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Public database of protein mass spectrometry data in Europe
The PRIDE (PRoteomics IDEntifications database) is a public data repository of mass spectrometry-based proteomics data, and is maintained by the European
Proteomics Identifications Database
Proteomics_Identifications_Database
Large-scale study of proteins
Proteomics is the large-scale study of proteins. The proteome is the entire set of proteins produced or modified by an organism or system. Proteomics
Proteomics
sequences can be found in a reference database such as the Proteomics Identifications Database. Proteogenomics helps eliminate this reliance on existing
Proteogenomics
Database of biological information
including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function
Biological_database
False-discovery Rate for Protein Identifications from Mascot Database Search Results". Molecular & Cellular Proteomics. 4 (6): 762–72. doi:10.1074/mcp
List of mass spectrometry software
List_of_mass_spectrometry_software
International working group
The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate
Proteomics Standards Initiative
Proteomics_Standards_Initiative
Data Bank Proteomics Identifications Database PsycINFO PubChem PubMed Central Questia – defunct Rate Your Music REBASE Restriction Enzyme Database RedLightGreen
List_of_online_databases
Shotgun proteomics refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance
Shotgun_proteomics
in high-throughput proteomics is called top-down proteomics and does not use proteolytic digestion. Essentially, bottom-up proteomics is a relatively simple
Bottom-up_proteomics
Topics referred to by the same term
European Space Agency (ESA) unmanned spaceplane project Proteomics Identifications Database, or PRIDE Boston Pride, a professional ice hockey team (2013–2023)
Pride_(disambiguation)
Data analysis software for proteomics
The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the
Trans-Proteomic_Pipeline
Mass spectrometry proteomic analysis software suite
of proteomics software are commonly used for peptide identification (protein ID) through de novo peptide sequencing assisted search engine database searching
PEAKS
Set of proteins that can be expressed by a genome, cell, tissue, or organism
(December 2007). "Viral proteomics: global evaluation of viruses and their interaction with the host". Expert Review of Proteomics. 4 (6): 815–829. doi:10
Proteome
Major developments include the following: Creation of GPMDB: a large proteomics database generated using GPM; Inclusion in the Human proteome project as a
Gpm_(proteomics)
protein identification using mass spectrometry (MS; Bottom Up proteomics). Top-down proteomics using mass spectrometry interrogates protein structure through
Top-down_proteomics
resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases PIR was established in 1984 by the
Protein_Information_Resource
Systematized collection of data in bioinformatics
proteomics and genomics. This sort of databases summarize books, articles, book reviews, dissertations, and annotations about gene-disease databases.
Gene–disease_database
approaches: a digestion-free, top-down method and bottom-up proteomics. Top-down proteomics is seldom used to analyse ancient proteins due to analytical
Ancient_protein
used in the small molecules mass spectra identification since the 1980s. In the early years of shotgun proteomics, pioneer investigations suggested that
Peptide_spectral_library
Database of protein sequences and functional information
Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation
UniProt
Protein identification software
certain to be spurious identifications, but we can't discriminate between true and false positives identified in the target database. FDR estimation was
Mascot_(software)
Application of mass spectrometry
Slavov, Nikolai (January 2022). "Scaling Up Single-Cell Proteomics". Molecular & Cellular Proteomics. 21 (1) 100179. doi:10.1016/j.mcpro.2021.100179. PMC 8683604
Protein_mass_spectrometry
Techniques used to study protein–small molecule interactions
Chemoproteomics (also known as chemical proteomics) entails a broad array of techniques used to identify and interrogate protein-small molecule interactions
Chemoproteomics
Type of mass spectrometry
spectrometer, this is called "bottom-up proteomics". Shotgun proteomics is a variant of bottom up proteomics in which proteins in a mixture are digested
Tandem_mass_spectrometry
American chemist
researchers in the world. His work is focused on developing tools and in proteomics and he specializes in mass spectrometry. He is best known for the development
John_R._Yates
spectrum is reported as the best identification for this spectrum. Bottom-up proteomics Mascot (software) Shotgun proteomics Jimmy K. Eng, Ashley L. McCormack
Sequest
Containers for scientific data
2012). "File formats commonly used in mass spectrometry proteomics". Molecular & Cellular Proteomics. 11 (12): 1612–21. doi:10.1074/mcp.R112.019695. PMC 3518119
Mass_spectrometry_data_format
Swedish-American physicist and mass spectrometrist
systems for automated analysis of large-scale proteomics data. Subsequently, he served as the Director of Proteomics at Genomic Solutions, and as Staff Scientist
David_Fenyő
Sub-discipline of biology
by Positional Proteomics. ACS Chem. Biol. 10, 1754-1764 (2015). Eckhard U., Marino G., Butler G. S., Overall C. M. Positional proteomics in the era of
Degradomics
Analytical technique for protein identification
results table. Protein mass spectrometry Shotgun proteomics Top-down proteomics Bottom-up proteomics Clauser KR, Baker P, Burlingame AL (1999). "Role
Peptide_mass_fingerprinting
Scientific project coordinated by the Human Proteome Organization
2008). "Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea". Proteomics. 8 (9): 1750–1753. doi:10.1002/pmic
Human_Proteome_Project
Sequencing of amino acid arrangement in a protein
additional evidence for protein identifications performed as above. The peptides matched during protein identification do not necessarily include the N-
Protein_sequencing
Biomolecule consisting of chains of amino acid residues
sets defines the field of proteomics, named by analogy to the related field of genomics. Key experimental techniques in proteomics include 2D electrophoresis
Protein
Branch of proteomics
Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing a phosphate group as a posttranslational modification
Phosphoproteomics
Mass spectrometry software
correct identifications. Tanimoto similarities are also given. The COSMIC confidence score assigns a confidence to CSI:FingerID structure identifications. The
SIRIUS_(software)
Species of venomous snake
and Antivenom Immunoprofiling: Identification of Key Toxin Targets for Antivenom Development". Journal of Proteomics. 119: 126–142. Bibcode:2015JProt
Black_mamba
of Canada. Her work on interaction proteomics, was awarded, alongside John Yates, the Discovery Award in Proteomics from the Human Proteome Organization
Anne-Claude_Gingras
Analytical chemistry technique
swiftly. LC–MS is used in proteomics as a method to detect and identify the components of a complex mixture. The bottom-up proteomics LC–MS approach generally
Liquid chromatography–mass spectrometry
Liquid_chromatography–mass_spectrometry
Protein-coding gene in the species Homo sapiens
"Phosphoproteomic analysis of the developing mouse brain". Mol. Cell. Proteomics. 3 (11): 1093–101. doi:10.1074/mcp.M400085-MCP200. PMID 15345747. Ota
TSEN2
Human gene database maintained by the Weizmann Institute of Science
GeneCards is a database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted
GeneCards
Small molecule (PROTAC)
protein degradation induced by a small molecule: En route to chemical proteomics". Bioorganic & Medicinal Chemistry Letters. 18 (22): 5904–5908. doi:10
Proteolysis_targeting_chimera
Chemical labels used to quantify biomolecules via mass spectrometry
Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance*[S]". Molecular & Cellular Proteomics. 18 (10): 2108–2120
Tandem_mass_tag
Functional Element SNPs Database (FESD) is a biological database of single nucleotide polymorphisms in molecular biology. The database is a tool designed to
Functional element SNPs database
Functional_element_SNPs_database
Study of large set of protein
proteins". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. Medical Proteomics. 1854 (6): 592–600. doi:10.1016/j.bbapap.2014.10.011. PMC 5524126
Immunoproteomics
Biological analysis approach
September 2016). "ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis". Scientific Reports. 6 (1) 32713
Multiomics
Software for understanding biological data
especially in computational biology and bioinformatics, including genomics, proteomics, microarrays, systems biology, evolution, and text mining. Prior to the
Machine_learning_in_biology
spectrometry Proteomics Mass spectrometry in the biological sciences James, P.; Quadroni, M.; Carafoli, E.; Gonnet, G. (1993-08-31). "Protein identification by
Peptide-mass_fingerprint
Scientific study of chemical processes involving metabolites
single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome is dynamic, changing
Metabolomics
independent analysis and hyper reaction monitoring". Expert Review of Proteomics. 10 (6): 551–566. doi:10.1586/14789450.2013.858022. ISSN 1478-9450. PMID 24206228
Data-independent_acquisition
biochemistry at The University of Texas at Austin, working in genetics, proteomics, and bioinformatics. Marcotte is an example of a computational biologist
Edward_Marcotte
Mammalian protein found in humans
PMID 2323781. S2CID 21989261. Aulak KS, Cicardi M, Harrison RA (June 1990). "Identification of a new P1 residue mutation (444Arg----Ser) in a dysfunctional C1 inhibitor
SERPING1
Swedish microbial culture repository
diagnosis of infectious diseases mainly by using molecular, genomic and proteomic approaches. "CCUG". European Culture Collections Organisation. 8 August
Culture Collection (University of Gothenburg)
Culture_Collection_(University_of_Gothenburg)
(2005). "Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines". Proteomics. 5 (16): 4082–95. doi:10.1002/pmic
Peptide_sequence_tag
Short length polypeptides
polypeptides are, in fact, translated from a sORF. Proteogenomics combines proteomics, genomics, and transciptomics. This is important when looking for potential
Micropeptide
Membrane enclosed compartments in chloroplasts and cyanobacteria
Peltier J, Friso G, Kalume D, et al. (2000). "Proteomics of the Chloroplast: Systematic Identification and Targeting Analysis of Lumenal and Peripheral
Thylakoid
Computational analysis of large, complex sets of biological data
species), or differences between populations. Bioinformatics also includes proteomics, which aims to understand the organizational principles within nucleic
Bioinformatics
Medical condition
Turk LS, Ozgul S, Kakehi S, von Daake S, Lopez N, et al. (June 2019). "A Proteomic Screen of Neuronal Cell-Surface Molecules Reveals IgLONs as Structurally
Anti-IgLON5_disease
Transcriptomics, Metagenomics, Proteomics, Metaproteomics, Metabolomics and Cloud Computing Bioinformatics for Proteomics (BioInfra.Prot): Members: Ruhr
German Network for Bioinformatics Infrastructure
German_Network_for_Bioinformatics_Infrastructure
Medical model that tailors medical practices to the individual patient
including health and disease, so proteomics is helpful in early diagnosis. In the case of respiratory disease, proteomics analyzes several biological samples
Personalized_medicine
Chemical changes in proteins following their translation from mRNA
(December 2011). "The First Identification of Lysine Malonylation Substrates and Its Regulatory Enzyme". Molecular & Cellular Proteomics. 10 (12) M111.012658
Post-translational modification
Post-translational_modification
Physical interactions and constructions between multiple proteins
2004). "Human protein reference database as a discovery resource for proteomics". Nucleic Acids Research. 32 (Database issue): D497–D501. doi:10.1093/nar/gkh070
Protein–protein_interaction
American pathologist (died 2021)
Allen Brain Atlas. Proteomics and Knowledge Mining - At Novartis, Boguski's division was responsible for the application of proteomics technologies and
Mark_Boguski
Technique used for determining crystal structures and identifying mineral compounds
(October 2006). "The impact of protein characterization in structural proteomics". Acta Crystallographica. Section D, Biological Crystallography. 62 (Pt
X-ray_crystallography
Species of bacteria, cause of plague
(November 2006). "Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics". Journal of Proteome Research. 5
Yersinia_pestis
Process in computational biology
active research in the various omics fields such as transcriptomics, proteomics, metabolomics, and more generally structural and functional genomics.
Gene_prediction
Swiss academic
developed proteomics software and databases, in particular the Melanie 2-D gel electrophoresis analysis software and the SWISS-2DPAGE database, as well
Ron_Appel
including microarray (MIAME), RNAseq (MINSEQE), metabolomics (MSI) and proteomics (MIAPE). Minimum information standards typically have two parts. Firstly
Minimum_information_standard
Largest known protein in human muscles
2021-02-13. Retrieved 2010-10-15. "ProtParam for human titin". ExPASy Proteomics Server. Swiss Institute of Bioinformatics. Archived from the original
Titin
Extinct species of mammoth
Orlando, L.; Willerslev, E.; Gilbert, M. T. P.; Olsen, J. V. (2012). "Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred
Woolly_mammoth
Chemical entity which can be bound by an antibody
peptide-based vaccines, and immunodiagnostic tools. Epitopes are often used in proteomics and the study of other gene products. Using recombinant DNA techniques
Epitope
Prediction of where a protein resides in a cell
"ProtSecKB (The Protist Secretome and Subcellular Proteome KnowledgeBase)". proteomics.ysu.edu. Retrieved 2017-09-17. Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber
Protein subcellular localization prediction
Protein_subcellular_localization_prediction
Molecular biology technique
possibility of a high number of false positive (and false negative) identifications. The exact rate of false positive results is not known, but earlier
Two-hybrid_screening
American life sciences company
nicking enzymes and DNA methylases. It pursues research in areas related to proteomics, DNA Sequencing, and drug discovery. NEB scientists also conduct basic
New_England_Biolabs
Protein-coding gene in humans
Zhao Y, White MA (June 2007). "Broad spectrum identification of SUMO substrates in melanoma cells". Proteomics. 7 (13): 2216–21. doi:10.1002/pmic.200600971
CPLANE1
Protein-coding gene in the species Homo sapiens
"Phosphoproteomic analysis of the developing mouse brain". Molecular & Cellular Proteomics. 3 (11): 1093–101. doi:10.1074/mcp.M400085-MCP200. PMID 15345747. Polci
NIMA-related_kinase_1
Data about other data
quantities of data, including results of genome or meta-genome sequencing, proteomics data, and even notes or plans created during the course of research itself
Metadata
Family of pufferfish
on land". Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. 1 (1): 153–157. doi:10.1016/j.cbd.2005.11.003. ISSN 1744-117X. Archived
Tetraodontidae
Prediction by observation and computation
Genome Institute provides an Integrated Microbial Genomes and Microbiomes database (JGI IMG) that has a phylogenetic profiling tool for single genes and gene
Protein–protein interaction prediction
Protein–protein_interaction_prediction
Scientific discipline
work to improve proteomics through the development of enrichment strategies, chemical affinity tags, and new probes. Samples for proteomics often contain
Chemical_biology
Key enzyme of photosynthesis involved in carbon fixation
Jwa NS, Rakwal R (February 2009). "Rice proteomics: ending phase I and the beginning of phase II". Proteomics. 9 (4): 935–963. doi:10.1002/pmic.200800594
RuBisCO
Detection of mRNA molecules
2% of the total. While knowledge of the precise proteins a cell makes (proteomics) is more relevant than knowing how much messenger RNA is made from each
Gene_expression_profiling
Genus of bacteria
PMID 15143043. Poetsch, A. (2011). "Proteomics of corynebacteria: From biotechnology workhorses to pathogens". Proteomics. 11 (15): 3244–3255. doi:10.1002/pmic
Corynebacterium
Method in natural language processing
representation can be widely used in applications of deep learning in proteomics and genomics. The results presented by Asgari and Mofrad suggest that
Word_embedding
Professor of biochemistry
2012-05-02. Retrieved 2022-09-15. "Cambridge Centre for Proteomics". Cambridge Centre for Proteomics, University of Cambridge. 2018-08-06. Retrieved 2022-09-15
Kathryn_S_Lilley
Field of science that uses cells for the creation of products
various areas, such as functional genomics, structural genomics, and proteomics, and forms a key component in the biotechnology and pharmaceutical sector
Biotechnology
Lung disease involving long-term poor airflow
"Advances in phosphoproteomics and its application to COPD". Expert Review of Proteomics. 19 (7–12): 311–324. doi:10.1080/14789450.2023.2176756. PMID 36730079
Chronic obstructive pulmonary disease
Chronic_obstructive_pulmonary_disease
Discipline in genetics
refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics. The related suffix -ome is used to address the objects
Genomics
Protein-coding gene in the species Homo sapiens
a novel protein, Frigg, as a protein kinase A substrate". Mol. Cell. Proteomics. 1 (7): 517–27. doi:10.1074/mcp.M200010-MCP200. PMID 12239280. Sun G,
SUN domain-containing protein 2
SUN_domain-containing_protein_2
Genus of bacteria
Wick, Charles H., ed. (2013). Identifying Microbes by Mass Spectrometry Proteomics. Hoboken: CRC Press. ISBN 978-1-4665-0496-7. Pabulo H, Rampelotto (2016)
Oceanobacillus
Biological process
the citrullinated residues, or detected using mass spectrometry-based proteomics technologies. Citrullination of arginine results in a monoisotopic mass
Citrullination
Single nucleotide in genomic DNA at which different sequence alternatives exist
(June 2019). "PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants"
Single-nucleotide polymorphism
Single-nucleotide_polymorphism
Family of digestive enzymes
Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping". Molecular & Cellular Proteomics. 19 (12): 2139–2157. doi:10.1074/mcp
Trypsin
Part of the University of New South Wales in Australia
in the development and application of bioinformatics for genomics and proteomics. Researchers at the facility include: Modifications generate conditional
UNSW_Faculty_of_Science
Open-Source Workflow Management Platform
(2020). "Scalable Data Analysis in Proteomics and Metabolomics Using Bio Containers and Workflows Engines". Proteomics. 20 (9) e1900147. doi:10.1002/pmic
Nextflow
Species of venomous snake
toxicity and antivenomics profiling of available antivenoms". Journal of Proteomics. 172: 173–189 [178]. doi:10.1016/j.jprot.2017.08.016. hdl:10261/279110
Eastern_green_mamba
Swiss bioinformatician
for protein analysis. Her efforts have been instrumental in advancing proteomics research, particularly through her contributions to the ExPASy (Expert
Elisabeth_Gasteiger
Protein-coding gene in the species Homo sapiens
Mann M (2001). "Mass spectrometry allows direct identification of proteins in large genomes". Proteomics. 1 (5): 641–50. doi:10.1002/1615-9861(200104)1
ZG16B
Study of biochemical processes in an individual cell
(August 2016). "Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes". Molecular & Cellular Proteomics. 15 (8): 2616–2627
Single-cell_analysis
Species of snake
and antivenom immunoprofiling: Identification of key toxin targets for antivenom development". Journal of Proteomics. 119: 126–142. doi:10.1016/j.jprot
Jameson's_mamba
Canadian protein biochemist (born 1958)
spectrometry to protein primary structure, with applications in the fields of proteomics and analytical biochemistry. He has developed methods for measuring the
Ronald_Beavis
travel, tourism, insurance
PROTEOMICS IDENTIFICATIONS-DATABASE
PROTEOMICS IDENTIFICATIONS-DATABASE
Girl/Female
German
Mighty with a spear. Note: 'This Database is Copyright Muse Creations Inc. 2000'.
Biblical
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Boy/Male
English
English surnames related to Bradley: broad clearing in the wood. Note: This Database is Copyright...
Girl/Female
English
Adventurous. Note: This Database is Copyright 2000, Muse Creations Inc.
Girl/Female
Native American
Power of the moon Note: 'This Database is Copyright Muse Creations Inc. 2000'.
Girl/Female
English
which is a . Note: 'This Database is Copyright Muse Creations Inc. 2000'.
Girl/Female
German
Bright angel Note: 'This Database is Copyright Muse Creations Inc. 2000'.
Girl/Female
Russian
crowned with laurels. Note: 'This Database is Copyright Muse Creations Inc. 2000'.
Boy/Male
Spanish
Conqueror. Note: This Database is Copyright 2000, Muse Creations Inc.
Surname or Lastname
English (chiefly West Midlands)
English (chiefly West Midlands) : (of Norman origin): habitational or regional name from Old French mansel ‘inhabitant of Le Mans or the surrounding area of Maine’. The place was originally named in Latin (ad) Ceromannos, from the name of the Gaulish tribe living there, the Ceromanni. The name was reduced to Celmans and then became Le Mans as a result of the mistaken identification of the first syllable with the Old French demonstrative adjective.English (chiefly West Midlands) : status name for a particular type of feudal tenant, Anglo-Norman French mansel, one who occupied a manse (Late Latin mansa ‘dwelling’), a measure of land sufficient to support one family.English (chiefly West Midlands) : some early examples, such as Thomas filius Manselli (Northumbria 1256), point to derivation from a personal name, perhaps the Germanic derivative of Mann 2 Latinized as Manzellinus.
Surname or Lastname
English (Devon)
English (Devon) : habitational name, probably from Morecombelake in Dorset (recorded as Mortecumbe in 1240). The second element of this is Old English cumb ‘short valley’, ‘combe’ (see Coombe); the first is probably either an Old English personal name, Morta (see Mort) or mort ‘young salmon or similar fish’. The surname is not from Morecambe in Lancashire, which is an 18th-century coinage, based on identification of Morecambe Bay with Morikambē ‘great gulf’ in the work of the ancient Greek geographer Ptolemy.
Boy/Male
Latin
Yearning; sorrow. Abbreviation of Desiderus.Note: This Database is Copyright Dogwood Technical...
Girl/Female
Polish
Christian. Note: 'This Database is Copyright Muse Creations Inc. 2000'.
PROTEOMICS IDENTIFICATIONS-DATABASE
PROTEOMICS IDENTIFICATIONS-DATABASE
PROTEOMICS IDENTIFICATIONS-DATABASE
PROTEOMICS IDENTIFICATIONS-DATABASE
PROTEOMICS IDENTIFICATIONS-DATABASE
PROTEOMICS IDENTIFICATIONS-DATABASE
PROTEOMICS IDENTIFICATIONS-DATABASE
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