scholarly journals A dry method for preserving tear protein samples

2017 ◽  
Author(s):  
Weiwei Qin ◽  
Chan Zhao ◽  
Linpei Zhang ◽  
Ting Wang ◽  
Youhe Gao
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Low Cost ◽  
Mass Spectrometry Analysis ◽  
Protein Patterns ◽  
Spectrometry Analysis ◽  
Disease Biomarkers ◽  
Tear Protein ◽  
Significant Difference ◽  
Biomarker Research

AbstractTears covering the ocular surface is an important bio-fluid containing thousands of molecules, including proteins, lipids, metabolites, nucleic acids, and electrolytes. Tears are valuable resources for biomarker research of ocular and even systemic diseases. For application in biomarker studies, tear samples should ideally be stored using a simple, low-cost, and efficient method along with the patient’s medical records. For this purpose, we developed a novel Schirmer’s strip-based dry method that allows for storage of tear samples in vacuum bags at room temperature. Using this method, tear protein patterns can also be preserved. Liquid chromatography-mass spectrometry/mass spectrometry analysis of proteins recovered from the dry method and traditional wet method showed no significant difference. Some tissue/organ enriched proteins were identified in tear, thus tear might be a good window for monitoring the change of these tissues or organs. This dry method facilitates sample transportation and enables the storage of tear samples on a large scale, increasing the availability of samples for studying disease biomarkers in tears.

Protein profile of the ovarian follicular fluid of brown brocket deer (Mazama gouazoubira; Fisher, 1814)

Zygote ◽  
2019 ◽  
Vol 28 (2) ◽  
pp. 170-173
Author(s):  
Thaís T.S. Souza ◽  
Maria J.B. Bezerra ◽  
Maurício F. van Tilburg ◽  
Celso S. Nagano ◽  
Luciana D. Rola ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Follicular Fluid ◽  
Protein Profile ◽  
Mass Spectrometry Data ◽  
Mass Spectrometry Analysis ◽  
Spectrometry Analysis ◽  
Significant Difference ◽  
Mazama Gouazoubira ◽  
Ovarian Follicular Fluid ◽  
Brocket Deer

SummaryThe aim of this study was to characterize the protein profile of ovarian follicular fluid (FF) of brown brocket deer (Mazama gouazoubira). Five adult females received an ovarian stimulation treatment and the FF was collected by laparoscopy from small/medium (≤3.5 mm) and large (>3.5 mm) follicles. Concentrations of soluble proteins in FF samples were measured and proteins were analyzed by 1-D SDS-PAGE followed by tryptic digestion and tandem mass spectrometry. Data from protein list defined after a Mascot database search were analyzed using the STRAP software tool. For the protein concentration, no significant difference (P > 0.05) was observed between small/medium and large follicles: 49.2 ± 22.8 and 56.7 ± 27.4 μg/μl, respectively. Mass spectrometry analysis identified 13 major proteins, but with no significant difference (P > 0.05) between follicle size class. This study provides insight into elucidating folliculogenesis in brown brocket deer.

Bio-Inspired Metaheuristic Optimization Algorithms for Biomarker Identification in Mass Spectrometry Analysis

2012 ◽  
Vol 3 (2) ◽  
pp. 64-85 ◽  
Author(s):  
Syarifah Adilah Mohamed Yusoff ◽  
Ibrahim Venkat ◽  
Umi Kalsom Yusof ◽  
Rosni Abdullah
Keyword(s):  
Mass Spectrometry ◽  
Chemical Properties ◽  
Feature Subset Selection ◽  
Mass Spectrometry Data ◽  
Mass Spectrometry Analysis ◽  
Computational Techniques ◽  
Feature Subset ◽  
Protein Patterns ◽  
Spectrometry Analysis ◽  
Biomarker Analysis

Mass spectrometry is an emerging technique that is continuously gaining momentum among bioinformatics researchers who intend to study biological or chemical properties of complex structures such as protein sequences. This advancement also embarks in the discovery of proteomic biomarkers through accessible body fluids such as serum, saliva, and urine. Recently, literature reveals that sophisticated computational techniques mimetic survival and natural processes adapted from biological life for reasoning voluminous mass spectrometry data yields promising results. Such advanced approaches can provide efficient ways to mine mass spectrometry data in order to extract parsimonious features that represent vital information, specifically in discovering disease-related protein patterns in complex proteins sequences. This article intends to provide a systematic survey on bio-inspired approaches for feature subset selection via mass spectrometry data for biomarker analysis.

scholarly journals Alternative proteins are functional regulators in cell reprogramming by PKA activation

2020 ◽  
Vol 48 (14) ◽  
pp. 7864-7882 ◽  
Author(s):  
Tristan Cardon ◽  
Julien Franck ◽  
Etienne Coyaud ◽  
Estelle M N Laurent ◽  
Marina Damato ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Epithelial Mesenchymal Transition ◽  
Gene Annotation ◽  
Mass Spectrometry Analysis ◽  
Cell Reprogramming ◽  
Pathway Enrichment Analysis ◽  
Mesenchymal Transition ◽  
Spectrometry Analysis ◽  
Biological Studies

Abstract It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.

Integrated plant proteomics — putting the green genomes to work

2003 ◽  
Vol 30 (5) ◽  
pp. 471 ◽  
Author(s):  
Joshua L. Heazlewood ◽  
A. Harvey Millar
Keyword(s):  
Mass Spectrometry ◽  
Data Storage ◽  
Large Scale ◽  
Protein Identification ◽  
Mass Spectrometry Analysis ◽  
Plant Science ◽  
Genomic Information ◽  
Plant Proteomics ◽  
Spectrometry Analysis ◽  
Complete Set

Protein analysis has been at the heart of plant science for many years, but with new questions emerging from an abundance of genomic information and further improvements in technology, there are now new opportunities to undertake large-scale analyses and to move to more complex systems than has been possible previously. This explosion of interest and data is often referred to simply as proteomics, which is the study of the complete set of proteins expressed at a given time and place, the proteome. As its name suggests proteomics is intricately linked to allied technologies such as genomics, transcriptomics and metabolomics. In this review of plant proteomics we outline a series of issues that face the practical user, particularly the largest problem that currently faces researchers, the myriad of options to choose from. The choices, problems and pitfalls of entering into gel-based and non-gel-based arraying techniques are discussed together with advances in pre-fractionation of samples, liquid chromatography separations and subcellular analyses. Issues relating to mass spectrometry analysis and the eventual protein identification are outlined, and the dilemmas of data storage and analysis are highlighted. During this tour we provide a series of references to the literature — experimental, theoretical and technical — to illustrate the breadth of current investigations using these techniques.

scholarly journals A New Drug Discovery Approach Based on Thermal Proteome Profiling to Develop More Effective Drugs

2021 ◽  
Vol 8 (2) ◽  
Author(s):  
Elham Gholizadeh ◽  
Mostafa Rezaei-Tavirani ◽  
Alireza Emadi ◽  
Reza Karbalaei ◽  
Ali Khaleghian
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Protein Extraction ◽  
Mass Spectrometry Analysis ◽  
Structural Stabilization ◽  
Proteome Profiling ◽  
Spectrometry Analysis ◽  
Drug Concentrations ◽  
Low Efficiency

: The search for disease-related targets and studying drug-protein and protein-protein interactions are central issues that would accelerate the clinical approval of a drug. Also, by developing an accurate method in this regard, time and resource consumption will significantly decrease. The low efficiency of some drugs in humans is a grave issue leading to a low rate of FDA approval after spending billions of dollars and decades of research. Several strategies and methods have been expanded to fill this gap, such as drug affinity responsive target stability (DARTS), stability of proteins from rates of oxidation (SPROX), cellular thermal shift assay (CETSA), and finally, thermal proteome profiling (TPP). The TPP is based on the combination of CETSA and quantitative mass spectrometry. Among recently introduced proteomics technologies, TPP demonstrates the ability to offer detailed proteomic profiles for the large-scale analysis of protein-ligand interactions, including endogenous ligands and proteins like cofactors and metabolites. TPP facilitates the identification of the markers governing drug efficacy and toxicity and provides an unbiased measure for estimating the rate of drug-target engagement. At a glance at TPP steps, after protein extraction, the molecule is exposed to different temperatures and drug concentrations. After discarding solubilized and stabilized proteins, the protein’s identity is investigated by mass spectrometry analysis. As a result of the protein’s structural stabilization after binding to its substrate, TTP helps to accurately identify target proteins with high throughput. In this study, we aimed to introduce the basics of this method and review most recent studies on this technique.

scholarly journals DIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift

2020 ◽  
Author(s):  
Ozge Karayel ◽  
André C. Michaelis ◽  
Matthias Mann ◽  
Brenda A. Schulman ◽  
Christine R. Langlois
Keyword(s):  
Mass Spectrometry ◽  
Systems Biology ◽  
Large Scale ◽  
E3 Ligase ◽  
Cellular Systems ◽  
Mass Spectrometry Analysis ◽  
High Throughput Analysis ◽  
Metabolic Switch ◽  
Spectrometry Analysis ◽  
Yeast Proteome

ABSTRACTYeast Saccharomyces cerevisiae is a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run data independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them, and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled new regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system read-out pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation novel targets of the GID E3 ligase. Moreover, our approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole proteome-based readouts can serve as comprehensive systems-level assay in all cellular systems.

Application of Mass Spectrometry Methods to the Analysis of Lipid Composition of the Human Brain

2021 ◽  
Vol 37 (5) ◽  
pp. 80-87
Author(s):  
A.I. Tkachev ◽  
M.S. Osetrova ◽  
D.N. Smirnov ◽  
O.I. Efimova ◽  
E.E. Khrameev
Keyword(s):  
Mass Spectrometry ◽  
Human Brain ◽  
Lipid Composition ◽  
Large Scale ◽  
Lipid Extraction ◽  
Simultaneous Detection ◽  
Molecular Organization ◽  
Mass Spectrometry Analysis ◽  
Spectrometry Analysis ◽  
The Brain

Abstract-Lipids make up more than half of the dry matter of the human brain and play a key role in its functioning. However, the lipid composition of the brain anatomical structures remains poorly understood. The first such studies were carried out more than 50 years ago, but since then, a small number of works have been published describing the concentration of lipids in only a few areas of the human brain. A fundamentally new step towards understanding the molecular organization of the brain and identifying the molecular basis of human cognitive abilities should be a detailed large-scale study of the brain lipidome. However, there is no description in the literature of methods optimized for studying the lipid composition of the human brain. In this work, we develop and present methods for lipid extraction and mass spectrometry analysis, which ensure simultaneous detection of the maximum amount of different lipid classes and individual substances in the human brain, as well as the approaches to bioinformatics analysis of the obtained data. Their use makes it possible to create a comprehensive picture of the molecular organization of the human brain, which has no analogues in the world in terms of its completeness. Key words: lipidome, brain, mass spectrometry, high-performance liquid chromatography, bioinformatics The reported study was funded by the Russian Foundation for Basic Research, project no. 20-34-70077.

scholarly journals DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

2020 ◽  
Vol 117 (51) ◽  
pp. 32806-32815
Author(s):  
Ozge Karayel ◽  
André C. Michaelis ◽  
Matthias Mann ◽  
Brenda A. Schulman ◽  
Christine R. Langlois
Keyword(s):  
Mass Spectrometry ◽  
Systems Biology ◽  
Large Scale ◽  
E3 Ligase ◽  
Cellular Systems ◽  
Mass Spectrometry Analysis ◽  
High Throughput Analysis ◽  
Metabolic Switch ◽  
Spectrometry Analysis ◽  
Yeast Proteome

The yeastSaccharomyces cerevisiaeis a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run, data-independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement, and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source-dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system readout pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation of targets of the GID E3 ligase. Moreover, this approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole-proteome–based readouts can serve as comprehensive systems-level assays in all cellular systems.

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