Biology Reference
In-Depth Information
The World-2DPAGE Repository
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(http://world-2dpage.expasy.org/
repository/), recently created as a supplement to the World-2DPAGE
Constellation, aims to host gel-based proteomics data with protein iden-
tifications published in the literature for laboratories that do not have the
means of hosting a database. Data from two publications
73,74
are already
accessible, including four 2-DE image maps with nearly 1200 identified
spots. Practically, the users are asked to upload gel image(s), spot identi-
fication list(s), and MS data (if any); and to give relevant information on
protocols, publications, etc. If a dataset was already submitted as MS
identification data to the PRIDE repository (http://www.ebi.ac.uk/
pride/),
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then the same file can be reused for submission to the World-
2DPAGE Repository without any additional work. The bidirectional
cross-references between World-2DPAGE and PRIDE have been set up
to offer a smooth navigation between both repositories (between gel and
MS data).
The World-2DPAGE Constellation, as well as some of the other PIG
developments described in the previous sections, is detailed in Fig. 3 in
one single and typical 2-DE analysis workflow.
5. Conclusion
The present chapter has described a set of proteomics tools and analysis
platforms developed in our group in the past decade or so. Throughout
the years, the common trait of this collection has remained the pro-
duction of collaborative work with other proteomics groups. On the
one hand, the exchange with other dry lab groups led to the integra-
tion of, or with, other tools; among them is the long-term relationship
with the Swiss-Prot group of SIB, where care is taken to develop tools
that consider as much information from UniProtKB/Swiss-Prot
and other derived tools as possible. On the other hand, interaction
with wet lab groups, in particular with the Geneva Hospital and the
University of Geneva Faculty of Medicine, has contributed to the inte-
gration of data in dedicated databases and the adaptation and fine-
tuning of software.
