NewS

Open data practices in proteomics: the why, the how and the what for?

The goal of the ETC Auditorium "Stylish Academic Writing" professional development webinar series is to help students and trainees improve their scientific writing skills. The 5th webinar featured Dr. Juan Antonio Vizcaino, Proteomics Team Leader at the European Bioinformatics Institute (EMBL-EBI), as the lecturer. The discussion focused on the latest trends in open data practices in proteomics. Dr. Deepti Jaiswal Kundu, a Scientific Curator at the PRIDE database (EMBL-EBI) served as the host and Dr. Tiannan Guo, a Tenured Associate Professor at Westlake University, participated as a panelist.

This webinar focused on the advantages of open data sharing in proteomics and its potential to drive research, collaboration, and innovation. Dr. Vizcaino highlighted the importance of data repositories, such as PRIDE, MassIVE, JPOST, iProX, and Panorama, in facilitating open data sharing. The webinar emphasized the FAIR data principles (Findable, Accessible, Interoperable, and Re-usable) and encouraged researchers to contribute their proteomics data and promote collaboration within the scientific community. Inspiring examples of data re-use were showcased, along with the bottlenecks associated with utilizing public proteomics data, such as data complexity and lack of metadata annotation. The webinar stressed the significance of proper metadata documentation and introduced the Sample Description and Result Format (SDRF) file format to improve metadata annotation and enable meaningful re-use of proteomics data. Lastly, the challenges of data privacy, intellectual property rights, data standardization, and data curation were addressed, with strategies and recommendations provided to promote responsible and effective sharing of proteomics data.

Dr. Vizcaino also addressed some live questions (Q & A):

1.     Q:  How do you envision the future of the data repositories, knowing that data sets are now containing more and more samples, like single cells or instruments producing large data?

A:  It’s a continuous struggle that usually happens. We keep on innovating in terms of infrastructure in terms of keeping and dealing with large data. We take the experience /suggestions from other EBI repositories (e.g. those devoted to DNA/RNA sequencing data) about how they manage large datasets.

2.     Q:  The availability of sample metadata is crucial for identifying samples which are an important aspect of open data practices. A single large amount of data in PRIDE have metadata missing in them. So, what are your suggestions for the submitters in PRIDE.

A:  When ProteomeXchange started on that time the emphasis was put on data provision. But now it is more and more clear the necessity of more metadata. And that’s why the SDRF annotation has been proposed which is now promoted by PRIDE to submitters.

3.     Q:  Many journals have dedicated data availability sections where accessions are mentioned. Have you considered using these top detect publications with PRIDE id?

A:  We do that. We check the abstract of the publication and the full text (in the case of open-access journals).

4.     Q:  Are there any options in PRIDE to keep the RAW data private even if the article is public?

A:  The policy of ProteomeXchange is as soon as publication is out, the data needs to be public. There are some exceptional cases when data is sensitive like clinical data. We do not have any mechanism yet for the controlled access data but in the future, we might have to include it.

A:  Datasets that are re-used the most are the ones that are more scientifically relevant, e.g. those published in high-profile journals. A second criterium includes those which are annotated better, where people don’t have to work on those.

A full video recording of the session including the talk and Q&A session is available on the HUPO YouTube channel website (https://www.hupo.org/Webinars-and-Virtual-Presentations).

For those with no access to YouTube, an alternative link is: https://www.bilibili.com/video/BV1Ph411c7ij/?spm_id_from=333.788.recommend_more_video.-1&vd_source=052ff6e1ca06b197e00a9a80affeda05.

The June HUPOST is now available.  Many updates this month, including important upcoming congress deadlines, ECR updates, ETC news....and much more!

The C-HPP is holding a workshop prior to the HUPO 2023 Congress in Busan, Korea at the Centum Premier Hotel in the "Chelsea and Liverpool rooms" on Sunday, 17th September, 09:30 –15:00.

Those who would like to be present are asked to register for free - the sign up sheet is here.

Please pass this onto your students and colleagues who might be attending.

Agenda

09:30 Meet and Greet coffee/tea

10:00-12:00 Session 1 

Welcome, quick Chromosome Team updates:

• neXtProt, human proteome numbers from the 2023-04-18 release (Lydie Lane, Eric Deutsch, Nuno Banderia),
• HPP (Cecilia Lindskog)
• JPR Special Issue (Chris Overall)
• Other business from matters arising from the PIC.
• Special presentation on “Chemoproteomics as an enabling technology for the aims of the C-HPP for PTM, MPs or CP50 research” by Ho Jeong Kwon, Director, Chemical Genomics Leader Research Initiative, Yonsei University, President-Elect, Korean Society for Biochemistry and Molecular Biology (KSBMB).

12:00 - 13:00 Lunch

13:00 Session 2: Future Aims and plans for the C-HPP/HPP and neXtProt

Discussions will include new directions for the C-HPP with an action plan for Human Proteome PTM, MPs, and CP50 (as part of the Grand Challenge) incorporating neXtProt.

15:00 Meeting closes

(15:30 HUPO Council)

Deadline extended to June 1st

The clock is ticking, and this is your last chance to seize the spotlight and share your ground-breaking work! The 3-Minute Thesis Competition challenges you to condense your research findings into a compelling and concise presentation, delivering it in just three minutes using a single static slide.

Whether you're investigating novel biomarkers, unraveling complex protein interactions, or developing cutting-edge analytical techniques, your research deserves to be heard and celebrated. The 3-Minute Thesis Competition allows you to distill your work to its essence and effectively communicate its significance to a non-specialist audience.

Selected finalists will have the exciting opportunity to compete in the final showdown, to be held during a dedicated session at HUPO 2023 Busan (September 17-21). To participate, simply submit a lay abstract via the HUPO 2023 abstract submission portal without scientific jargon that describes your Ph.D. thesis research topic for a general, non-expert audience. Abstract text should not exceed 300 words and entrants must be enrolled in a Ph.D. program.

Submit your abstract here.

Deadline extended to June 1st

Last call to participate in the HUPO 2023 Poster Competition! This is your chance to showcase your research findings, innovative methodologies, and exciting discoveries to a global audience. All graduate students (Master’s and Ph.D.), as well as postdocs, are encouraged to participate in the HUPO 2023 poster competition taking place on September 17-21, 2023 in Busan, South Korea.

This competition provides a platform for you to present your work in a visually engaging format, fostering discussions and collaborations with fellow researchers. Presenting a poster allows you to highlight the significance and impact of your research while fostering meaningful interactions with colleagues from around the world. To participate, simply indicate your interest in the competition while submitting your abstract by checking the appropriate box. A set of posters will be selected as finalists and will be evaluated during the conference by a jury. Winners in both categories (graduate students and postdocs) will each receive cash prizes.

Submit you abstract here today!

The Journal of Proteome Research is preparing to publish its 11th annual special issue dedicated to highlighting the progress made on the HUPO Human Proteome Project (HPP). The editorial team invites you to submit a manuscript for consideration by August 15, 2023.

For this special issue, the editorial team will consider research papers encompassing the HUPO HPP Grand Challenge, Chromosome-Centric Human Proteome Project (C-HPP) and the Biology and Disease Human Proteome Project (B/D-HPP), as well from the HPP Resource Pillars (Antibody, MS, Pathology, and Knowledgebase), and short definitive reports, submitted in the Letters format, on the discovery of a missing protein(s).

More details are available at the JPR website.

The 10th HUPO HPP Special Issue has been published in the April issue of the Journal of Proteome Research (https://pubs.acs.org/toc/jprobs/22/4). As a consequence of lab shut downs in the pandemic, a smaller and later Special Issue was necessary. The hallmark anchor paper of every Special Issue is the HPP Metrics paper, lead by Dr Gil Omenn and the leaders of neXTprot, the Peptide Atlas, the HPP, C-HPP and B/D-HPP: “The 2022 Report on the Human Proteome from the HUPO Human Proteome Project” by Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch (https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00498)

ABSTRACT: The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, “A Function for Each Protein”.

For 2024, the format of the 11th HUPO HPP Special Issue will differ. Papers focused on the HPP, the neXt-MP50, the neXt-CP50, and the Grand Challenge will be published in regular JPR issues after acceptance during this year. In December 2023 a HUPO HPP Virtual Issue will be compiled of these HPP papers and related articles published over the year.

For reports on missing protein discovery, authors must use the 2023-04-18 release of neXtProt and the checklist for the credible identification of missing proteins (https://www.nextprot.org/news/new-release-with-updated-proteomics-data).

An example of the HPP Virtual Issue is now online  HUPO Human Proteome Project Virtual Special Issue, Associate Editor, Dr Chris Overall. This collection includes papers published this past year as part of the 10th HUPO HPP Special Issue, now online, along with highly cited papers from HUPO HPP SI’s of years past.

DATE: Thursday, May 25, 2023

TIME:  8:00 am EDT / 1:00 pm BST

LECTURER: Dr. Juan Antonio Vizcaino, Proteomics Team Leader, European Bioinformatics Institute (EMBL-EBI)

PANELISTS:

• Dr. Tiannan Guo (host), Tenured Associate Professor, Westlake University
  
• Dr. Deepti Jaiswal Kundu, Scientific Curator (PRIDE archive), EMBL-EBI

After registering, you will receive a confirmation email containing information about joining the webinar.

The May HUPOST is now available.  There's lots of updates including congress info, Single Cell webinar, ECR news, HUPO Awards and Elections....and much more!

The HUPO Early Career Researcher (ECR) Initiative is delighted to welcome Darien Tayba Schell and Seanantha Baros-Steyl.

Darien Tayba Schell is a Ph.D. student at the University of Cape Town, South Africa, supervised by Prof. Jonathan Blackburn. Her research aims to better understand host responses to mycobacterial phosphatases during infection using phosphoproteomic methods. She is skilled in mass spectrometry, microscopy, and R programming. During her BMedSci Hons degree, specializing in structural biology, she became intrigued by mass spectrometry in relation to proteomics. She hopes that her findings contribute to the field of Tuberculosis research and provides a framework for the development of more effective TB treatments in the future. Darien looks forward to contributing to the future growth of the ECR.

Seanantha Baros-Steyl is a Ph.D. student at the University of Cape Town, South Africa, working under the supervision of Prof. Jonathan Blackburn. Her current research focuses on identifying host-pathogen protein-protein interactions within the context of tuberculosis. She employs mass spectrometry-based proteomic and phosphoproteomic pipelines to uncover the mechanisms driving disease progression and identify potential therapeutic targets. She also has a strong interest in leveraging programming languages, particularly Python and R, to enhance mass spectrometry data analysis and visualisation. Seanantha is passionate about diseases of the developing world and strives to use her expertise to contribute to the advancement of drug discovery and development and improve the lives of people affected by these diseases. She is committed to making a positive impact within the HUPO community.