Biology Reference
In-Depth Information
6
Discussion
The HUPO Proteomics Standards Initiative's developments are
nowadays crucial for proteomics data interpretation, sharing and
reprocessing. The defi nition of standards formats and the provision
of tools that read and write these formats are particularly benefi cial
for highly collaborative scientifi c projects in which different pro-
teomics laboratories with different equipment are exchanging data.
This is also true for centralizing data and meta-data from variable
sources in a repository such as PRIDE and therefore facilitates
compliance with journals' requirements on data deposition.
However, a minimal “quality control” (i.e., in the sense of MIAPE
compliance) on proteomics data is desired in order to ensure that
any reported, shared or published proteomics work has the mini-
mum information that will allow a clear review of the performed
procedures and produced data, as well as to allow a potential rec-
reation of the work. We have described in this chapter a number of
different bioinformatics resources that are available to help users to
comply with required guidelines.
With this chapter, we present PSI standardization develop-
ments to the scientifi c community, in particular the MIAPE
guidelines and related resources. These guidelines and associated
tools are useful to help the community in producing, exchanging,
interpreting and fi nally publishing proteomics data using a com-
mon language. In this era where datasets can live and exist by
themselves, where they can obtain a DOI and become citable as
proposed by the proteomeXchange consortium (
www.proteom-
exchange.org
)
, it is of interest for the whole community to appro-
priately generate well annotated datasets that can be reused and
reinterpreted if needed.
Acknowledgments
This publication was supported by the Spanish National Research
Council (CSIC), the Spanish National Proteomics Institute
(ProteoRed-ISC III) (grant number 2005X747_3) and by the EU
FP7 “ProteomeXchange” (EU FP7 grant number 260558) grants.
The Swiss-Prot group is part of the SIB Swiss Institute of
Bioinformatics. This activity is supported by the Swiss Federal
Government through the The State Secretariat for Education,
Research and Innovation SERI and by the European Union proj-
ect “ProteomeXchange” (EU FP7 grant number 260558).
