Current instrumentation, methodologies and workflows
Equipment. Currently the following instruments are operational at the facility:
Search engines/computer software
- Database search servers: MASCOT, SEQUEST Cluster, Proteome discorverer and MaxQuant. The Sequest cluster is running on a dedicated 8 node double processor server.The proteome discovere is running on a 32 procesor computer server.
- PEAKS (from Bioinformatics solutions). new software tool for protein identification and quantization, de novo peptide seqiuencing. To download a viewer click here.
- HDExaminer (from Sierra Analytics) is now our prefer software for analysis of protein dynamics by HDX MS
Some of the tools used at our facility have been custom build:
- HDXFinder (software for D/H Exchange analysis): A set of web-based computer applications for assisted Deuterium Exchange Mass Spectrometry Analyisis. Access to this portal is free to academic users. Optimized for Mozilla Firefox. A draft of the manual can be downloaded here. Programer: Danny Miller. A project in collaboration with A. Fenton:
- SAIDE: a cooling chamber for DX MS experiments. This is an interface for HPLC and MS build by Mecour.
- M.T. Villar, D. E. Miller, A.W. Fenton and A. Artigues: SAIDE: A Semi-Automated Interface for Hydrogen /Deuterium Exchange Mass Spectrometry. (2010) Proteomica 6:63-69.
- We are currently working in a fully automatic version of this interface with capability to measure H/DX at the subsecond time scale.
Our new cell is a combo, a shorter version of the SS that has a transparent insert that can be used for sample loading.
Feb 08, 2017