Japan Partnering Award: Establishment of an Integrative proteomics bioinformatics platform to enable novel analysis approaches

Lead Research Organisation: European Bioinformatics Institute
Department Name: Proteomics Services Team

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Publications

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Deutsch E (2017) The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition in Nucleic Acids Research

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Deutsch EW (2020) The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. in Nucleic acids research

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Deutsch EW (2023) Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. in Journal of proteome research

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Deutsch EW (2017) Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. in Journal of proteome research

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Deutsch EW (2021) Universal Spectrum Identifier for mass spectra. in Nature methods

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Deutsch EW (2023) The ProteomeXchange consortium at 10 years: 2023 update. in Nucleic acids research

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Jarnuczak AF (2017) Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets. in Current protocols in bioinformatics

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Perez-Riverol Y (2019) The PRIDE database and related tools and resources in 2019: improving support for quantification data. in Nucleic acids research

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Perez-Riverol Y (2022) The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. in Nucleic acids research

 
Title jPOST becomes a member of ProteomeXchange 
Description jPOST (https://jpost.org/) is a proteomics data resource developed by various Japanese organisations (PI is Prof. Yasushi Ishihama). In the context of this grant, jPOST joined ProteomeXchange, the international Consortium of proteomics resources (www.proteomexchange.org). 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact jPOST is now a member of the ProteomeXchange Consortium 
URL http://www.proteomexchange.org
 
Description PSI Spring Meeting 2017 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface).

The 2017 PSI Spring Workshop was held in Beijing, China at the National Center for Protein Sciences, Beijing (Phoenix Center). The workshop was chaired by Eric Deutsch and the local organizer, Henning Hermjakob. The opening session featured presentations by researchers who have implemented the standards and formats developed by the PSI to further their research work or tool development. Henry Lam (Hong Kong University of Science and Technology) described his work developing applications using spectral libraries in proteomics. In his talk, Lam argued that the process of spectral library building can be improved by first clustering by similarity and then selecting high-quality and confidently identified clusters to be included in the library. Although clustering spectra by similarity is more computationally intensive than simply grouping spectra by identifications, this process is a more robust mechanism for quality control and the detection of errors in spectral libraries. Finally, given the important role of spectral libraries and archives as an information hub and shared community resource, he challenged the PSI to develop a standardized data interchange format, which is currently sorely lacking. Such a standardized format will greatly simplify software development and enable better integration and interoperability of workflows involving spectral libraries and archives.

Jun Qin, Director of the Phoenix Center, updated the attendees on the status of proteomic sciences in China. The Phoenix Center groups have achieved fast proteome sequencing, although there is still an issue with low abundance proteins, which first need to be enriched in a sample. The institute is developing Firmiana, a one-stop proteomic cloud platform for data analysis and processing.8 The aim is to reduce the cost of medicine, with the China Human Proteome Project (CNHPP) focusing on the 10 cancers most prevalent in China.

The chairs from the different working groups gave an update on their activities, including nonpurely PSI activities such as ProteomeXchange and the status of metabolomics data standards. The workshop then split into parallel work-tracks for each of the developing formats and standards for the next 2 days, combining presentations with discussion and hands-on development work. A final plenary session reviewed the results of the working groups' activities at the end of the workshop.
Year(s) Of Engagement Activity 2017
URL http://www.psidev.info/content/hupo-psi-meeting-2017