NewS

“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.

The HUPO ECR Mentoring Sessions provide a space for mentors and mentees to come together and openly discuss relevant topics on navigating an early career in proteomics. Three insightful sessions will take place at HUPO 2024 in Dresden, Germany with the following mentors and topics:

Career Paths: What’s Next in Your Career? (Sunday, Oct. 20, 14:15 - Conference Room 3-4)

• John R. Yates III (Scripps Research)
• Christoph Krisp (Bruker Daltonics GmbH & Co. KG)
• Maurine Fucito (Evosep)
• Uli Ohmayer (NEOsphere Biotechnologies GmbH)
  
  

Mental Health: Building Resilience to Manage Work and Job Search Stress (Tuesday, Oct. 22, 15:15 - Conference Room 3-4)

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

Mastering Mentorship: Navigating Conflicts and Personalities (Wednesday, Oct. 23, 15:00 - Conference Room 3-4)

• Chiara Francavilla (Danish Technical University)
• Parag Mallick (Stanford University)
• Blandine Chazarin (PRISM laboratory)

These sessions are designed to foster lively discussions and offer practical advice to help you navigate your career. Don't miss the opportunity to learn and ask your questions to experienced mentors and connect with peers facing similar challenges!