NewS

The ECR Mentoring Sessions provide a space for mentors and mentees to come together and openly discuss relevant topics about navigating an early career.

These sessions highlighted the importance of opening a dialogue about the many factors that influence our careers. Thank you to all the speakers listed below for their honest advice and to the many early career researchers who attended and took the opportunity to ask questions!

Mental Health: Building resilience to manage work and job search stress
Chairs:

• Ireshyn Govender (Council for Scientific and Industrial Research, South Africa, ZA)
• Martha Ingola (Bayer AG, Preclinical Development, Germany, DE)

Speakers:

• Jennifer Geddes-McAlister (University of Guelph)
• Stuart Cordwell (The University of Sydney)
• Adriana Franco Paes Leme (Brazilian Biosciences National Laboratory)

The mental health mentoring session at HUPO 2024 shed light on the importance of managing one’s mental health throughout their scientific journey. Presentations showed an intimate look into the personal experiences of the three speakers which were well received by everyone, including senior researchers and ECRs.

The speakers all shared valuable tips for maintaining a positive outlook especially in the light of rejection which is a common occurrence in the scientific world. Listening to their experiences brought a sense of comfort knowing that rejection happens to everyone and it is not personal.

Finally, the panel discussion afforded attendees an opportunity to directly engage with the panelists. A wide array of questions were posed from participants at different career stages.

This led to fruitful discussions where the panelists and other attendees shared their thoughts and advice.

Mastering mentorship: Navigating conflicts and personalities
Chairs:

• Livia Rosa-Fernandes (Centre for Motor Neuron Disease Research, Sydney / AU)
• Daniel Garama (Monash University, Melbourne / AU)

Speakers:

• Dr. Blandine Chazarin (Postdoctoral Scientist at PRISM laboratory, France)
• Dr. Chiara Francavilla, (Associate Professor at DTU Bioengineering, and an honorary Senior Research Fellow, University of Manchester)
• Dr. Parag Mallick (Associate Professor at Stanford University and Chief Scientist at Nautilus Biotechnology, a next-generation proteomics company)

The mentoring session "Mastering Mentorship: Navigating Conflicts and Personalities," was a captivating convergence of professionals from diverse geographical regions and various career stages in both industry and academia.

The session provided a platform for speakers to share their career paths and the significant impact of conflict situations on their professional growth.

Attendees gained insights into the characteristics of challenging personalities and acquired strategies to manage, mitigate, and resolve conflicts effectively. A common thread among the concerns shared by attendees was the profound effect of difficult situations on career progression and mental health, including the potential loss of employment or projects, and the pervasive influence of a toxic work environment on the overall group dynamics.

The diverse backgrounds of the speakers contributed to a nuanced discussion about the attendees' worries, which included navigating jealousy and favoritism, as well as other detrimental dynamics that can be often found well-established in research groups.

Moreover, the session delved into the essential qualities of effective leadership and set expectations for the mentor-mentee relationship. The speakers maintained a positive outlook on conflict resolution, advocating for the expression of concerns in a respectful and considerate manner as the initial step towards addressing challenging scenarios. They also emphasized the importance of being open to constructive criticism and recognizing one's role within the dynamics of the relationship.

Career Paths: What’s Next in Your Career?
Chairs:

• Jessica Del Castillo (Sanquin, Utrecht University, Amsterdam, NL)
• Christian Moritz (University Hospital CHU of Saint-Étienne, FR)

Speakers:

• Christoph Krisp (Application Development Specialist Proteomics at Bruker Daltonics, DE)
• Maurine Fucito (Application Specialist at Evosep, DK, and President of the Young Proteomics Investigators Club)
• Uli Ohmayer (Co-founder and Head of Mass Spectrometry at NEOsphere Biotechnologies, DE)
• John Yates (Editor-in-Chief, Journal of Proteome Research, and Professor at the Scripps Research Institute, US)

The Career Paths: What’s Next in Your Career? session kicked off HUPO 2024 with Early Career Researchers eager to hear firsthand insights from experienced professionals across academia and industry. Speakers shared valuable lessons from their own career journeys, discussing essential moments and strategies that helped shape their paths.

The speakers emphasized the importance of self-reflection to understand one's goals, the role of networking to build professional relationships, and the added value of international experience in today’s globalized scientific landscape.

During the lively panel discussion, attendees asked pressing questions, including practical advice for those who find networking challenging—particularly for introverts.

The session concluded with an interactive “standing table” format, where attendees gathered around their preferred speakers for small-group discussions. This allowed for deeper conversations and immediate networking training. The informal setting stimulated open dialogue and practical advice. A big thank you to all the speakers and attendees who contributed to making this mentoring session a source of inspiration and practical guidance!

“The Past, Present and Future of Quadruple Ion Trap Mass Spectrometers in Proteomics”

Dr. Philip Remeš, a Senior Research Scientist at Thermo Fisher Scientific, presented an educational seminar on ion trap mass spectrometers. In addition to discussing how ion traps work fundamentally, Dr. Remeš covered the strengths and weaknesses of ion traps for proteomics, as well as how ion traps are likely to be used for proteomics in the near future. Approximately 50 participants were in attendance.

Ion traps have played a critical role in the birth of mass spectrometry-based proteomics. He began by tracing the historical development of ion traps, starting from their invention in the 1950s by Wolfgang Paul. Initially used in physics to manipulate ions, ion traps were later adapted for mass spectrometry, with significant improvements made by George Stafford and colleagues in the 1970s and 1980s that enhanced their efficiency and suitability for proteomics applications. From a historical perspective, Dr. Remeš highlighted the gradual increase of ion utility with ion traps relative to triple quadrupole mass spectrometers in commercial instruments. He discussed how linear ion traps have improved upon earlier 3D designs and how linear traps have changed throughout the last quarter century.

Dr. Remeš discussed the evolution of data acquisition technologies in proteomics, emphasizing the transition from qualitative analyses using data-dependent acquisition (DDA) to more quantitative approaches like data-independent acquisition (DIA) and parallel reaction monitoring (PRM). He explained that while DDA, often coupled with Tandem Mass Tags (TMT) for sample multiplexing, is effective for peptide identification, it faces quantitation challenges due to interference. DIA has emerged as a powerful method that enhances throughput and coverage by simultaneously acquiring data on all ions and generating extensive peptide lists. He then highlighted that advancements in ion trap technology have made PRM highly effective for quantitative proteomics. He pointed out that ion traps can now achieve quantitation performance comparable to, or even surpassing, that of Orbitraps and time-of-flight mass spectrometers, especially in targeted assays, thus broadening their applicability in modern proteomics workflows.

Several criticisms of ion trap usage in proteomics have been waged. In particular, ion traps have markedly lower mass resolution than Orbitraps or time-of-flight (ToF) mass spectrometers. Dr. Remeš emphasized that this lower mass accuracy is still generally sufficient for proteomics applications. Since peptides produce multiple fragment ions during mass spectrometry, a sufficient number of fragment ions generally remain interference-free even with low mass resolution. With technological advancements like automatic gain control (AGC) and the integration of deep learning tools that predict peptide fragmentation patterns, ion traps have become highly quantitative, even at low input levels. Therefore, despite their inherent limitations in mass accuracy, ion traps remain valuable and effective instruments in the field of proteomics due to their sensitivity, efficiency, and the sufficiency of their resolution for most proteomic analyses.

This session included an extended Q&A session with the audience, guided by Brian Searle (Ohio State University, USA). A full video recording of the session, including the Q&A session, is available on the HUPO Proteomics Webinars and Virtual Presentations website (https://hupo.org/Webinars-and-Virtual-Presentations).If you haven’t had the chance yet, please check out the webinar. Share it with your colleagues, coworkers, or friends.
Cheers!

During the years, the scientists from the entire world, especially the ones involved in the Human Proteome Project (HPP) have accumulated massive knowledge on human proteins. Since 2012, the advance of the Chromosome-centric HPP (C-HPP) defined stringent criteria of protein existence. All of this information was collected in the neXtProt database. It became a valuable resource of human protein research. In 2023, a mirror site of neXtProt was established by Chi-Biotech in Shenzhen, China, facilitating the access from Asian countries.

In 2024, the neXtProt database was discontinued. Therefore, a new HUPO-branded knowledgebase, named HPP Portal, is under construction by the team of Dr. Gong Zhang (Jinan University, China) and Chi-Biotech.

The HPP Portal aimed to continue the idea of neXtProt, cataloging the knowledges to each human protein. It contains the information to UniProt, Human Protein Atlas, etc., and includes the Protein Evidence (PE) levels. A notable change is that the annotation is now based on GENCODE. This facilitates the connection to the genome and transcriptome data, and reduces the inconsistency when processing multiomics datasets. In addition, Function Evidence (FE) levels of each protein is provided, summarizing the current knowledge on protein functions. For those proteins without known functions, the predicted functions will be also included. The HPP Portal, fully HUPO and HPP branded, is the knowledge hub supporting the HPP Grand Challenge.

Are you tired of the lack of sun during the northern hemisphere winter and  looking to learn more about proteomics at one of the most well-received sun-soaked proteomics summer schools currently available? The Ubuntu Proteomics Summer School brings together an amazing list of speakers for our third event, being held in February 2025 in Durban, South Africa.

Join us and listen to talks from the likes of Jesper Olsen, Bernhard Küster, Kathryn Lilley and more (see full program here).

The Ubuntu Proteomics Summer School (UPSS) is a one week residential school with a concepts and applications track. The summer school aims to help researchers:

Explore galleries from the 2023 and 2024 schools, view the YouTube channel, X and LinkedIn profiles.

If you are interested in attending, please apply here, or spread the word to any interested parties.

#ubuntuproteomics

OBO the UPSS organizing committee

Attention HUPO Members!
We are excited to announce a special opportunity for all members to showcase their creativity and passion for the -omics world through our " Proteomics Essay Corner." We invite you to write essays or poems that explore and endorse the vast and fascinating landscape of proteomics and related fields.

Submission Guidelines:
Length: It is up to author; however, we would encourage to not go over 1000 words.

Anonymity: You may submit your work anonymously if you prefer.

Content: Your piece can reflect personal experiences, insights into the -omics revolution, or creative interpretations of the impact of proteomics on science and society.

This initiative is not only a chance to express your thoughts but also to foster a sense of community among HUPO members who share a passion for the ever-evolving -omics world. Whether you’re a seasoned researcher or a budding enthusiast, we encourage your unique voice to be heard!

Why Participate?
Share Your Perspective: Engage with fellow members and contribute to the discourse surrounding proteomics.

Inspire Others: Your words might inspire others to delve deeper into -omics research and applications.

Visibility: Selected submissions will be featured in our upcoming newsletter and online platforms, providing you with a chance to reach a broader audience.

How to Submit: Please send your essays or poems to [Justyna.Fert-Bober@cshs.org; blandine.chazarin@gmail.com]. There is no due date, but we wish to share the work on monthly basis. Feel free to include a title and a brief description of your work if you wish.

Let’s celebrate the -omics world together over coffee and creativity! We look forward to your submissions and to enriching our community with your thoughts and inspirations.

Happy writing!
For more information about the -omics field and recent advancements, check out resources available on the HUPO website or other scientific platforms.

The October HUPOST is now available!  Chock full of the latest HUPO 2024 news, finalists and info about the upcoming ECR events, the C-HPP Workshop, career opportunities and more!

Sponsored by Expert Review of Proteomics Taylor and Francis

The Proteomics Highlights of the Year plenary session at HUPO 2024 will take place on Monday, October 21st at 17:45 in the Plenary Hall at the International Congress Center Dresden. This exciting session features the finalists from the ECR Manuscript Competition, who will present some of the most innovative recent work in proteomics from emerging scientists. We are thrilled to introduce the three finalists who will present their cutting-edge research in a plenary session:

• Stacy Malaker (Yale University, USA); view Stacy's bio here.
• Marc van Oostrum (Max Planck Institute for Brain Research, Germany); view Marc's bio here.
• Leyuan Li (Beijing Proteome Research Center, CN); view Leyuan's bio here

The winner of the competition will be determined based on their oral presentation, and will take home $1,000; runners-up will be awarded $500.

This week, we are shining a light on our last, but certainly not least, finalist, Leyuan Li, who will present her manuscript entitled: “Revealing proteome-level functional redundancy in human gut microbiome using ultra-deep metaproteomics.” Her research focuses on using metaproteomics and other advanced techniques to unravel the complexities of our internal microbial ecology. Take a look hereat her short bio. 

The proteomics community is a vibrant and dynamic group of scientists, researchers, and professionals, all bound by a shared passion for understanding the complexities of proteins. As part of the HUPO community, we know that proteomics isn't just a field of study - it's a global network of collaboration, innovation, and discovery. What makes you love being a part of this amazing community?

HUPO wants to hear from you! Whether it’s the groundbreaking research, the collaborative spirit, or the sense of belonging, your story can inspire others and highlight the incredible diversity of experiences within HUPO. Submit your personal reflections or professional anecdotes and help us highlight some very special moments in the proteomics community. We’re going to feature them in the HUPO booth (looping video presentation) at HUPO 2024 in Dresden!  

Ruth Huttenhain, Assistant Professor, Stanford: “I love HUPO because it unites a vibrant and diverse community of scientists who share a passion for exploring protein function.”

Mathieu Lavallée-Adam, Associate Professor, University of Ottawa: "The HUPO World Congress is where I found my postdoctoral job! Networking within HUPO has helped me build new collaborations and friendships." 

Send your short stories (and photo) to office@hupo.org by October 11. Help us celebrate what makes HUPO an exceptional community for proteomics professionals worldwide!

The 2024 General Assembly of Members (GAM) will be held during HUPO 2024 in Dresden, Germany just prior to the Awards Ceremony and Closing Session:

Date: Wednesday, October 23, 2024
Time: 1615-1645 (local Time)
Location: Plenary Hall, International Congress Center Dresden

HUPO members are invited to attend for important HUPO updates and networking. Contact the HUPO Office (office@hupo.org) for more information.

neXtProt has not been updated since October 2023 and solutions are being sought to revive this major database. In the meantime, the resource remains available for users at both nextprot.org and nextprot.cn with a very large number of visitors each month.

To support the HPP as they move forward, UniProt has taken on the role of running the Proteomics Identification pipeline. This has involved upgrading existing UniProt MS peptide identification pipeline to meet the stringency of the HPP3.0 guidelines, and working with Eric Deutsch (PeptideAtlas) and Nuno Bandeira (MassIVE) to ensure all additional criteria for data evaluation are met.

UniProt release 2024_04 shows that 18,417 proteins now have PE1 level evidence, out of a total of 19,835 candidate entries (93%). The data will be visible in the UniProt Feature Viewer and accessible via an API and a full analysis will be published in the 2024 report on the proteome from the HUPO Human Proteome Project, currently in preparation. UniProt has long supported the data generated using HUPO Proteomics Standards Initiative data standards.

In addition to the peptide pipelines, we are working with Eric Deutsch, Andy Jones (U. Liverpool) and Juan Antonio Vizcaino (EMBL-EBI) to use deposited MS data to identify additional high-confidence PTM sites and these will be added to UniProt human protein records over the next few months. Protein interactions and complexes generated by the IMEx databases are already accessible through our records. The UniProt database is committed to supporting the HUPO HPP with its next Grand Challenge of identifying a function for every human protein and looks forward to a closer working relationship with this group in the future.