We curate images displaying protein co-purification banding patterns resulting from affinity capture followed
by e.g. SDS-PAGE and protein staining. We store the conditions of the experiment and link to the resulting banding
patterns so purifications under different conditions can be compared to one another.
We currently curate Saccharomyces cerevisiae, Escherichia coli, Mus Musculus and Homo sapiens genes and proteins. For more information on the
specification format for these species, please see our HOWTO page.
You may view gels currently in our public database,
which has been seeded with data resulting from our recently developed
affinity capture conditions screening process (Hakhverdyan et al),
and also create an account
if youíd like to upload
and manage your own gels. Your data are kept private until you choose to release them to the public (e.g. after publication).
For more details, please see the About page.
This is public beta version 0.9 of this site and it will continually evolve to meet the needs of curating and data
mining affinity capture co-purification experiments - as well as incorporating the latest appropriate "minimum information" standards.
feedback and collaboration
from the community.
* We have added support for the curation of Mouse genes via MGI systematic naming.
* A new feature has been added so that users can share Projects and Experiments with other users of the system.
* When conducting experiments either a single reagent or multiple reagents may used to separate the proteins
within a single lane of a gel. The decision to conduct an experiment either way can have an effect on results.
Comparing gels using different methods (single vs multiple) may cause issues in comparing data. The ability to
flag a lane as Single Reagent or Multiple Reagent has been added to the processing. Further, in searching gels for
further analysis, a researcher now has the ability to choose to include only Single Reagents or to include Multiple Reagents.
* The ability to assign a protein or possible proteins to gel data has now been added. At the lane level,
an XML file from a MS Search Engine may be assigned and used for further analysis. Currently, four search
engines are accepted: XTandem, SEQUEST, Mascot, MSGFPlus. In addition, proteins may be assigned at the band level.
This may be done by assigning a protein name to the band based on one of three Protein ID Methods (Western Blot, Mass
Spectrometry, or Other). When choosing MS, a file must be assigned as well just as in the lane assignment.
Interested in keeping abreast of our work on affinity capture optimization and data curation? Please enter your contact email
address here and we'll update you with the latest developments...
This site was created by Sarah Keegan, Zhanna Hakhverdyan, John LaCava and David Fenyo - and is supported and maintained
by The NCDIR and The Fenyo Lab.