NewS

Dr. Pavel Sinitcyn
Morgridge Institute For Research, United States

Pavel Sinitcyn is a distinguished Morgridge Interdisciplinary Postdoctoral Fellow at University of Wisconsin-Madison, conducting cutting-edge research in Dr.Joshua Coon’s lab. With a strong background in developing software solutions for proteomics data processing, Dr. Sinitcyn has played a pivotal role in developing tools such as MaxQuant, MaxDIA, Perseus, and Deep Proteomic Sequencing Methods.

Dr. Pavel Sinitcyn was a finalist in the HUPO 2023 ECR Manuscript Competition, for which he presented his manuscript, “Global Detection of Human Variants and Isoforms by Deep Proteome Sequencing”, in a plenary session. To get the inside story, we asked Dr. Sinitcyn a few questions about his experience in the competition. Read what he had to say below!

1. What is your current position and affiliation?
I am a postdoctoral researcher in the Coon lab at University of Wisconsin-Madison, United States. In June 2024, I will be starting my own group at Utrecht University in The Netherlands

2. How would you like your work to contribute to the field of proteomics?
I would like to see a change in the definition of protein coverage in the field. Rather than merely discussing protein coverage as the number of detected proteins out of the many annotated protein-coding genes, we should consider coverage as the portion of amino acids covered by a few detected peptides. This shift will enable a more comprehensive quantitative measurement of sequence isoforms, small amino acid variations, and post-translational modifications on a global scale.

3. What have you found in the HUPO community/congress?
I greatly appreciate the international mindset of the HUPO community. This conference goes beyond the opportunity to listen to great talks/posters and meet colleagues and friends in one place; it allows for the exploration of the landscape of the field on a global scale, spanning various countries and regions.

4. How was your experience/what did it mean to present your work at HUPO?
I thoroughly enjoyed my experience presenting my work at HUPO, especially within the HUPO ECR community. Returning to HUPO is always a pleasure. The conference's well-tuned schedule and scale allowed for a comprehensive experience without the usual need to constantly choose between simultaneous must-visit sessions. The vibrant atmosphere of the poster session and bioinformatics hub added to the overall positive experience. And finally, attending this conference was particularly meaningful for me as it was the first one after the birth of my son, giving me the opportunity to fully participate in the session organized by Moms in Proteomics.

Check out the latest edition of the HUPOST featuring HUPO 2024 Program, ECR Manuscript Competition and Online Panel, ETC Webinar Series, Upcoming Events and much more 

Date: Wednesday February 28, 2024
Time: 4pm GMT (5pm CET)

Are you a Ph.D. student, postdoc, or early career researcher looking to get recognised for your work? Join the next HUPO Early Career Researcher online panel discussion, "Getting recognised for your work", at 4pm GMT (5pm CET) on Wednesday February 28.

The panel will feature Dr. Laurent Gatto (Associate Professor of Bioinformatics, UCLouvain), Dr. Stacy Malaker (Assistant Professor of Chemistry, Yale University), and Dr. Juan Antonio Vizcaino (Scientist and Team Leader, Proteomics, European Molecular Biology Laboratory).

This will be the perfect opportunity to ask any questions that you may have about getting recognised for your work and putting yourself in a favourable position for your future career.

REGISTER HERE

The C-HPP is holding a workshop Madrid, Spain, at the National Center for Biotechnology, CSIC, Campus of the University Autónoma of Madrid, Darwin, 3, Spain.

A workshop hotel is being organized where registrants can book and cover their own accommodation. The hotel will be near the train station for a short 15-minute ride to the University Autónoma.

Registration and most meals and coffee are free and we invite members of the C-HPP, B/D-HPP, and HPP to register as soon as possible to help with planning.

REGISTER HERE

AGENDA

Wednesday, April 24

13:00-14:30 Welcome Lunch

Preworkshop Working Group on Protein Identification and Function Guidelines
(Chairs: Rob Moritiz + Charles Pineau)

14:30 – 16:30: Discussion on guidelines for (i) assigning protein function for the Grand Challenge, incorporating, (ii) With HUPO’s loss of support from neXtprot, also to be discussed will be a new repository for HPP progress on completing the Human Proteome Project and where the data will reside for functional annotation of the Human Proteome, (iii) SWATH/DIA data into the HPP.

16:30 Coffee

17:00 Finalize recommendations and action items on the three aims.

18:00 Dinner ad hoc in central Madrid, Tapas!

Thursday, April 25

Session One: Grand Challenge (Chairs Charles Pineau + Fernando Corrales)

9:00 Chris Overall. Welcome and outline of workshop.

9:15 Charles Pineau. C-HPP in Le Grand Challenge: (20 min + 10 mins)

9:45 General Discussion on the Grand Challenge and HPP Database Management

11:00 Coffee break

11:30 Gong Zhang(20 min + 10 mins): “Proteome-wide Functional Annotation Using Deep-Learning-based Protein Structures”.

12:00 Uwe Volker. Discussion Summary: Challenges in the Grand Challenge. (20 min + 10 mins)

12:30 - 14:00 Lunch

Session Two: Mission of the C-HPP (Chairs: Gong Zhang + Heeyoun Hwang)

14:00 Chris Overall. Outline of the C-HPP Mission Statement.

14:15 – 15:15 General Discussion on the C-HPP Mission Aims. Including gender and geographic diversity in the leadership of teams and EC, inactive teams/team renewal.

15:15 Yong-In Kim (Chr 9) (ECR) (15 min + 5 min): “Exploring Uncharacterized Proteins on Chromosome 9: Current Progress and Insight”

15:35 Alejandra Delgado (ECR) (15 min + 5 min): “Investigating the Function NDUFAF4 in the Context of Cholestasis”.

16:00 Much-needed coffee break

16:30 Sergio Encarnación-Guevara(20 min + 10 mins): “Chromosome 19: Progress in the characterization of proteins without assigned function.”

17:00 Heeyoun Hwang (20 min + 10 mins): “uPE1 Study with Cholangiocarcinoma and PDAC Proteome Data”

17:30 Rob Moritz (20 min + 10 mins): Collective Thoughts on the C-HPP Mission and Direction

18:00 Session Close

Retire to hotels to freshen up and then meet for aperos and dinner at a destination to be announced by Madrid Natives (Fernando).

Friday, April 26:

Session Three: Meeting the Challenge (Chairs Cecilia Lindskog + Sergio Encarnación-Guevara)

9:00 Cecilia Lindskog (Incoming Chair HPP): (20 min + 10 mins) “Solve the Protein Puzzle – The Grand Challenge to Understand the Different Pieces of the Human Proteome”

9:30 Min-Sik Kim (new Chr 13 Head, Korea): (20 min + 10 mins) “Breast Cancer Proteome and Chromosome 13”

10:00 Chris Overall (Chair C-HPP): (20 min + 10 mins) “Physiological vs. Pathological Functions of Proteins in the Grand Challenge”

10:30 Coffee break

11:00 Frank Schmidt (new Head, Chr 21, Qatar Team): (20 min + 10 mins) “How can Olink Contribute to the HPP project?”

11:30 – 12:30 Open Discussion on technologies, approaches, and bioinformatics to meet the Grand Challenge.

12:30 Meeting Close

Campus Restaurant fine dining and departure.

REGISTER HERE

The hallmark update paper each year is the HPP Metrics publication, is now online, lead by Dr Gil Omenn and the leaders of neXTprot, the Peptide Atlas, the HPP, C-HPP and B/D-HPP:

“The 2023 Report on the Human Proteome from the HUPO Proteome Project”, by Gilbert S. Omenn,* Lydie Lane, Christopher M. Overall, Cecilia Lindskog, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch.

ABSTRACT: Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1−4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

The HUPO Early Career Researcher (ECR) Committee is delighted to welcome Pathmanaban Ramasamy. Keep reading to know more about him!

Pathmanaban Ramasamy (Paddy) is a junior post-doc in the CompOmics group at Ghent University in Belgium. During his joint Ph.D. program between Ghent University and Vrije Universiteit Brussel, he leveraged his expertise in structural bioinformatics and proteomics informatics to unravel the role of local amino acid interactions in protein folding, fold stability, and the location of post-translational modifications (PTMs). He endeavors to unravel the "where, how, and why" of protein PTMs through a comprehensive large-scale investigation that spans these modifications within sequence, structure, and biophysical contexts.

He has been extremely active in bringing the MS proteomics and structure communities together at the European scale, investing heavily in an ELIXIR Europe-funded cross-over study between the three key communities: the 3D-BioInfo (protein structure), Intrinsically Disordered Proteins, and MS Proteomics communities. Paddy is enthusiastic about becoming a member of the HUPO-ECR and looks forward to actively contributing to the support of young proteomics researchers through his involvement with HUPO-ECR and YPIC.

Prof. Hong Wang
Institute Of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, China

1. What is your current position and affiliation?
   
   I am presently employed as a Principal Investigator (tenure-track Assistant Professor) at the National Key Laboratory of Blood Science, within the Institute of Hematology & Blood Diseases Hospital at the Chinese Academy of Medical Sciences & Peking Union Medical College. Concurrently, I hold the positions of Director at the Center for Advanced Technologies and Founding Director of the Mass Spectrometry Center at Haihe Laboratory of Cell Ecosystem. 
   
   
2. How would you like your work to contribute to the field of proteomics?
   
   In my current role at the foremost blood diseases research hospital in China and the innovative Haihe Laboratory of Cell Ecosystem, I aspire to make significant contributions to the field of proteomics. By integrating mass spectrometry-based omics with other advanced technologies, I aim to collaborate closely with clinicians to address complex clinical questions. My goal is to propel these technologies towards translational medicine, facilitating the translation of precision biomarkers and therapeutic targets into practical clinical applications. This approach seeks to bridge the gap between cutting-edge research and real-world patient care. 
   
   
3. What have you found in the HUPO community/congress?
   
   HUPO serves as my academic home, and participating in the HUPO congress feels akin to a holiday homecoming to reunite with family and friends. Each congress is a source of continual inspiration, fostering valuable collaborations, and exposing me to new technologies that I eagerly incorporate into my work. The sense of community and shared knowledge at HUPO events consistently propels my research forward and enriches my professional journey.
   
   
4. How was your experience/what did it mean to present your work at HUPO?
   
   Presenting my work at HUPO was an enriching experience, marked by valuable and insightful feedback. The positive reception and recognition of my multidisciplinary efforts within my field provided a significant boost of confidence. This affirmation encourages me to advance further in exploring the novel concept of the blood ecosystem that we introduced, reinforcing my commitment to pioneering work at the intersection of diverse disciplines.

The PSI meeting 2024 will take place from March 18-20th 2024 at the Kyoto University, Japan.

View event details here.

The meeting is sponsored by: JPOST (JST-NBDC) and JPDM (JSPS).

Organizers: Yasushi Ishihama & Shujiro Okuda.

Program:  The provisional agenda will be posted soon.

Registration:  Registration for attending the meeting is now open.

The January HUPOST is now available.....check out the latest HUPO 2024 news, ETC Webinars, ECR Manuscript Competition, upcoming events & much more...

The HUPO Early Career Researcher (ECR) Initiative is delighted to welcome Nick Riley and Mahshid Moballegh Nasery.

Nick Riley is an assistant professor of chemistry at the University of Washington. With a background in mass spectrometry instrumentation, proteomics, and glycobiology from his graduatework with Prof. Josh Coon at University of Wisconsin-Madison and his postdoctoral work with Prof. Carolyn Bertozzi at Stanford University, he now leads a research program focused on innovative bioanalytical and chemical biology technologies to investigate essential principles of glycocode regulation and dysregulation. Nick has been involved with HUPO and US HUPO for a number of years and is excited to join the HUPO ECR committee to support the vibrant and supportive communities that help early career scientists build their scientific careers in proteomics research.

Mahshid Moballegh Nasery pursued a diverse academic journey, beginning with a Bachelor's in Chemistry and delving closer into biology with a Master's in Medical Toxicology, where her focus on cancer led to publications in articles and a chapter book. Her passion for proteomics started to grow as she attended her proteomics course and attended an ECR day meeting! Currently engaged in research at the University of Debrecen, under the supervision of Dr. Eva Csosz. Her recent membership in YPIC (Young Proteomics Investigators Club) reflects her eagerness to expand her network and engage actively with fellow proteomics scientists. She aims to deepen her involvement in various activities, leveraging her multi-disciplinary background, to contribute meaningfully to the scientific community. Driven by a thirst for knowledge and a desire to make impactful contributions, Mahshid is passionate about exploring within the vibrant realm of proteomics and biochemistry.