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Systematic Protein Investigative Research Environment
Systematic Protein Investigative Research Environment (SPIRE) provides web-based experiment-specific mass spectrometry (MS) proteomics analysis in order to identify proteins and peptides, and label-free expression and relative expression analyses. SPIRE provides a web-interface and generates results in both interactive and simple data formats. Methodology Spire's analyses are based on an experimental design that generates false discovery rates and local false discovery rates (FDR, LFDR) and integrates open-source search and data analysis methods. By combining X! Tandem, OMSSA and SpectraST SPIRE can produce an increase in protein IDs (50-90%) over current combinations of scoring and single search engines while also providing accurate multi-faceted error estimation. SPIRE combines its analysis results with data on protein function, pathways and protein expression from model organisms. Integration with other information SPIRE also connects results to publicly available proteomics d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Seattle Children's Research Institute
Seattle Children's, formerly Children's Hospital and Regional Medical Center, formerly Children's Orthopedic Hospital, is a children's hospital in the Laurelhurst neighborhood of Seattle, Washington. The hospital specializes in the care of infants, children, teens, and young adults aged 0–21 in several specialties. History The hospital was founded as the seven-bed Children's Orthopedic Hospital in 1907 by Anna Herr Clise after her 5-year-old son, Willis, died of inflammatory rheumatism in 1898. It was originally a ward of the downtown Seattle General Hospital. It moved to a cottage on Queen Anne Hill the next year, and in 1911 influential community members including Herbert Gowen and Mark A. Matthews dedicated a full 40-bed hospital at the same location. The library at the hospital was founded in 1946. In 1953, Children's moved to a new campus in Laurelhurst, east of the University of Washington. A research division, Seattle Children's Research Institute (SCRI), was es ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionized, for example by bombarding it with a beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragments) are then separated accordin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of 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 proteome is the entire set of proteins produced or modified by an organism or system. Proteomics enables the identification of ever-increasing numbers of proteins. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefited greatly from the genetic information of various genome projects, including the Human Genome Project. It covers the exploration of proteomes from the overall level of protein composition, structure, and activity, and is an important component of functional genomics. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
False Discovery Rate
In statistics, the false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the expected proportion of "discoveries" (rejected null hypotheses) that are false (incorrect rejections of the null). Equivalently, the FDR is the expected ratio of the number of false positive classifications (false discoveries) to the total number of positive classifications (rejections of the null). The total number of rejections of the null include both the number of false positives (FP) and true positives (TP). Simply put, FDR = FP / (FP + TP). FDR-controlling procedures provide less stringent control of Type I errors compared to family-wise error rate (FWER) controlling procedures (such as the Bonferroni correction), which control the probability of ''at least one'' Type I error. Thus, FDR-controlling procedures have greater power, at the co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry Software
Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. Proteomics software In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and ''de novo'' search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data. Database search algorithms De novo sequencing algorithms De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels ''et al.'' (1990). Homology searching algorithms MS/MS peptide quantification Other software See also * Mass spectrometry data format: for a list of mass spectrometry data viewers and format converters. * List of protein ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multi-Omics Profiling Expression Database
The Multi-Omics Profiling Expression Database (MOPED) was an expanding multi-omics resource that supports rapid browsing of transcriptomics and proteomics information from publicly available studies on model organisms and humans. As to date (2021) it has ceased activities and is unaccessible online. Systematic Protein Investigative Research Environment MOPED is designed to simplify the comparison and sharing of data for the greater research community. MOPED employs the standardized analysis pipeline SPIRE to uniquely provide protein level absolute and relative expression data, meta- analysis capabilities and quantitative data. Processed relative expression transcriptomics data were obtained from the Gene Expression Omnibus (GEO). Data can be queried for specific proteins and genes, browsed based on organism, tissue, localization and condition, and sorted by false discovery rate and expression. MOPED empowers users to visualize their own expression data and compare it with existing ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of 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 proteome is the entire set of proteins produced or modified by an organism or system. Proteomics enables the identification of ever-increasing numbers of proteins. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefited greatly from the genetic information of various genome projects, including the Human Genome Project. It covers the exploration of proteomes from the overall level of protein composition, structure, and activity, and is an important component of functional genomics. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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