The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.
Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.
The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
Genome-based peptide fingerprint scanning (GFS) is a system in bioinformatics analysis that attempts to identify the genomic origin of sample proteins by scanning their peptide-mass fingerprint against the theoretical translation and proteolytic digest of an entire genome. This method is an improvement from previous methods because it compares the peptide fingerprints to an entire genome instead of comparing it to an already annotated genome. This improvement has the potential to improve genome annotation and identify proteins with incorrect or missing annotations.
Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrumentations have been developed for its many uses. Its applications include the identification of proteins and their post-translational modifications, the elucidation of protein complexes, their subunits and functional interactions, as well as the global measurement of proteins in proteomics. It can also be used to localize proteins to the various organelles, and determine the interactions between different proteins as well as with membrane lipids.
In proteomics, GPM stands for "Global Proteome Machine". It is a web-based, open source user interface for analyzing and displaying protein identification data. It was originally designed by Rob Craig and Ron Beavis and first released in 2003. The interface creates a series of web browser page views of tandem mass spectrometry data that has been assigned to protein sequences. The underlying data documents are stored in BIOML format files.
Marc R. Wilkins is an Australian scientist who is credited with the defining the concept of the proteome. Wilkins is a Professor in the School of Biotechnology and Biomolecular Sciences at the University of New South Wales, Sydney.
CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) is a scientific research institute devoted primarily to biological research. It is a part of Council of Scientific and Industrial Research (CSIR), India.
Proteogenomics is a field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides. Proteogenomics is used to identify new peptides by comparing MS/MS spectra against a protein database that has been derived from genomic and transcriptomic information. Proteogenomics often refers to studies that use proteomic information, often derived from mass spectrometry, to improve gene annotations. The utilization of both proteomics and genomics data alongside advances in the availability and power of spectrographic and chromatographic technology led to the emergence of proteogenomics as its own field in 2004.
Secretomics is a type of proteomics which involves the analysis of the secretome—all the secreted proteins of a cell, tissue or organism. Secreted proteins are involved in a variety of physiological processes, including cell signaling and matrix remodeling, but are also integral to invasion and metastasis of malignant cells. Secretomics has thus been especially important in the discovery of biomarkers for cancer and understanding molecular basis of pathogenesis. The analysis of the insoluble fraction of the secretome has been termed matrisomics.
The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization. Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome.
Mitali Mukerji is a Professor and Head of the Department of Bioscience and Bioengineering, IIT Jodhpur. She was formerly a Chief Scientist at the CSIR Institute of Genomics and Integrative Biology with notable achievement in the field of human genomics and personalized medicine. She is best known for initiating the field of "Ayurgenomics" in partnership with her colleague Dr. Bhavana Prasher under the mentorship of Prof. Samir K. Brahmachari. Ayurgenomics is an innovative study, blending the principles of Ayurveda- the traditional Indian system of medicine- with genomics. Mukerji is also a major contributor in the Indian Genome Variation Consortium, a comprehensive database that is producing "the first genetic landscape of the Indian population", and has been an author in many publications that use IGV databases to study population genomics. Mukerji has done extensive research on hereditary ataxias, and is involved in many other projects related to tracking disease origins and mutational histories. She is the recipient of the prestigious Shanti Swarup Bhatnagar Award in 2010 for her contribution in the field of Medical Sciences.
Ronald Charles Beavis is a Canadian protein biochemist, who has been involved in the application of mass spectrometry to protein primary structure, with applications in the fields of proteomics and analytical biochemistry. He has developed methods for measuring the identity and post-translational modification state of proteins obtained from biological samples using mass spectrometry. He is currently best known for developing new methods for analyzing proteomics data and applying the results of these methods to problems in computational biology.
Zeng Rong is a Chinese biochemist researching and developing technology for proteomics research. She is currently a professor at the Institute of Biochemistry and Cell Biology at the Shanghai Institutes for Biological Sciences.
David Fenyö is a Hungarian-Swedish-American computational biologist, physicist and businessman. He is currently professor in the Department of Biochemistry and Molecular Pharmacology at NYU Langone Medical Center. Fenyö's research focuses on the development of methods to identify, characterize and quantify proteins and in the integration of data from multiple modalities including mass spectrometry, sequencing and microscopy.
The Institute of Bioinformatics, often referred to as IOB, is an Indian not-for-profit academic research organization based in Bangalore, India. It is involved in research in the fields of bioinformatics, multi-omics, systems biology and neurological disorders. In 2002, the institute was set up by The Genomics Research Trust and the Johns Hopkins University of Baltimore, Maryland. This organization is recognized as a 'Scientific and Industrial Research Organization' (SIRO) of the Department of Scientific and Industrial Research, Government of India. Renowned Proteomicist Akhilesh Pandey, Professor at Department of Laboratory Medicine and Pathology, Center for Individualized Medicine of Mayo Clinic in Rochester, Minnesota, USA is the Founding and current Director of IOB, and eminent Proteomicist Ravi Sirdeshmukh, Founder President of the 'Proteomic Society of India' is the current Associate Director of IOB.
Shoba Ranganathan is an Indian Australian biochemist who is a professor of bioinformatics at Macquarie University. Her research considers computational biology and bioinformatics, genome annotation and structural bioinformatics.
Ravi Sirdeshmukh is an Indian cancer biologist and proteomicist. He is a distinguished scientist and incumbent associate director of the Institute of Bioinformatics (IOB) in Bangalore, founding president of the Proteomics Society of India and senior research advisor at the Mazumdar Shaw Center for Translational Research (MSCTR) in Bangalore. He is also an elected member of the Council of Human Proteome Organization. He is most noted for his contributions in the Human Proteome Project where he served as the Group Leader for the countries like India, Singapore, Taiwan and Thailand. Sirdeshmukh is also an invited member of the Council of Asian Oceanean HUPO (AOHUPO).
