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[edit]
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[edit]
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[edit]
- ^ 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[edit]
- 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.