SummaryAlthough computational mass spectrometry (MS) has greatly boosted proteomics research, software for MS searches is generally underutilized. When using MS software, scientists face three obstacles: fiddly software chaining, time-consuming execution, and unfriendly user interfaces. Due to these obstacles, using such software becomes a laborious, tedious, and error-prone experience. To alleviate the struggling, some researchers bring in integrated software platforms that automate the worst of the whole process. However, MS searches grow complex quickly and so do obstacles, which grow faster than most platforms can accommodate and therefore we often end up tailoring them, but in vain. To address this problem, our ProteoSAFe Proteomics Environment is Scalable in utilizing distributed computing, Accessible via reconfigurable, easy-to-learn user interfaces, and Flexible in tool chaining.
WorkflowsVersion 1.2.3 of ProteoSAFe contains the following pre-defined workflows:
- InsPecT - protein identification database search (with MS-Cluster)
- MS-Alignment - database search with blind PTM discovery (with MS-Cluster)
- PepNovo - de novo peptide sequencing
Installation information and other documentation can be found here.
A powerful tool for PTM discovery (Jan 2008, Journal of Proteome research, Vol 7. Issue 1)
From spectral networks to shotgun sequencing (June 2007, Nature Methods, Vol. 4 No. 6)
Identifying peptides without a database (May 2007, Journal of Proteome Research)
UCSD Computer Scientist Wins Young Investigator Award, Research on Snake Venom Proteins Highlighted (Nov 2006, UCSD)