Proteomics and its applications
Proteomics involves the analysis of the entire complement of proteins in a cell, tissue or organism. It assesses protein activities, modifications, localization and interactions. Proteomics uses techniques like gel electrophoresis, mass spectrometry and liquid chromatography to separate and identify proteins. These techniques can be applied to discover disease biomarkers, develop diagnostic tools, and gain insights into disease pathogenesis and treatment. Proteomics has applications in studying various diseases including cancer, diabetes and infections. It provides insights into cellular processes and systems biology.
With the DNA sequences of more than 90 genomes completed, as well as a draft sequence of the human genome, a major challenge in modern biology is to understand the expression, function, and regulation of the entire set of proteins encoded by an organism—the aims of the new field of proteomics. This information will be invaluable for understanding how complex biological processes occur at a molecular level, how they differ in various cell types, and how they are altered in disease states. The term proteomics describes the study and characterization of a complete set of proteins present in a cell, organ, or organism at a given time.
In general, proteomic approaches can be used (a) for proteome profiling, (b) for comparative expression analysis of two or more protein samples, (c) for the localization and identification of posttranslational modifications, and (d) for the study of protein-protein interactions. The human genome harbours 26000–31000 protein-encoding genes; whereas the total number of human protein products, including splice variants and essential posttranslational modifications (PTMs), has been estimated to be close to one million. It is evident that most of the functional information on the genes resides in the proteome, which is the sum of multiple dynamic processes that include protein phosphorylation, protein trafficking, localization, and protein-protein interactions. Moreover, the proteomes of mammalian cells, tissues, and body fluids are complex and display a wide dynamic range of proteins concentration one cell can contain between one and more than 100000 copies of a single protein.
A rapidly emerging set of key technologies is making it possible to identify large numbers of proteins in a mixture or complex, to map their interactions in a cellular context, and to analyze their biological activities. Mass spectrometry has evolved into a versatile tool for examining the simultaneous expression of more than 1000 proteins and the identification and mapping of posttranslational modifications. High-throughput methods performed in an array format have enabled large-scale projects for the characterization of protein localization, protein-protein interactions, and the biochemical analysis of protein function. Finally, the plethora of data generated in the last few years has led to approaches for the integration of diverse data sets that greatly enhance our understanding of both individual protein function and elaborate biological processes.
With the DNA sequences of more than 90 genomes completed, as well as a draft sequence of the human genome, a major challenge in modern biology is to understand the expression, function, and regulation of the entire set of proteins encoded by an organism—the aims of the new field of proteomics. This information will be invaluable for understanding how complex biological processes occur at a molecular level, how they differ in various cell types, and how they are altered in disease states. The term proteomics describes the study and characterization of a complete set of proteins present in a cell, organ, or organism at a given time.
In general, proteomic approaches can be used (a) for proteome profiling, (b) for comparative expression analysis of two or more protein samples, (c) for the localization and identification of posttranslational modifications, and (d) for the study of protein-protein interactions. The human genome harbours 26000–31000 protein-encoding genes; whereas the total number of human protein products, including splice variants and essential posttranslational modifications (PTMs), has been estimated to be close to one million. It is evident that most of the functional information on the genes resides in the proteome, which is the sum of multiple dynamic processes that include protein phosphorylation, protein trafficking, localization, and protein-protein interactions. Moreover, the proteomes of mammalian cells, tissues, and body fluids are complex and display a wide dynamic range of proteins concentration one cell can contain between one and more than 100000 copies of a single protein.
A rapidly emerging set of key technologies is making it possible to identify large numbers of proteins in a mixture or complex, to map their interactions in a cellular context, and to analyze their biological activities. Mass spectrometry has evolved into a versatile tool for examining the simultaneous expression of more than 1000 proteins and the identification and mapping of posttranslational modifications. High-throughput methods performed in an array format have enabled large-scale projects for the characterization of protein localization, protein-protein interactions, and the biochemical analysis of protein function. Finally, the plethora of data generated in the last few years has led to approaches for the integration of diverse data sets that greatly enhance our understanding of both individual protein function and elaborate biological processes.
Functional proteomics, methods and toolsKAUSHAL SAHU
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Proteomics and its applications in phytopathologyAbhijeet Kashyap
Dear friends, I Abhijeet kashyap presenting the basics of proteomics to you all . Proteomics is the large-scale study of proteins, particularly their structures and functions.Proteomics helps in understanding the structure and function of different proteins as well as protein-protein interactions of an organism.
Genomics, Transcriptomics, Proteomics, Metabolomics - Basic concepts for clin...Prasenjit Mitra
This set of slides gives an overview regarding the various omics technologies available and how they can be used for improvement in clinical setting or research
Transcriptomics is the study of RNA, single-stranded nucleic acid, which was not separated from the DNA world until the central dogma was formulated by Francis Crick in 1958, i.e., the idea that genetic information is transcribed from DNA to RNA and then translated from RNA into protein.
it will help you to understand how the protein microarrays are made, what are the different types and what all purposes they are used for. its very useful ppt
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
Proteomics is the study of the proteome, the full protein complement of organisms e.g. plasma, cells and tissue.
Understanding the proteome allows for:
Characterisation of proteins
Understanding protein interactions
Identification of disease biomarkers
Functional proteomics, methods and toolsKAUSHAL SAHU
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Proteomics and its applications in phytopathologyAbhijeet Kashyap
Dear friends, I Abhijeet kashyap presenting the basics of proteomics to you all . Proteomics is the large-scale study of proteins, particularly their structures and functions.Proteomics helps in understanding the structure and function of different proteins as well as protein-protein interactions of an organism.
Genomics, Transcriptomics, Proteomics, Metabolomics - Basic concepts for clin...Prasenjit Mitra
This set of slides gives an overview regarding the various omics technologies available and how they can be used for improvement in clinical setting or research
Transcriptomics is the study of RNA, single-stranded nucleic acid, which was not separated from the DNA world until the central dogma was formulated by Francis Crick in 1958, i.e., the idea that genetic information is transcribed from DNA to RNA and then translated from RNA into protein.
it will help you to understand how the protein microarrays are made, what are the different types and what all purposes they are used for. its very useful ppt
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
Proteomics is the study of the proteome, the full protein complement of organisms e.g. plasma, cells and tissue.
Understanding the proteome allows for:
Characterisation of proteins
Understanding protein interactions
Identification of disease biomarkers
A genome is an organism’s complete set of DNA or complete genetic makeup, The entire DNA complement. It describes the identity and the sequence of genes of an organism.
Genomics is the study of entire genomes(structure, function, evolution, mapping, and editing of genomes)
Executing the sequencing and analysis of entire human genome enables more rapid and effective identification of disease associated genes and provide drug companies with pre validated targets.
Proteomics is the systematic high-throughput separation and characterization of proteins within biological systems./ large scale study of protein and their functions.
Proteomics measures protein expression directly, not via gene expression, thus achieving better accuracy. Current work uses 2-dimensional polyacrylamide gel electrophoresis(2D- PAGE) and mass spectrometry.
New separation and characterization technologies, such as protein microarray and high throughput chromatography are being developed.
Introduction to proteomics, techniques to study proteomics such as protein electrophoresis, chromatography and mass spectrometry and protein database analysis, case studies derived from scientific literature including comparisons between healthy and diseased tissues, new approaches to analyse metabolic pathways, comprehensive analysis of protein-protein interactions in different cell types.
protein microarray_k.b institute (m.pharm pharmacology) .pptxNittalVekaria
1: Introduction
Welcome to our presentation on Protein Microarrays.
Discover the revolutionary technology transforming protein analysis and biomolecular research
2: What are Protein Microarrays?
Protein microarrays are high-throughput platforms for studying protein-protein interactions, protein function, and biomarker discovery.
They consist of thousands of immobilized proteins on a solid surface, allowing for simultaneous analysis of multiple proteins.
3Components of Protein Microarrays
Substrate: Glass slides, membranes, or beads.
Proteins: Target proteins immobilized on the substrate.
Detection System: Fluorescent dyes, antibodies, or other probes.
Imaging System: Scanners or cameras for data acquisition.
4: Types of Protein Microarrays
Analytical Microarrays: Used for studying protein-protein interactions, protein expression profiling, and protein function analysis.
Antibody Microarrays: Utilized for detecting and quantifying specific proteins or antibodies in biological samples.
Reverse-Phase Protein Arrays (RPPAs): Designed for high-throughput protein expression profiling and signaling pathway analysis.
5:Applications of Protein Microarrays
Biomarker Discovery: Identification of disease-specific biomarkers for diagnosis, prognosis, and treatment monitoring.
Drug Discovery: High-throughput screening of drug candidates and target validation.
Functional Proteomics: Mapping protein-protein interactions, post-translational modifications, and protein function analysis.
Clinical Diagnostics: Detection of infectious diseases, cancer biomarkers, and autoimmune disorders.
6: Workflow of Protein Microarray Experiment
Protein immobilization: Spotting or printing target proteins onto the microarray substrate.
Sample incubation: Incubating the microarray with biological samples containing proteins of interest.
Detection and analysis: Using fluorescent probes or antibodies to detect bound proteins and quantifying the signals.
Data interpretation: Analyzing and interpreting the results to extract meaningful biological insights.
7: Advantages of Protein Microarrays
-High-throughput analysis of thousands of proteins in parallel.
Small sample volume requirement.
Enables multiplexed assays for comprehensive protein profiling.
Facilitates rapid biomarker discovery and validation.
8: Challenges and Considerations
Standardization of protocols and reagents.
Optimization of protein immobilization and detection methods.
Data analysis and interpretation complexities.
Cost and accessibility of microarray platforms.
9: Future Perspectives
Integration with other omics technologies for holistic biological insights.
Development of miniaturized and portable microarray platforms for point-of-care diagnostics.
Advancements in data analysis algorithms and bioinformatics tools.
Expanding applications in personalized medicine and precision healthcare
10: Conclusion
Protein microarrays offer a powerful and versatile tool for protein analysis and biomarker discover
protein microarray_k.b institute (m.pharm pharmacology) .pptxNittalVekaria
1: Introduction
Welcome to our presentation on Protein Microarrays.
Discover the revolutionary technology transforming protein analysis and biomolecular research
2: What are Protein Microarrays?
Protein microarrays are high-throughput platforms for studying protein-protein interactions, protein function, and biomarker discovery.
They consist of thousands of immobilized proteins on a solid surface, allowing for simultaneous analysis of multiple proteins.
3Components of Protein Microarrays
Substrate: Glass slides, membranes, or beads.
Proteins: Target proteins immobilized on the substrate.
Detection System: Fluorescent dyes, antibodies, or other probes.
Imaging System: Scanners or cameras for data acquisition.
4: Types of Protein Microarrays
Analytical Microarrays: Used for studying protein-protein interactions, protein expression profiling, and protein function analysis.
Antibody Microarrays: Utilized for detecting and quantifying specific proteins or antibodies in biological samples.
Reverse-Phase Protein Arrays (RPPAs): Designed for high-throughput protein expression profiling and signaling pathway analysis.
5:Applications of Protein Microarrays
Biomarker Discovery: Identification of disease-specific biomarkers for diagnosis, prognosis, and treatment monitoring.
Drug Discovery: High-throughput screening of drug candidates and target validation.
Functional Proteomics: Mapping protein-protein interactions, post-translational modifications, and protein function analysis.
Clinical Diagnostics: Detection of infectious diseases, cancer biomarkers, and autoimmune disorders.
6: Workflow of Protein Microarray Experiment
Protein immobilization: Spotting or printing target proteins onto the microarray substrate.
Sample incubation: Incubating the microarray with biological samples containing proteins of interest.
Detection and analysis: Using fluorescent probes or antibodies to detect bound proteins and quantifying the signals.
Data interpretation: Analyzing and interpreting the results to extract meaningful biological insights.
7: Advantages of Protein Microarrays
-High-throughput analysis of thousands of proteins in parallel.
Small sample volume requirement.
Enables multiplexed assays for comprehensive protein profiling.
Facilitates rapid biomarker discovery and validation.
8: Challenges and Considerations
Standardization of protocols and reagents.
Optimization of protein immobilization and detection methods.
Data analysis and interpretation complexities.
Cost and accessibility of microarray platforms.
9: Future Perspectives
Integration with other omics technologies for holistic biological insights.
Development of miniaturized and portable microarray platforms for point-of-care diagnostics.
Advancements in data analysis algorithms and bioinformatics tools.
Expanding applications in personalized medicine and precision healthcare
10: Conclusion
Protein microarrays offer a powerful and versatile tool for protein analysis and biomarker discover
Typical molecular biomarkers include proteins, genetic mutations, and aberrant methylation patterns. abnormal transcripts, miRNAs, and other biological molecules. Protein biomarkers are considered reliable indicators of the disease state and clinical outcome as they are the endpoints of biological processes. Remarkable innovations in proteomic technologies in the last few years have greatly accelerated the process of biomarker discovery. https://www.creative-proteomics.com/services/proteomics-service.htm
Proteomics: types, protein profiling steps etc.Cherry
Proteome is a set of proteins produced in an organism, system, or biological context or entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain expressed time in a given set of condition. Proteomics is the study of all the proteins produced by a cell.
Presentation about how much bioinformatics involved in the medical field. This was presented at the University of Colombo in 2007 for an undergraduate seminar
Biological screening of herbal drugs: Introduction and Need for
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This presentation was provided by Steph Pollock of The American Psychological Association’s Journals Program, and Damita Snow, of The American Society of Civil Engineers (ASCE), for the initial session of NISO's 2024 Training Series "DEIA in the Scholarly Landscape." Session One: 'Setting Expectations: a DEIA Primer,' was held June 6, 2024.
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Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
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2. Proteomics
• The analysis of the entire protein complement
in a given cell, tissue, body fluid and organism
• Proteomics assesses activities, modifications,
localization, and interactions of proteins in
complexes.
4. • Proteome indicates the total proteins expressed by a genome in a cell or tissue
• Proteomics is increasingly being used to discover potential biomarkers
noninvasively.
• Biomarkers detection might allow identification of patients who would benefit
from further evaluation.
• With the development of proteomic techniques, proteome analysis provides a
fast, non-invasive diagnostic tool for patients with various diseases.
• The advent of highly sensitive proteomic technologies can identify proteins
associated with development of diseases well before any clinically identifiable
alteration.
• MS has a high resolving power and identifies proteins with more accuracy
• Proteomic technologies can be applied for an un-biased examination to detect
novel biomarkers that could play a critical role in disease diagnostics, treatment
monitoring and prognosis.
5. History of proteomics
• SDS-PAGE discovered by Laemmli in 1970.
• O’Farrell (1975) applied IEF to protein samples
prior to SDS-PAGE to pioneer the concept of 2-
DE.
• JJ Thomson (1913) identified M/Z ratio
• Hillenkamp (1988) developed MALDI-MS.
• Fenn (1988) developed ESI-MS
• In 1993, Henzel et al. reported the first work
related to the identification of protein from the
2DE.
• Marc Wilkins coined the word ‘proteome’ in
1995 PROTEins complement of the genOMICS
6. 2002 Nobel Prizes in
Chemistry
Mass spectrometry for macromolecules
"for their development of soft desorption
ionisation methods for
MS analyses of biological macromolecules"
Koichi Tanaka John B. Fenn
8. Experimental Work flow
Protein identification
(Sequest & Mascot)
Proper sample collection and storage
Sample pre-processing
Protein identification LC-MS/MS
Immuno depletion/protein concentration etc
In gel Tryptic digestion/ in-solution digestion
Bioinformatic Analysis
Protein separation by
1D SDS-PAGE/ 2DE
Or
Fractionation by LC
9. Proteomic techniques
• Gel based
– SDS-PAGE
– 2-DE
• Off gel base
– LC (SCX, RP-LC, Immuno affinity)
• Quantitative proteomics
– iTRAQ, ICAT, SILAC
• MS
– MALDI, LC-MS, SLDI, CE-MS
10. Data bases
• Data analysis search engines
• Sequest
• MASCOT
• X tandam
• Peaks
• Protein data bases
• NCBS
• Swiss port
12. • What is SDS-PAGE?
– SDS-PAGE a type of gel electrophoresis.
• What is the purpose of doing gel
electrophoresis?
– It has been seen that by running a gel we are able
to identify more proteins from the sample.
13. • An electric current is applied across the gel, causing proteins
will differentially migrate based on their molecular mass.
• Staining will be done by using Coomassie Blue dye R-250,
colloidal CBB G-250, Sypro ruby and silver stain
• periodic acid-Schiff (PAS), will be used to detect
glycoproteins.
14. 2-DE• Proteins separates based on
• PI
• MW
“You’ve got one protein missing …”
“No, you’ve one extra protein !”
19. Importance of Proteins
• they serve as catalysts that maintain metabolic processes in the cell.
• they serve as structural elements both within and outside the cell.
• they are signals secreted by one cell or deposited in the extracellular
matrix that are recognized by other cells.
• they are receptors that convey information about the extracellular
matrix to the cell.
• they serve as intracellular signaling components that mediate the effects
of receptors.
• they are key components of the machinery that determines which genes
are expressed and whether mRNAs are translated into proteins.
• they are involved in manipulation of DNA and RNA through processes
such as: DNA replication, DNA recombination, RNA splicing or editing.
20. applications
• What is Omics good for?
• WHAT? Biomarker / Drug target
• Establishing and mining proteome from
different species
21. • At least 200 different PTMs have been
identified.
22. • Expression proteomics
• Functional proteomics
• Mining: identification of proteins (catalog
the proteome)
• Protein-expression profile: identification of
protein interest in a particular state of the
tissue/organism
• Protein-network mapping: protein
interactions in living systems
• Mapping of protein modifications: how and
where proteins are modified.
25. • Proteomic applications in Diabetes
• Helps in protein changes duo to glycation
• molecular mechanisms underpinning disease
processes and the effects of treatment
• To understand the impact of: stress,
environmental stimuli, food, genetic and obesity,
etc.
• Tissue proteomics to understand pathophysiology
and drug target.
• Helps in early diagnosis of diabetic
complications.
• identifying new targets for therapeutic
development.
26. • Identification of surrogate markers looking at the
plasma/urine/tissue proteome at different stages
of development of diabetes, its complications.
• To study the signal transduction network of the
insulin receptor and/or other cell surface
receptors.
• Characterization of the proteome or a subset of
the proteome of animal and cell models
• Identification of novel signaling molecules and
pathways involved in cell development,
differentiation, communication, function and
destruction, etc.
• for studying the regulation, synthesis, secretion,
and action of hormones and cytokines
27. • Proteomic applications in Cancer
• Proteins serve as hallmark for the
physiological status of cell
• The ability of physicians to effectively treat
cancer is directly dependent on their ability
to detect cancers at their earliest stages.
• Proteomic technologies hold recently great
promise in the search of new biomarkers for
the early detection and the discovery of new
therapeutic targets.
28. • Proteomics technologies to identify unique
biosignatures and biomarkers responsible for the
diagnosis, prognosis and therapeutic prediction
of such disease.
• Biomarkers found in blood, other body fluids, or
tissues that are a sign of a normal or abnormal
process, or disease. They may also be used to see
how well the body responds to a treatment for a
disease or condition.