT aSyn under physiological and pathological conditions, we investigated their subcellular distribution patterns in normal aged and PD brains using highly-selective antibodies in combination with 3D multicolor STED microscopy. We show that CTT aSyn localizes in mitochondria in PD patients and controls, whereas the organization of Ser129-p in a cytoplasmic network is strongly associated with pathology. Nigral Lewy bodies show an onion skin-like architecture, with a structured framework of Ser129-p aSyn and neurofilaments encapsulating CTT aSyn in their core, which displayed high content of proteins and lipids by label-free CARS microscopy. The subcellular phenotypes of antibody-labeled pathology identified in this study provide evidence for a crucial role of Ser129-p aSyn in Lewy body formation.

scholarly journals Påvisning av nye biomarkører i plasma-proteomet

2009 ◽  
Vol 16 (1) ◽  
Author(s):  
Jens P. Berg ◽  
John Henninge ◽  
Terje Lund
Keyword(s):  
Diagnostic Procedures ◽  
Prophylactic Surgery ◽  
Clinical Samples ◽  
Plasma Proteome ◽  
Post Translational Modifications ◽  
Novel Proteins ◽  
In Vitro Diagnostic ◽  
Close Cooperation ◽  
New Biomarkers

<p>Svar på laboratorieanalyser er av avgjørende betydning for ressursbruk i helsevesenet i forbindelse med utredning, behandling og oppfølgning av pasienter. Undersøkelser fra USA viser at ca. 70% av alle beslutninger som foretas i helsevesenet i stor grad er basert på resultater fra laboratoriene (1). Størst betydning for bruk av ressurser og folkehelse har laboratorieanalyser som kan brukes til å identifisere personer med økt risiko for sykdom som kan forebygges eller kureres. De mest dramatiske eksempler på dette finner man for noen dominant arvelige kreftformer hvor en enkelt genetisk undersøkelse kan påvise personer som trenger ekstra oppfølgning og i enkelte tilfeller profylaktisk kirurgisk behandling. Blod utgjør det viktigste materialet for laboratorieundersøkelser. I denne artikkelen vil vi beskrive noen av mulighetene som finnes i letingen etter nye biomarkører i form av proteiner og peptider i plasmaproteomet som betegner det totale uttrykket av proteiner i plasma. Utviklingen av immunometriske og massespektrometriske metoder har åpnet nye muligheter til å finne nye sykdomsmarkører både som ”nye” proteiner og i form av modifikasjoner som er dannet etter at proteinet er syntetisert (post-translasjonelle modifikasjoner). Effektiv testing av kombinasjoner av flere titalls markører gjør det mulig å lete etter sykdomsspesifikke ”fingeravtrykk” i proteomet. Plasma-proteomet karakteriseres imidlertid også av at bare noen få proteiner utgjør kvantitativt det meste av proteomet og av store konsentrasjonsforskjeller mellom de ulike proteinene. God tilgang på godt karakteriserte kliniske materialer er helt nødvendig for å kunne validere nytten av en ny biomarkør. Et effektivt samarbeid mellom metode-utviklere og biobanker er derfor av avgjørende betydning for hvor raskt en ny biomarkør kan bli en diagnostisk eller prognostisk faktor.</p><p><em>Determination of new biomarkers in the plasma proteome.</em> Decision making and use of health care resources depend to a large extent on data from in vitro diagnostic procedures. Laboratory results may have its largest impact on diseases that can be prevented or cured. Most dramatically a single genetic analysis can in certain dominantly inherited diseases differentiate between subjects who are at high risk of developing cancer and subjects who have a risk comparable to the general population. Ultimately, the test may identify individuals eligible for curative prophylactic surgery. Blood is the most important specimen for laboratory investigations. This paper describes some of the possibilities that are emerging in the search for new protein and peptide biomarkers in the plasma proteome, which is the total expression of proteins in plasma. The development of new immunometric and mass spectrometric methods has opened new strategies to identify disease markers both as novel proteins and differences in their post-translational modifications. Efficient testing of combinations of tens of markers simultaneously makes it technically possible to search for fingerprints of specific diseases in the proteome. However, a few plasma proteins dominate quantitatively and there are huge concentration differences among the proteins. Access to well characterized clinical samples is of great importance for the validation of new candidate markers. Close cooperation between biomarker hunters and serum or plasma biobanks is a crucial determinant for the transition of a biomarker candidate to a potential diagnostic of prognostic factor</p>

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