Systematic Protein Investigative Research Environment

Systematic Protein Investigative Research Environment
Content
Description web based mass spectrometry (MS) proteomics analysis tool
Contact
Research center Seattle Children's Research Institute
Laboratory Bioinformatics & High-throughput Analysis Laboratory
Authors Eugene Kolker
Primary citation Kolker, et al.[1]
Release date 2011
Access
Website SPIRE

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 data through its Multi-Omics Profiling Expression Database (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.

References

  1. ↑ Kolker E, Higdon R, Morgan P, Sedensky M, Welch D, Bauman A, Stewart E, Haynes W, Broomall W, Kolker N (December 2011). "SPIRE: Systematic protein investigative research environment". J Proteomics. 75 (1): 122–6. doi:10.1016/j.jprot.2011.05.009. PMID 21609792.

Further reading

  • Stelzer G, Dalah I, Stein TI, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, Krug H, Perco P, Mayer B, Kolker E, Safran M, Lancet D (October 2011). "In-silico human genomics with GeneCards". Hum. Genomics. 5 (6): 709–17. doi:10.1186/1479-7364-5-6-709. PMC 3525253. PMID 22155609.
  • Kolker E, Higdon R, Haynes W, Welch D, Broomall W, Lancet D, Stanberry L, Kolker N (January 2012). "MOPED: Model Organism Protein Expression Database". Nucleic Acids Res. 40 (Database issue): D1093–9. doi:10.1093/nar/gkr1177. PMC 3245040. PMID 22139914.
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