Table 3.
Community-built informatics tools integrated into the Skyline ecosystem.
| Tool | Creator | Integration Date | Purpose |
|---|---|---|---|
| BiodiversityPlugin | Computational Proteomics Group, Pacific Northwest National Laboratory (Payne et al 2015) | 2015 Jun 10 | mass spectrometry data retrieval by organism and biological pathway |
| MPPReport | Agilent Technologies | 2014 Sep 9 | data export for use in Agilent’s Mass Profiler Professional multivariate statistics software |
| MS1Probe | Gibson Lab, The Buck Institute for Research on Aging (Schilling et al 2012) | 2014 Apr 16 | high throughput statistical quantification of MS1 Filtering datasets |
| MSstats | Vitek Lab, Purdue University (Choi et al 2014) | 2015 Jul 30 | statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics |
| Population Variation | Computational Proteomics Group, Pacific Northwest National Laboratory (Fujimoto et al 2014) | 2013 Dec 20 | protein variant lookup from dbSNP and the 1000 Genome project |
| Prego | MacCoss lab, University of Washington (Searle et al 2015) | 2015 Jun 23 | peptide SRM response prediction |
| Protter | Wollscheid Lab, ETH Zurich (Omasits et al 2014) | 2015 Dec 19 | transmembrane protein topology visualization |
| QuaSAR | Carr Lab, Broad Institute of MIT and Harvard (Mani, Abbatiello, and Carr 2012) | 2014 Oct 23 | QC, statistical analysis, and visualization of data from quantitative MRM-MS |
| SProCoP | Bereman Lab, North Carolina State University (Bereman et al 2014) | 2014 Dec 3 | Visualization, detection, and identification of assignable causes of variation in LC-MS |