Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative

The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative

During the last 10 years, the Proteomics Standards Initiative from the Human Proteome Organization (HUPO-PSI) has worked on defining 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 experimental 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 publishing proteomics experiments particularly in specialized proteomics journals. Finally, we describe existing bioinformatics resources that generate MIAPE compliant reports or that check proteomics data files for MIAPE compliance.

The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/.

Enabling proteomics: the need for an extendable 'workbench' for user-configurable solutions

Proteomics has the capability to generate overwhelming quantities of data in relatively short timescales, and it is not uncommon to see experimenters investing substantially more time in data analysis than in data gathering. Although several sophisticated tools for data reduction and analysis are available, they lack the flexibility to cope with increasingly innovative experimental strategies and new database resources that encode both qualitative and quantitative data. I will outline a specification of a flexible proteomics tool that could address many current bottlenecks and deficiencies.

Proposal for a standard representation of two-dimensional gel electrophoresis data

The global analysis of proteins is now feasible due to improvements in techniques such as two-dimensional gel electrophoresis (2-DE), mass spectrometry, yeast two-hybrid systems and the development of bioinformatics applications. The experiments form the basis of proteomics, and present significant challenges in data analysis, storage and querying. We argue that a standard format for proteome data is required to enable the storage, exchange and subsequent re-analysis of large datasets. We describe the criteria that must be met for the development of a standard for proteomics. We have developed a model to represent data from 2-DE experiments, including difference gel electrophoresis along with image analysis and statistical analysis across multiple gels. This part of proteomics analysis is not represented in current proposals for proteomics standards. We are working with the Proteomics Standards Initiative to develop a model encompassing biological sample origin, experimental protocols, a number of separation techniques and mass spectrometry. The standard format will facilitate the development of central repositories of data, enabling results to be verified or re-analysed, and the correlation of results produced by different research groups using a variety of laboratory techniques.

Proteomics: A Paradigm Shift

Proteome--the protein complement of a genome--has become the protein renaissance and a key research tool in the post-genomic era. The basic technology involves the routine usage of gel electrophoresis and spectrometry procedures for deciphering the primary protein sequence/structure as well as knowing certain unique post-translational modifications that a particular protein has undergone to perform a specific function in the cell. However, the recent advancements in protein analysis have ushered this science to provide deeper, bigger and more valuable perspectives regarding performance of subtle protein-protein interactions. Applications of this branch of molecular biology are as vast as the subject is and include clinical diagnostics, pharmaceutical and biotechnological industries. The 21st century hails the use of products, procedures and advancements of this science as finer touches required for the grooming of fast-paced technology.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

Identification of protein associations in organelles, using mass spectrometry-based proteomics

Recent literature that highlights the power of using mass spectrometry (MS) for protein identification from preparations of highly purified organelles and other large subcellular structures is covered in this review with an emphasis on techniques that preserve the integrity of the functional protein complexes. Recent advances in distinguishing contaminant proteins from "bonafide" organelle-localized proteins and the affinity capture of protein complexes are reviewed, as well as bioinformatic strategies to predict protein organellar localization and to integrate protein-protein interaction maps obtained from MS-affinity capture methods with data obtained from other techniques. Those developments demonstrate that a revolution in cellular biology, fueled by technical advances in MS-based proteomic techniques, is well underway.

BioBuilder as a database development and functional annotation platform for proteins

Background

The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development.

Results

BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database , a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange.

Conclusions

As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.

Unraveling protein interaction networks with near-optimal efficiency

The functional characterization of genes and their gene products is the main challenge of the genomic era. Examining interaction information for every gene product is a direct way to assemble the jigsaw puzzle of proteins into a functional map. Here we demonstrate a method in which the information gained from pull-down experiments, in which single proteins act as baits to detect interactions with other proteins, is maximized by using a network-based strategy to select the baits. Because of the scale-free distribution of protein interaction networks, we were able to obtain fast coverage by focusing on highly connected nodes (hubs) first. Unfortunately, locating hubs requires prior global information about the network one is trying to unravel. Here, we present an optimized 'pay-as-you-go' strategy that identifies highly connected nodes using only local information that is collected as successive pull-down experiments are performed. Using this strategy, we estimate that 90% of the human interactome can be covered by 10,000 pull-down experiments, with 50% of the interactions confirmed by reciprocal pull-down experiments.

Update on chloroplast proteomics

Currently, relatively few proteomics studies of chloroplast have been published, but the field has just started emerging and is likely to develop more rapidly in the future. While the complex membrane structure of the chloroplast makes it difficult to study its entire proteome by global approaches, proteomics has considerably increased our knowledge of the proteins of single compartments such as, for instance, the envelope and the thylakoid lumen. Proteomics has also succeeded in the subunit characterisation of select protein complexes such as the ribosomes and the cytochrome b (6)f complex. In addition, proteomics was successfully applied to find new potential target pathways for thioredoxin-mediated signal transduction. In this review, we present an overview of the latest developments in the field of chloroplast proteomics and discuss their impact on photosynthesis research. In addition, we summarise the current state of research in proteomics of the photosynthetic cyanobactrium Synechocystis sp. PCC 6803.