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In-Depth Information
guidelines laying the foundations for a set of MIAPE guideline
modules would be published during the following years.
The MIAPE guidelines, as defi ned by HUPO-PSI, aim at list-
ing the information that should be provided while describing a
proteomics experiment. As a complete proteomics experiment can
be divided into smaller experimental and data analysis steps, the
various HUPO-PSI working groups, composed of experts from
different proteomics fi elds, has defi ned one or more MIAPE mod-
ules each covering one of these steps. The different MIAPE mod-
ules are the result of discussions between working group experts,
software developers, hardware developers and end users. The doc-
uments have further followed the formal review process internally
defi ned by PSI [
3
] and are available on the HUPO-PSI Web site
(
www.psidev.info
)
. In most of the cases, these guidelines have also
passed the review process of Nature Biotechnology as they have
been published there as well.
Subsequently, several joint sessions between HUPO-PSI and
publication committees were held [
4
,
5
], in which journals fed
back their opinions about how to ensure proteomics data quality
before publishing it; how to allow the reprocessing of the data;
whether to require raw data deposition in a public repository or
not; and how to tackle the adoption of MIAPE guidelines in their
respective instructions for authors. Most importantly, proteomics
journals have been taking part in these meetings, such as Nature
Biotechnology, Molecular and Cellular Proteomics, Proteomics,
Journal of Proteomics and Journal of Proteome Research. As a
result, several of these journals have been encouraging MIAPE
compliance [
1
,
8
,
10
] to submit manuscripts for several years.
It is quite important for the scientifi c community that MIAPE
guidelines become a standard that regulates the minimum infor-
mation compiled by every proteomics scientifi c publication, since
they will turn into a quality stamp to ensure a critical review and a
potential repetition of the results. In addition, it is also crucial that
tools are available to help authors of proteomics manuscripts as
well as proteomics data producers to reach compliance with mini-
mal technical burden.
2
The Proteomics Standards Initiative
Initiated on 2002, the Proteomics Standards Initiative (PSI) is an
open community and one of the 13 scientifi c initiatives of HUPO
that involves researchers, database providers, vendors, software
developers and publishers. Its mission statement is: HUPO-PSI
defi nes community standards for data representation in proteomics
to facilitate data comparison, exchange and verifi cation. Five main
