Systematic Protein Investigative Research Environment (SPIRE) provides web-based experiment-specific

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 use ...

(MS)

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 ...

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 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 expe ...

s 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 data through its

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) ...

(MOPED). SPIRE can provide analysis and annotation for user-supplied protein ID and expression data. Users can upload data (standardized appropriately) or mail in data files.

Methodology

Integration with other information

References

Further reading