NewS

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.

We are pleased to announce the results of the 2023 HIPP election. We would like to thank Jenn Abelin, Nicola Ternette and Wei Wu for agreeing to stand for election. The newly elected members of the HUPO-HIPP leadership team are:

Chair:  Nicola Ternette Co-chair: Jenn Abelin
University of Oxford   Broad Institute

A word from our newly elected Chair:

Thank you all for your participation in the HUPO-HIPP elections 2023! I am very honoured to take on the position as Chair of HUPO-HIPP together with Jenn Abelin. We would like to take this opportunity to thank Michal Bassani for her excellent leadership throughout the past two years, which enabled us to present and discuss important findings in the field in three high-profile webinars and allowed us to hold the 2nd HUPO-HIPP Summer School in Oxford, UK last year.

Jenn and I will continue our efforts to facilitate discussions in the field of immunopeptidomics together with the executive committee, with its current members Michal Bassani, Pouya Faridi, Annika Nelde, Krystel Vincent, and Wei Wu. We would also like to welcome Susan Klaeger to the executive committee, as our first industry representative.  We are keen to learn whether there are suggestions or nominations for additional members of our committee, and or hearing from you what would be a priority for the HUPO-HIPP team from your perspective. Do not hesitate to contact us at hupo.hipp@gmail.com. 

We will get in touch soon with more information on the establishment of working groups and activities not to miss in the immunopeptidomics community.

All best wishes,

Nicola & Jenn

DATE:  Tuesday, May 2, 2023

TIME:   8 am PDT / 10 am CDT / 11 am EDT

SPEAKERS AND PRESENTATION TOPICS:

1. Vadim Demichev: “Using Slice-PASEF to maximise proteomics sensitivity.”
2. Manuel Matzinger: “High throughput single cell proteomics using ultrashort gradients and Wide-Window Acquisition to reach unprecedented proteome coverage and quantitative accuracy.”
3. Ben Osborn: ”Applying single cell proteomics to answer questions in human pharmacology”
4. Claudia Ctortecka: “Versatile and reproducible single-cell protein profiles define cell sub-populations at high throughput”
5. Sarah Parker: “Single Cell Proteomic Analysis of Complex Tissue: Case study in the Aorta”

REGISTER HERE

Join us for the 4th ETC Auditorium - Writing: The Key to Funding Your Research

DATE: Wednesday, April 12, 2023

TIME:   7 am PDT / 9 am CDT / 10 am EDT

Writing a successful grant application is hard work—regardless of your career level. Once you've convinced yourself that you have a compelling research project, you have to find a way to convince the reviewers and then the funding agency to support you. This webinar will cover fundamental essentials of a successful research proposal, including choice of grant category, PI and collaborators/co-investigators in addition to writing style, organization, and documentation. Guidance about shared instrumentation grant applications will also be presented.

SPEAKER: Dr. Susan Weintraub has been been actively engaged in biomedical mass spectrometry since 1971. She is a co-author of more than 180 scientific papers published in peer-reviewed journals in addition to six book chapters. She completed a six-year term on the Board of Directors of the American Society for Mass Spectrometry (ASMS), serving as Vice President for Programs (2010 - 2012), President (2012 - 2014) and Past President (2014 - 2016). She is currently a member of the HUPO Council and chair the HUPO Mass Spectrometry Resource Pillar. She is also an Associate Editor for the Journal of Proteome Research, with a primary assignment of computational mass spectrometry manuscripts. In 2018, she was elected a Fellow of the American Association for the Advancement of Science. Dr Weintraub's publications can be found in her PubMed Bibliography

PANELISTS:

• Giuseppe Palmisano: Professor - Department of Parasitology, University of Sao Paulo, Brazil
• Brian Searle: Assistant Professor - Department of Biomedical Informatics, State Ohio University Medical

REGISTER HERE

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

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 3rd event featured Ruedi Aebersold from ETH Zurich, Switzerland. Prof. Ruedi Aebersold is an emeritus Professor at ETH Zurich who is an international leader in proteomics field and mentored many scientists. Ruedi's lab has pioneered several widely-used techniques and tools that have contributed to today's proteomics research. His publications have been cited 196,000 times with an h-factor of 214, according to Google Scholar.

The talk emphasized a number of key ideas on why and how paper writing contributes to a successful scientific career as a significant factor, including:

• A paper only matters if it describes progress in the field
• Publishing your work in a way that supports your career goals
• The reason why prestigious journals have a high IF is that they manage to include a small number of papers that have >100-1000s citations
• Publications that are more cooperative generally have a higher impact, especially those describing research at the interface of disciplines
• Make the text easier and clear: One paper one message
• Before you start writing: define the science story and tell it to the lab and other audiences who are not scientists
• Use a foolproof structure and track through the main topics e.g., the discussion should be focused on putting the new results in context and point out limitations
• Developing writing skills by practicing writing and structured talks and using short clear sentences
• Before you submit: anticipate what reviewers might object to and make sure every co-author agrees with the paper.
• Grow a "thick skin" towards rejections: never take the rejection personally and improve and address the criticism factually.
• Talk to the editors to adjust expectations for additional data and grievances with reviewers.
• Avoid frequent problems: write one paper at a time- but do it.
• Perfection is an elusive goal: freeze the story at the point of saturation and let reviewers define the path to perfection.
• After publishment: increase the paper's visibility and impact through social media and conferences.

Ruedi also addressed some voted live questions from PollEverywhere, such as his views on ChatGPT and how that would affect scientific writing.

The session was hosted by Yansheng Liu (Yale University School of Medicine), Blandine Chazarin (Cedars-Sinai Heart Institute), and Deepti J Kundu (PRIDE and EBI).

A full video recording of the session including the figure clinic and Q&A session is available on the HUPO YouTube channel. An alternative link for those who don’t have access to YouTube can be viewed here.

The manuscript competition is a great opportunity for early career researchers to showcase their work. Each year three finalists are selected to present their manuscripts in a plenary session during HUPO’s world congress. We reached out to last year’s finalists and asked a few questions to learn about their experience in the competition at HUPO 2022 in Cancun, Mexico. Take a look at what they had to say.

Ling Hao’s Interview:

Dr. Ling Hao was a finalist in the 2022 HUPO ECR manuscript competition, for which she presented her work: Thiol-Cleavable Biotin for Chemical and Enzymatic Biotinylation and its Application to Mitochondrial TurboID Proteomics in a plenary session. We asked a few questions to Dr. Hao about her experience in the competition. Read what she had to say below!

What is your current position and affiliation?

I am an Assistant Professor of Chemistry in the George Washington University in Washington, DC, USA. 

How would you like your work to contribute to the field of proteomics?

I hope that our research work can lead to both proteomics method advancements and a deeper understanding of molecular mechanisms of brain diseases. I also hope to support students and postdocs through classroom teaching and individual mentoring, so that they can enjoy research and pursue their dream careers in the proteomics field. 

How was your experience and what did it mean to you to present your work at the HUPO World Congress?

It was a tremendous honor and encouragement to present our research during the 2022 HUPO ECR manuscript competition and also be selected as the HUPO Rising Star Award. I received a lot of valuable feedback to improve our research work. I felt much empowered to continue our research, pushing our science forward and supporting young researchers in the field. 

What have you found in the HUPO community/congress?

I deeply appreciate and value both the exciting science and supportive environment in the HUPO community. My proteomics journey started when I was a graduate student in Prof. Lingjun Li's group in University of Wisconsin-Madison. Learning how cutting-edge proteomics techniques were developed to advance diverse aspects of human health (both in the Li Lab and during HUPO Congress) were eye-opening experiences. During the 2022 HUPO Congress, I learned about the exciting new pi-hub project as the proteomic navigator of the human body. I was also super impressed by how amazing and supportive the HUPO ECR group is. 

Wout Bittremieux’s Interview:

Dr. Wout Bittremieux was a finalist and first prize winner in the 2022 HUPO ECR manuscript competition. He presented his work on:  A learned embedding for efficient joint analysis of millions of mass spectra.

What is your current position and affiliation?

I recently started as an assistant research professor at the University of Antwerp, Belgium.

How would you like your work to contribute to the field of proteomics?

Building on recent breakthroughs in artificial intelligence that have led to disruptive advances across many scientific domains, my career is oriented towards developing powerful computational solutions to uncover novel biological and biomedical insights from proteomics data.

What have you found in the HUPO community/congress?

HUPO has an extremely vibrant and welcoming community. I was especially impressed by the various dedicated activities for early career researchers, as well as the open and friendly atmosphere throughout the entire conference.

How was your experience/what did it mean to present your work at HUPO? 

The HUPO 2022 World Congress was my first time attending the HUPO meeting and I had a blast. With engaging discussions in the Bioinformatics Hub, an exciting scientific program, participating in the ECR Manuscript Competition, and even a little bit of beach time in between, HUPO 2022 was the year's highlight.

Ready to apply? Click here to learn more about how you can submit your work for the competition.