Chris Overall (Chair), Young-Ki Paik (Co-Chair), Lydie Lane (co-chair), Gilberto B. Domont (MAL), Fernando Corrales (MAL), Pengyuan Yang (MAL) and Péter Horvatovich (Secretary General).

The Annual HUPO Congress in 2019 in Adelaide, Australia had a rich C-HPP and HPP program and activities on the future directions of the (C-)HPP programs.

The HPP investigators day, September 16, 2019

The HPP investigators Program was held on Sunday, September 15, 2019. The program included a long introduction to “The Human Proteome Project” by Mark Baker, followed by updates and reports on C-HPP and JPR HPP special issue by the C-HPP Chair, Chris Overall, the B/D-HPP by Fernando Corrales, Knowledgebase Pillar by Eric Deutsch, Mass Spectrometry Pillar by Sue Weintraub, Antibody/Affinity Pillar by Jochen Schwenk and the fourth new Pathology Pillar by Dan Chen.

The program was followed by C-HPP and B/D-HPP Principal Investigator Council meetings in parallel sessions and then by the HPP Workshop on “Illuminating the dark proteome to understand human biology and disease”, where Eric Deutsch presented the HPP Data interpretation Guidelines version 3.0 and Lydie Lane provided an update on new neXtprot developments, such as the support of the PSI Extended Fasta Format (PEFF), which includes annotation of the protein sequences with PTMs and sequence variants using controlled vocabulary, changes on protein evidence levels, definition of protein function serving the basis of uPE1 definition and changes of the number of proteins with known and unknown functions in the current neXtprot release (Jan-2019) compared to the previous release in Jan-2018, integration of variant frequencies from gnomAD database and the future integration of I-TASSER/COFACTOR protein function predictor tools.

Paola Roncada provided a summary on the Food and Nutrition Proteomics highlighting importance of proteomics in allergen identification such as partially digested shrimp tropomyosin. The Human Kidney and Urine proteome initiative progress was presented by John Arthur, while Meggie Lam presented the PubMed literature analysis of the HPP completed with visualization using VOSviewer.

HPP Workshop Day, September 19, 2019

HPP Workshop day started with an intensive and animated discussion on the highlights of HUPO 2019 and current progress and future directions of the HPP by Jennifer van Eyk. Then the future directions of the HPP was highlighted by C-HPP EC by Chris Overall and Young-Ki Paik, B/D-HPP (Ileana Christea), the Pathology Pillar (Dan Chan), and Ab/Affinity Pillar, by the new Chair, Cecilia Lindskog. Discussion led to the presentation of current and future HPP Pillars plans and how to increase in general the visibility of proteomics in the scientific community.

Th eSPecial Invited C-HPP speaker, Seán O’Donoghue, presented an illuminating lecture on the “The dark proteome of structural biology”, where “dark” represent regions in proteins where there is no known or predicted structure based on every sequence with a structure in the PDB from all species, a brilliant tour de force in bioinformatics and data visualizations using the AQUARIA tool. Missing protein searches in rare tissues such as human bone was summarized by Chris Overall leading to uncomfortable conclusions concerning the likelihood of finding MPs in such tissues, while Fernando Corrales summarized popular and less popular proteins in disease.

Mike Snyder presented a multi-omics strategy of human health over several years of active monitoring and Lydie Lane the use of SPARQL to query multiple complex databases among others neXtProt allowing to gain more comprehensive information on life-science curated data as strategy for better HPP outreach.

C-HPP Poster Session

Three winners of the C-HPP Poster Awards each received a certificate and cheque of USD200 from John Wilson, Protifi at the closing ceremony. The awardees are, Chae-Yeon Kim (Yonsei University, Seoul, Korea), Chengxin Zhang (University of Michigan, Ann Arbor, MI, USA) and Yuanling Zhang, (Siqi Liu Lab, Beijing Institute of Genomics, China).

Bioinformatics Hub

Again, Eric Deutsch has mastered a wide ranging and practical program on bioinformatics challenges in MP hunting, data analysis and implementing the new Human Proteome Project Data Interpretation Guidelines (Version 3.0) in a friendly atmosphere that encourages Q & A and for attendees to come away truly knowing the answer to their questions. The program with some of presentations is available at http://bit.ly/hupohub2019.

The C-HPP Wiki

The C-HPP wiki was updated with slides of many presentations and a dedicated session of the Bioinformatics hub was provided on how to edit C-HPP Wiki, which is based on Tiki Wiki content management system (version 18.1). We ask input from the individual chromosome teams to fill the C-HPP Wiki with further content regarding resources, achievements, available ProteomeXchange datasets and any information, which is relevant for C-HPP participants and in general for the HPP community.

Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

Submit your original research, communications or review manuscripts that combine proteomics with other omics techniques to this special issue by 31 May 2020. Find out more here: https://www.mdpi.com/journal/biomolecules/special_issues/multiomics_biomedical_research

Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

The laid-back city of Adelaide provided a relaxing backdrop for an intensive week of HUPO2019 - a big thank you and congratulations to the local organizing committee!

In addition to cutting edge science, HUPO Executives, HUPO Council and Presidents of National Proteomics Societies had extensive discussions on future strategies for HUPO. Several areas of development were identified, including:

• Foster active HUPO community on social media.
• Add value to HUPO membership and attract new members.
• Inform the broader public on the importance of proteins.

It is envisaged that small groups of volunteers will drive specific tasks towards the identified goals, generally within short time frames. We would like to invite members with practical ideas and time to volunteer through this online form. Feedback on current barriers and potential drivers to increase the engagement can also be provided through the same.

Early Career Researchers (PhD students and postdocs) are particularly encouraged to help build our HUPO community!

Early Career Research (ECR) Committee

The HUPO ECR committee has an open position for a member at the post-doctoral fellow or junior faculty level. This member would be responsible for the communications of the initiative. The member’s tasks would include, but not limited to:

• Interacting and participating with the ECR committee to grow and support proteomics for early stage investigators.
• Maintaining and upgrading the HUPO ECR website,
• Managing the HUPO ECR social media accounts (Twitter, Facebook, Instagram),
• Assembling material for the HUPO HUPOST monthly emails.
• Participating in the planning ECR events at International HUPO and other HUPO related events.

In addition, the member would be expected to participate to the monthly calls with all committee members.

This position represents a fantastic opportunity for early career researchers to network with other junior scientists and also several senior leaders in the Proteomics field. The member will also have the occasion to develop his own leadership and management skills in an international organization.

The member should be ready for a commitment of two years to the ECR initiative.

Interested candidates can contact Mathieu Lavallée-Adam (mathieu.lavallee@uottawa.ca) if they have any questions or to signify their interest before September 8th. It should be noted that the ECR initiative is committed to equity, diversity and inclusion principles and that these, along with geographic diversity will be considered to fill this position.

Early Career Researcher Committee

The Early Career Researcher (ECR) initiative has prepared numerous exciting activities for the upcoming HUPO World Congress. The following activities will highlight ECR talents and provide junior scientists with unique development opportunities.

1. All ECRs are invited to register and attend the ECR Mentoring Day on September 15th, where they will interact with senior mentors and learn how to communicate, manage and network more effectively. For more information, please visit: https://www.hupo2019.org/mentoring-day-2/

2. The three finalists of the Early Career Researcher Manuscript Competition will be giving talks at the World Congress. Come hear about their research during the following sessions:

• Bioinformatics and Statistics, (Maggie Lam - Sept 17, 10:40AM – 12:40PM),
• Proteogenomic, (Ankit Sinha - Sept 17, 3:15PM - 5:15PM)
• The Interactome (Eneko Villanueva - Sept 18, 1:30PM - 3:30PM).

For more details about the finalists, please visit: https://hupo.org/Early-Career-Researcher-Competition-2019

3. The eight finalists of the Ph.D. Poster competition will be giving short talks in Adelaide. All are invited to discover their work. The competition finalists are listed here.

Péter Horvatovich, University of Groningen, Netherlands 

The Newsletter summarizes all C-HPP related news and activities from May 2018 to July 2019. The Newsletter starts with the Editorial of Christopher Overall, C-HPP Chair, summarizing the current status of the international efforts to find evidence on missing proteins (PE2-4), making c.a. 89% completion and future direction of neXt-CP50. Next, the article entitled “Services for cDNA clones: New Resources for the Dark Proteome Research” by Joshua LaBaer presents the world’s largest collection of unique, full-length Gateway plasmids representing more than 89% (covering 17,362 unique genes) of 19,522 human protein-coding genes made by the chromosome 10 team. These clones and the cloning facility to prepare new clones for sequence variants are available at Arizona State University and can be used to prepare recombinant proteins that can support both confirmation of missing proteins and functional characterization of uPE1 proteins.

The Newsletter also gives highlights on recent C-HPP Workshops such as the 19th C-HPP workshop in Santiago, Spain, June 16-17, 2018, the 20th HPP Post-Congress Workshop as follow-up of HUPO 2018, in Orlando, USA on October 4, 2018, and the 21st C-HPP Workshop entitled “Illuminating the Dark proteome”, Saint Malo, France, May 11-14, 2019. Besides workshop highlight organizational changes such as introduction of new neXt-CP50 program, election of new (co-)chairs and chromosome PIs. The update of the neXt-MP50 project documented the evidence for new candidates of 104 MPs, which are listed in the Editorial of JPR 2018 issue. Also other highlighted are the summary on JPR 2018 special issue, plans for the 23rd HUPO C-HPP HPP symposium (C-HPP2020) "From chromosome-centric project to the human proteome" which will be taking place in Russia from 22 to 26 May, 2020. This workshop will be happen aboard on a ship traveling from Saint Petersburg to Valaam Island and back.

Click here to view the C-HPP Newsletter No.8.

Vera Ignjatovic,University of Melbourne, Australia

With the HUPO 2019 Congress fast approaching in the table below we present a compact guide of the variety of B/D-HPP activities taking place and urge the HUPO attendees to schedule these in their congress calendar.

Justyna Fert-Bober, Cedars-Sinai Medical Center, USA

Adelaide, Australia (September 15, 2019) — The HUPO World Congress is proud to announce the Fifth Annual International Mentoring Day on September 15, 2019.

If asked to name a mentor that has helped to shape you, would you be able to identify one? What are your expectations of such a mentor? What characteristics define a remarkable mentor? As a mentee what can you offer to your mentor? These questions and more, will be discussing during the HUPO Mentoring day.

The focus of the annual Mentoring Day being held during the HUPO World Congress 2019 is on mentor-mentee relationship and how to establish productive networks needed for early career scientists. This year, the program covers the following topics:

1. Mental and Health Wellness - Yours and the people around you.

2. The art of self-promotion and lab-promotion.

3. Bad manuscript review, bad grant review. - How to respond to them!

4. Selling proteomics and bioinformatics to scientists outside the field

During this workshop, mentees will meet and interact with a stellar group of mentors that have established themselves as international leaders in proteomics, including (in alphabetic order): Dr. Stuart Cordwell (Australia), Dr. Daniel Figeys (Canada); Dr. Martin Larsen (Denmark), Dr. Merry Lindsey (USA), Dr. Birgit Schilling (USA) and Dr. Jennifer Van Eyk (Canada/USA).

Each mentor is coming from different cultural and sociological background. They all took different pathways to become PIs, but they all have one thing in common, they are all passionate about sharing their experience with early career scientists. This workshop promotes face-to-face discussions, friendly roundtable exercises and lots of career advice. Self-promotion is a very subtle art. It requires building relationships, and this workshop is an excellent opportunity to start creating new ones.

Please see below our mentors’ biographies:

Stuart Cordwell is a professor of Analytical Chemistry at the University of Sydney, who has co-supervised 16 PhD students and more than 20 Honours students. Stuart obtained his PhD at the University of Sydney. He was an author on the manuscript that defined the term ‘proteome’ in 1995 and has been involved in proteomics research throughout his career. He also established the first laboratory-based undergraduate Proteomics course in Australia. Dr. Cordwell’s vision for the Australasian Proteomics Society is to provide an inclusive society and support network that encourages the participation of Early and Mid-Career Researchers, as well as providing financial and travel support for students and consistent high-quality meetings of international standard.

Quote: ‘Get angry, get emotional, channel the energy into your reply; then sleep on it, consider it, remove the emotion and your argument will be strong’

Daniel Figeys is professor in the Department of Biochemistry, Microbiology and Immunology at the University of Ottawa. He is the founding director of the Ottawa Institute of Systems Biology and is the co-founding director of the Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology. Dr Figeys obtained his Ph.D. in Chemistry from the University of Alberta and did his postdoctoral studies at the University of Washington in Molecular Biotechnology. Daniel was previously Senior Vice-President at MDS-Proteomics and more recently co-founded MedBiome and Biotagenics, two early start-up biotech companies. His laboratory has published over 180 papers and has been cited over 14,000 times. Through starting new companies and transferring technology to industry Daniel has experience in “Selling the power of proteomics and bioinformatics to scientists outside the field”. He is also responsible for a professional skill development program that amongst other skills includes wellness, networking and self-promotion.

Quote “I wish these types of training had been available when I was a student/postdoc instead of having to learn on the fly”

Merry Lindsey is Chair of the Department of Cellular and Integrative Physiology and Founding Director of the Nebraska Center for Heart and Vascular Research (NE-CHVR). Her research is focused on using proteomics to understand extracellular matrix responses to cardiac injury. Specifically, her lab develops multidimensional approaches to examine the mechanisms whereby the left ventricle responds to injury with the goal to develop therapeutic strategies to prevent, slow, or reverse the progression to heart failure. She is also dedicated to disseminating scientific results to the general, scientific, and medical communities and educating the next generation of scientists. Dr. Lindsey serves as Deputy Editor for the American Journal of Physiology- Heart and Circulatory Physiology and is on the editorial boards for Circulation Research and Basic Research in Cardiology. She is actively involved in the American Physiological Society, the American Heart Association, and the American Society of Matrix Biology and has presented her research at over 150 national and international venues. Her trainees routinely publish high impact articles, win research awards for excellence, and successfully transition to independent faculty positions.

Quote: The trick to answering reviewer comments is to make sure future reviewers can never make the same comment

Rob Rivers is a Program Director at the United States National Institute of Diabetes and Digestive and Kidney Diseases which is a part of the National Institutes of Health. He holds a Ph.D. degree in Chemistry from the University of Cambridge and a B.S. degree in Chemistry from Kentucky State University. In his current role he funds graduate students and post-doctoral fellows, as well as managing programs designed to foster the recruitment and training of minority and underrepresented biomedical investigators. Dr. Rivers trained early graduate students and early stage investigators on the importance of clear communication for promotion of science as well as ensuring wellness both physically and mentally.

Previously he worked at as Program Official at the Office of Cancer Clinical Proteomics Research with a focus on funding proteogenomic research on colon and ovarian cancers. He is active in the local and global community and was instrumental in starting the international non-profit organization Umbrella Initiatives Foundation that helps in providing improved educational opportunities to children living in poverty in Peru, Bolivia and the United States (www.umbrellainitiatives.org).

Importance of Wellness:
“Physical and mental wellness is integral in sustaining research pursuits over one’s career. When we don’t look after ourselves, then the quality of our work will decline as well.”-Rob Rivers

Quote If you don’t have time for wellness, then sooner or later you will be making time for illness.
-Adapted from Edward Stanley

Brigit Schilling is an Assistant Professor and the Director of the Mass Spectrometry Core at the Buck Institute for Research on Aging in California, with an Adjunct Professor appointment at the University of Southern California (USC). The Schilling lab develops and implements innovative protein analytical technologies to advance basic biology and biomedical research related to aging research. Research projects include investigation of protein phosphorylation, acetylation, and other posttranslational modifications, as well as differential expression of proteins during disease and aging processes. The Schilling lab has been highly successful in adopting novel proteomic technologies to achieve comprehensive and sensitive quantification capabilities. Dr. Schilling has mentored several postdoctoral fellows and research associates and provided strong support for them to achieve their career goals and offer them opportunities, such as attending conferences and educational courses.

Quote: Sharing scientific ideas with others and being able to discuss and present posters or talks at conferences is a big step towards building your own scientific network and establishing contacts that can be fostered throughout your career.

John R. Yates is an American chemist and professor of chemical biology at The Scripps Research Institute in La Jolla, California. His work is focused on developing tools and in proteomics and he specializes in mass spectrometry. Dr. Yates III is the recipient of the 2019 ASMS John B. Fenn Award for a Distinguished Contribution in Mass Spectrometry, for development of automated, large-scale interpretation of peptide tandem mass spectral data. Dr. Yates’ SEQUEST algorithm laid a critical foundation for the field of proteomics and has enhanced the accuracy and effectiveness of mass spectrometry to understand important biological and clinical questions. He also received the Thomson Medal in 2018. He has trained MSc/PhD students, post-doctoral fellows and PhD students. His strengths in leadership and mentoring help many to transited into independent faculty positions

Quote: Every 4-5 years you have to throw yourself onto the job market to see what you’re worth.

Jennifer (Jenny) Van Eyk is a Professor of Medicine at Cedars-Sinai Medical Center, Director of the Basic Science Research in the Barbra Streisand Woman’s Hearth Center and Director of the new Advance Clinical Biosystems Institute that has the motto “from discovery to patient care”. She co-director of the Cedars Sinai Precision Health, focused on in-hospital and population individualization of health care. Dr. Van Eyk is an international leader in the area of clinical proteomics and her lab focuses on developing analyical pipelines for de novo discovery and large-scale quantitative mass spectrometry methods. The aim is to maximize throughput and reproducibility to move targeted and robust discovery methods into continuous large population assessment and to develop clinical grade assays for neurological and cardiovascular diseases. To this extent she, oversees the new Cedars-Sinai Precision Biomarker Laboratories which consists of the Translational and CAP/CLIA certified clinical lab.

Dr. Van Eyk was a technician prior to obtaining her PhD from the University of Alberta (Canada) and doing her postdoctoral research in Heidelberg and University of Illinois in Chicago. Her first faculty position was at Queen’s University in Kingston Canada where she started her first company. She was recruited to Johns Hopkins University and then to Cedars-Sinai Medical Center. She has mentored over 30 graduate students and post-doctoral fellows who are now successful in many different science-related jobs.

Quote: Fill your life and lab with wonderful amazing people and create an environment where they can become the best they can be.

Methods are essential in all omics domains, including proteomics and metabolomics. JPR has therefore created a biannual Special Issue that will highlight novel and/or significantly updated methods for proteomics, metabolomics and omics studies in general. For readers, this Methods Special Issue will be an easily identifiable source of methods that have been specifically reviewed for their applicability and ease of adoption. For authors, the Special Issue provides visibility and wider adoption of methods in the proteomics community through dissemination and documentation. In addition, the Special Issue will become a facile platform to publish significantly updated and improved methods that may have been already published.

The Methods Special Issue will be managed by JPR Associate Editor Josh Labear with guest editors Laurence Florens and Meng-Qiu Dong and will cover all subdisciplines within the scope of the Journal of Proteome Research.

Scope

• Authors must present either a complete description of a relevant novel method (“Research Article” submission) or a substantial and meaningful update of a previously published method (“Technical Note” submission). The focus of the paper should be on the unique functionality of the method. It should be clear to any reader what questions the method addresses and how it is used.
• Demonstration of at least one example of an important application of the method should be included in the paper. Data generated to illustrate a method should be supported by an appropriate number of replicates and statistical analyses. In addition, there should be sufficient detail about the method to allow easy replication.
• Data associated with demonstrating the method must be submitted to an appropriate repository at the time of submission, along with full access information to the data provided in the manuscript (dataset identifier(s), username, and password).

Instructions for submission

Manuscripts must adhere to the guidelines available on the Journal of Proteome Research Information for Authors page and in Martens et al., J. Proteome Res. 2015, 14(5):2002-4; doi: 10.1021/pr501318d, and be submitted electronically through the ACS Paragon Plus portal.
In Paragon, specify manuscript type, and activate the special issue feature to designate the paper for Methods for Omics Research. In addition, include a statement in your cover letter that the paper is being submitted for the special issue. Provide names and contact information for at least four suggested reviewers who can meaningfully comment on the described method.

The deadline for submission of manuscripts for the 2020 Special Issue on Methods is August 7, 2019. Manuscripts will be screened for suitability for the Special Issue.

Open Access
There are diverse open-access options for publications in American Chemical Society journals. Please see http://acsopenaccess.org/.

Sudhir Srivastava, US National Insititutes of Health, National Cancer Institute USA

The Human Proteome Organization has established a HUPO External Initiative (HEDI) committee to foster interaction between the HUPO membership and international thought leaders who are responsible for developing strategy for funding proteomic-centric projects in their respective countries. HEDI will be chaired by Dr. Sudhir Srivastava, Chief, Cancer Biomarkers Research Group, National Cancer Institute, National Institutes of Health along with co-chairs Dr. Rob Moritz, HUPO Vice President and Institute for Systems Biology, Seattle WA USA and Dr. Mike Snyder (HUPO Past President and Stanford University, CA USA). The objectives of this initiative are:

• Identifying emerging scientific opportunities, rising public health challenges, or scientific knowledge gaps that merit further research by international funding agencies, non-profit governmental organizations and foundations, hereafter called Funders.
• Understanding scientific priorities and strategic planning of Funders globally in developing and applying resources (databases, analytic tools, and methodologies) and producing specifications for new resources in support of proteomic research
• If requested, assisting the Funders to address areas of emerging scientific opportunities and public health challenges effectively
• Proactively discussing and providing technical assistance to Funders in the development of proteomic-based initiatives.

The first inaugural meeting of this committee will take place during the HUPO Annual Meeting, September 15-19, 2019 to be held in Adelaide, Australia. Planning is underway to invite thought leaders, funding officials and other policy makers to discuss their ongoing and future proteomic projects in their own countries. The format of the meeting will encourage deep interaction among the participants to learn of each other’s needs and the participatory process that culminates in development of proteomic centric projects.