Biology Reference
In-Depth Information
Chapter 53
The Minimal Information About a Proteomics Experiment
(MIAPE) from the Proteomics Standards Initiative
Salvador Martínez-Bartolomé , Pierre- Alain Binz , and Juan P. Albar
Abstract
During the last 10 years, the Proteomics Standards Initiative from the Human Proteome Organization
(HUPO-PSI) has worked on defi ning standards for proteomics data representation as well as guidelines
that state the minimum information that should be included when reporting a proteomics experiment
(MIAPE). Such minimum information must describe the complete experiment, including both experi-
mental protocols and data processing methods, allowing a critical evaluation of the whole process and the
potential recreation of the work. In this chapter we describe the standardization work performed by the
HUPO-PSI, and then we concentrate on the MIAPE guidelines, highlighting its importance when pub-
lishing proteomics experiments particularly in specialized proteomics journals. Finally, we describe existing
bioinformatics resources that generate MIAPE compliant reports or that check proteomics data fi les for
MIAPE compliance.
Key words
Proteomics, HUPO-PSI, MIAPE, Standards, Reporting, Guidelines, Semantic validator
1
Introduction
With the growing number of variations of high-throughput pro-
teomics techniques in the last 10 years, the scientifi c community
soon detected the need to defi ne reporting guidelines that ensure
some minimal data and meta-data quality and consistency as a
requirement prior to publish protein and peptide identifi cation
data. Following this, a group of experts proposed the so-called
PARIS guidelines in 2004 [
1
]—later revised in 2005—and then
implemented in the instructions for authors by the journal
Molecular and Cellular Proteomics. Then, during 2006 and 2007,
the Proteomics Standards Initiative (PSI) [
2
] from the Human
Proteome Organization (HUPO), developed the concept of the
set of Minimal Information about a Proteomics Experiment
(MIAPE) guidelines, based on the experience of the micro-array
community with their MIAME guidelines. A MIAPE parent docu-
ment [
3
,
4
] which defi nes the principles and objectives of MIAPE
