• 24 Jul 2018 3:42 PM | Anonymous member (Administrator)

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

    Do you wonder how proteomics contributes to understanding of biology or management of disease? Are you interested in contributing to a BD-HPP initiative but not sure how to start? With many options to choose, HUPO 2018 is a perfect time to get involved. 

    Click here to check out the enticing sample menu!

    Note - There are subsidized fees of $60 for Sunday and $100 for Thursday to defray the extra costs of these activities on top of the Congress registration.

  • 28 Jun 2018 2:49 PM | Anonymous member (Administrator)

    Etienne Caron, ZTH Zurich, Switzerland

    The large collection of peptides associated to human leukocyte antigens (HLA) is referred to as the human immunopeptidome. Deciphering the composition of the human immunopeptidome is of paramount importance to understand the immune system and to guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases and cancers. Until now, mass spectrometry (MS) is the only available technology to interrogate the immunopeptidome in an accurate, systematic and unbiased manner. Therefore, the development of advanced analytical MS workflows is of great importance to enable the deciphering of the immunopeptidome at increasing depth and robustness.

    Foundation of the Human Immuno-Peptidome Project
    The Human
    Immuno-Peptidome Project (HUPO-HIPP) was created to accelerate research toward robust and comprehensive analysis of immunopeptidomes (https://hupo.org/human-immuno-peptidome-project/). On May 4–5th, 2017, 40 leading scientists and industry representatives from 18 universities and 9 companies convened in Zurich, Switzerland, for the first international HUPO-HIPP workshop (see picture).  During this event, participants identified specific challenges toward the goal of HUPO-HIPP, and within this framework, described the structure of a multipronged program aimed at addressing these challenges and implementing solutions at a community-wide level. The identified programs are: (1) method and technology development, (2) standardization, (3) effective data sharing, and (4) education (see details in Caron et al. Immunity, 2017)

    1st HUPO-HIPP summer school: September 10-13 2018, Madrid, Spain
    Members of HUPO-HIPP recognized that implementation of robust analytical workflows is a major hurdle to the expansion of the immunopeptidomics field. To circumvent this limitation and to disseminate the expertise on currently adopted methods by the immunopeptidomics community, the 1st HUPO-HIPP summer school was launched (http://www.hipp-summerschool.com/). Thus, the major goal of the summer school is to provide attendees with critical information about the main challenges of immunopeptidomics approaches with special emphasis on sample preparation, liquid chromatography-MS/MS analysis, bioinformatics and data sharing. Most importantly, the HUPO-HIPP summer school will contribute to boost the accessibility to immunopeptidomic technologies and to open this scientific niche to a bigger audience.

    Next steps
    HUPO-HIPP will soon publish the Minimal Information about an Immuno-Peptidomics Experiments (MIAIPE) to provide technical guidelines that represent the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. HUPO-HIPP also plans to 1) establish partnerships with MS developers and other initiatives (e.g. Human Vaccines Project) to increase the impact of MS-based immunopeptidomics, 2) establish partnerships with journals’ editors and funding agencies (NIH and EC) to enforce sharing of immunopeptidomic data, 3) further develop the SysteMHC Atlas (https://systemhcatlas.org) for deposition and open sharing of immunopeptidomic datasets, 4) launch an international human immunopeptidome project consortium (HIPPC), and 5) continuously promote the visibility of HUPO-HIPP in publications, conferences, workshops and elsewhere. Progress and future plans will be discuss at HUPO-Orlando 2018.

    If you would like to become a member of HUPO-HIPP complete the attached Membership Form and email to the address provided.

  • 28 Jun 2018 2:34 PM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    June 16-17, 2018

    The 19th C-HPP Symposium/workshop organized by Fernando J. Corrales, Concha Gil and Young-Ki Paik was held in conjunction with the EuPA 2018 Congress with a scientific theme, “Translating Genome into Biological functions”. During this meeting, 13 Chromosome teams (Chr 2, 5, 6, 9, 11, 13, 14, 15, 16, 17, 18, X and Mt.) presented their progress on missing protein identification and uPE1 (PE1 proteins of unknown function) characterization. The workshop program started with an update of the Human Proteome Project (HPP Chair and Chr 17 PI, Gilbert Omenn), on neXt-CP50 initiative, (C-HPP Chair and Chr 13 PI, Young-Ki-Paik) and progress reports on each team according to neXt-MP50 teams, Bioinformatics teams, neXt-CP50 teams and Young Investigators. The final session was devoted to discussion on the C-HPP organization long-term plans.

    Here are some highlights from the talks: Gilbert Omenn presented a new computational approach I-TASSER and COFACTOR algorithms to predict function of uPE1 proteins based on primary amino acid sequence. The talk presented predicted gene ontology-based functions of biological, molecular processes and cellular component of 66 uPE1 of Chromosome 17. A new challenge termed neXt-CP50, which aims to characterize at least 50 uPE1s in 3 years, and subsequent long-term plans with experimental strategies on uPE1s were presented and discussed by Young-Ki Paik. Jong Shin Yoo from chromosome 11 team presented and discussed a next generation proteomics pipeline to identify missing proteins (MPs) and protein sequence variants such alternative splicing and single amino acid variants in proteomics datasets. His group identified multiple MPs, splice junctions and single amino acid variant peptides in human brain tissue using deep proteomics and LC-MS/MS with ETD & CID fragmentation. Charles Pineau from chromosome 14 gave an update status on identification of missing proteins from human sperm and build of Human sperm proteome database in collaboration with MASSIVE. He also discussed the contribution of Epididymis proteome to the detection of MPs. Lydie Lane from chromosome 2 showed earlier uPE1 works on zebrafish and human cells. In particular she presented the characterization of enzymes such as APIP, involved in the methionine salvage pathway, mitochondrial proteins such as C11orf82, and developmental proteins such as C2orf62. Elena Ponomarenko and Ekaterina Ilgisonis from chromosome 18 team presented bioinformatics strategies including text mining in PubMed and protein-protein interaction (STRING) databases. Several options for reorganization of the C-HPP were presented and extensively discussed that included continuing a selected chromosome approach by only the currently active chromosome teams, plus the addition of new teams dedicated for bioinformatics/annotation teams, targeted MP stalking, identification of whole families of proteins in a chromosome agnostic manner and in protein – protein interaction data from large scale BioID and similar studies in human cells. The materials presented in this meeting will be available at C-HPP Wiki as soon as consent from the authors is received. More highlights from this meeting will also be presented in the C-HPP section of HUPOST in August 2018.

  • 01 Jun 2018 2:25 PM | Anonymous member (Administrator)

    The Human Proteome Project (HPP) MS-Pillar now extends is Phosphopeptide challenge resource to include affinity capture. Participants are invited to contribute to both phases of phosphopeptide identification methods development by analyzing a set of phosphopeptides by their favorite method and now follow up with an affinity purification step to see improvements in their methods. Together with our launch partner, SynPeptide Co. Ltd in Shanghai (www.synpeptide.com), the MS Resource Pillar has partnered with Resyn Biosciences Pty Ltd in South Africa (www.resynbio.com) to provide a comprehensive phosphopeptide purification kit to use on the SynPeptide-HUPO phosphopeptide mixtures. The Resyn MagReSyn® kit including the magnet separator valued at over US$1000 each are provided free to HUPO members.

    The MS-Pillar Phosphopeptide challenge samples are a complex set of human phosphopeptides (Ser, Thr or Tyr) singly and multiply phosphorylated) and their unphosphorylated counterparts that can be used for method development and verification for phosphopeptide enrichment, sequence analysis by mass spectrometry and bioinformatic evaluation.

    The first stage of this initiative is for interested members of the HUPO community to obtain a set of the peptides and apply their own methods and bioinformatic analysis to fully characterize the peptides as a neat mixture and in a tryptic digest background. Samples are still available by contacting the email below.

    The second stage is now to compare your methods used with the Resyn purification kit for phospho-enrichment and peptide clean-up. The kit contains 2mL of each MagReSyn® Ti-IMAC, Zr-IMAC, and HILIC, and 4-place magnetic separator. As a result of this collaborative endeavor, multiple purification schemes, analytical protocols and data processing strategies will be evaluated, making it possible to determine the approach(es) that provide the highest coverage of phosphopeptides in the mixture.

    By partnering with Resyn and SynPeptide the peptide sets and purification kit are being provided free-of-charge to all HUPO members, with the understanding that the analytical and data processing methods and results will be returned to the HPP MS Resource Pillar committee so they can be collated and reported at the HUPO 2018 meeting.

    Free aliquots of the peptide mixtures and MagReSyn k it can be obtained by sending an email to HUPO@resynbio.com.

  • 29 May 2018 4:19 PM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    On May 1, 2018, the C-HPP Consortium released the 7th C-HPP Newsletter summarizing 2017 C-HPP activities. Selected highlights from this C-HPP Newsletter are:

    • Reporting two C-HPP PIC decisions with respect to future directions of C-HPP consortiums made in HUPO 2017, Dublin: (1) an extension of C-HPP period to 2027: This action was necessary for completion of the human proteome mapping and identification of at least three post-translational modifications of each human protein (2) launch of neXt-CP50 challenge: This aims to discover function(s) of 50 PE1 proteins of unknown functions termed uPE1 by chromosome-centric approach in three years (list of uPE1 is available in neXtProt using SPARQL query NXQ_00022).
    • Prospective article of Ekaterina Poverennaya and Andrey Lisitsa from Orekhovich Institute of Biomedical Chemistry (Moscow, Russia, Chromosome 18 team) on the use of various gene editing technologies to found function(s) of uPE1 proteins in cell lines.
    • Lydie Lane from SIB provides a summary on the new neXtProt release (2018-1-17). Noted were an increase of PE1 human protein from 17008 to 17470 compared to the previous release (2017-1-17) and list new features of neXtProt such as viewing SRM peptides of human proteins and new SPARQL queries to list high proline content proteins (NXQ_00225). In particular, one can see the list of proteins detected in blood plasma, urine, or cerebrospinal fluid, which aims to support biomarkers research. For the detection claim of missing proteins, it usually requires at least two uniquely mapping peptides with length larger than 9 amino acids (NXQ_00226). However, in identifying proteins with experimentally determined long alpha helices (defined as a length longer than 75 amino acids), the new release provides an example query of proteins having a specific secondary structure (NXQ_00230).
    • HUPO Award for “Discovery in Proteomic Sciences” was given to Chris Overall for his career-long achievements to discover new chemical labeling approaches to study N- and C- termini of proteins such as TAILS, PICS and ATOMS which have been highly useful for studying protease substrates and cleavage sites and establishing new research field of degradomics.
    • Highlights form 17th C-HPP Workshop in Tehran (April 27-28, 2017, Iran) and 18th C-HPP Workshop in Dublin (September 17 and 21, 2017, Ireland) summarizing C-HPP progress, achievements and discussion on future directions.
    • Updated scientific program of upcoming 19th C-HPP Workshop which will be held in Santiago de Compostela (June 16-17, 2018, Spain) in conjunction with 2018 EuPA Congress. 
  • 29 May 2018 3:55 PM | Anonymous member (Administrator)

    Nicolle Packer, Macquarie University, Australia

    Performance of current software for automated intact glycopeptide identification and MS/MS spectral annotation in glycoproteomics

    Aim of study: To assess the performance of current glycoproteomics software for automated intact N- and O-glycopeptide identification from high resolution MS/MS spectral data across laboratories.

    Note - We would need to get your feedback by June 30, 2018 so that we can present the preliminary outcomes of this study at HUPO 2018 in Orlando. You will of course be a co-author on the manuscript that will be a compilation of the results of the study.

    Please let us know the following:

    1. Whether you will be a participant

    2. Whether you are a developer and/or user

    Introduction: Glycoproteomics, the study of intact glycopeptides in complex biological systems, is a growing discipline [1]. Analytical advances have now facilitated LC-MS/MS-based glycoproteomics studies reporting hundreds and even thousands of unique intact glycopeptides from a single experiment. However, significant bottlenecks clearly exist in the accurate annotation of the large volumes of resulting MS/MS spectral data and in the confident identification and reporting of the corresponding intact glycopeptides. The identification of intact glycopeptides has previously relied heavily on manual interpretation and expert curation support. However, as the field of glycoproteomics transitions to rely increasingly on the use of large data sets in our experimental designs, the development of efficient software for accurate automated glycopeptide identification becomes absolutely essential.

    Over the past 5-10 years the field of glycoproteomics has seen the development of multiple exciting tools that show promise for automated or semi-automated annotation and identification of glycopeptides from MS/MS spectral evidence [2].

    This first study of the newly established HUPO Glycoproteomics Initiative (HGI) sets out to study the performance of the current informatics capabilities in this specialised field. Documenting the current status of glycoproteomics is vital to drive further technological developments and promote applications of system-wide glycopeptide analysis.

    Overview of study: This informatics-focused glycoproteomics study consists of two parts:

    Part A) Comparative study in which developers of glycoproteomics software (of academic and industrial origin) identify and report intact glycopeptides from provided LC-MS/MS glycopeptide datasets using exclusively their own developed software. The developers may improve their existing software in this process but need to provide an exact description of how their software was utilised to obtain the reported glycopeptides and provide software access and experimental conditions to the study committee to allow them to reproduce and interrogate the reported findings.

    Part B) Comparative study in which expert users (research teams) in Glycoproteomics (from academic and industrial origin) identify intact glycopeptides from the same (as in A) provided LC-MS/MS glycopeptide datasets using one or more tools, which they routinely use for glycopeptide analysis including manual interpretation as support. Users must report how they obtained their findings.

    Most participants will fit in either Part A or B; however, a research group can contribute to both parts, but must adhere to the provided guidelines and must provide separate reports from these two efforts. Two LC-MS/MS datasets containing mixtures of intact O- and N-glycopeptide data are provided to all involved participants, which should be reported on according to the provided guidelines.

    Study details and the fine-print:

    About the analysed glycoprotein samples: Human serum containing a complex mixture of N- and O-linked glycoproteins was used in this study (Thermo Fisher Scientific #31876). Briefly, the proteins were reduced, carbamidomethylated and digested exhaustively with porcine trypsin. The resulting peptide mixtures were split and analysed in their native form after enrichment using two different LC-MS/MS acquisition styles.

    About the two LC-MS/MS acquisition style and access to the provided data: The glycopeptides were separated using nano-LC (C18) separation and detected in positive polarity using alternating fragmentation modes (HCD, ETciD, EThcD and CID, see “Terminology” below for definition) on a Thermo Orbitrap Lumos LC-MS/MS platform [3]. Complementary fragmentation types were used within the same LC-MS/MS run to satisfy various software packages for glycopeptide identification. Precursor and product ions were recorded in “profile” mode at high resolution in the Orbitrap (OT) and at low resolution in the ion trap (IT). Two unprocessed data (raw) files acquired using two different acquisition styles are provided to participants:

    Data file A: HCD (OT) – ETciD (OT) – CID (OT) (File: “A_glycopepnew_HCDETciDOTCIDpeptide.raw”)

    Data file B: HCD (OT) – EThcD (OT) – CID (IT) (File: “B_glycopepnewHCDEThcDiTCIDpeptide.raw”)

    https://cloudstor.aarnet.edu.au/plus/index.php/s/koiUv4LCOjobrih (Password:HGI2017)

    Since some participants may not have access to Thermo (proprietary) software for data processing, the data files are also provided after .mgf or .mzxml. conversion. The link also provides access to other critical files for the glycopeptide identification and the reporting template.

    About the proposed identification and reporting of intact glycopeptides: Participants are requested to report on identified intact glycopeptides in a tabulated form using a provided Excel template. The template also hosts detailed guidelines for the identification of intact glycopeptides (e.g. Protein and Glycan search space) and the requirements for the data reporting. The developers (Part A) are also expected to provide annotated MS/MS spectra of the identified (reported) glycopeptides (PDF/PPT preferred) if their software allows for this since annotated spectral evidence is a requirement of many journals in the reporting of glycopeptide data sets. Users are encouraged to do the same.

    About the data comparison, disclosure of participant reports and dissemination of outcome: The reported data of the participants will be compiled by the HGI study committee. The identity of the participating developers and their software as well as the relative performance of their software (compared to other software and the user groups) will be disclosed. Should participating developers decide to not return their findings for various reasons, their identity and participation will not be disclosed in any dissemination of the study outcome. User groups will remain anonymous. Results will be compiled, compared, published and presentation (see below). All participants (developers and users alike) that return glycopeptide reports adhering to the study guidelines will be acknowledged for their efforts by being offered a co-authorship in the publication(s) arising from this study and mentioned by name in oral/poster presentations.

    Time-line for 1st HGI study:

    Sep 2016: HGI formed. Head and committee selected.

    July 2017: LC-MS/MS glycoproteomics data generated by Thermo and quality validated by committee.

    2017: Calls for participation in HGI study.

    Sep 2017: HGI study introduced at World HUPO 2017.

    March 2018: Data files and reporting template made available to registered participants.

    30 June 2018: Deadline participant reporting of data.

    July-September 2018: Compilation and comparison of data.

    Sep 2018: Preliminary data presented World HUPO 2018.

    Early – Mid 2019: Outcome(s) published.

    Sep 2019: Outcomes presented at World HUPO 2019.

    HGI study committee:

    ·HGI chair: Prof. Nicolle H. Packer, Macquarie University, Sydney, and Glycomics Institute, Griffith University, Gold Coast, Australia (nicki.packer@mq.edu.au)

    ·HGI deputy chair: Dr. Morten Thaysen-Andersen, Macquarie University, Sydney, Australia (morten.andersen@mq.edu.au)

    Additional HGI study committee members:

    ·A/Prof. Daniel Kolarich, Griffith University, Gold Coast, Australia (d.kolarich@griffith.edu.au)

    ·Prof. Kai-Hooi Khoo, Academia Sinica, Taiwan (kkhoo@gate.sinica.edu.tw)

    ·Prof. Katalin Medzihradszky, UCSF, CA (folkl@cgl.ucsf.edu)

    ·Prof. Joe Zaia, Boston University, MA (jzaia@bu.edu)

    ·Prof. Goran Larson, Gothenburg, Sweden (goran.larson@clinchem.gu.se)

    ·Dr. Stuart Haslam, Imperial College, UK (s.haslam@imperial.ac.uk)

    ·Prof. Giuseppe Palmisano, University of Sao Paulo, Brazil (palmisano.gp@usp.br)

    ·Prof. Jong Shin Yoo, Korea Basic Science Institute, Korea (jongshin@kbsi.re.kr)

    Acknowledgement: Dr Rosa Viner (Thermo) is thanked for providing valuable samples and high quality LC-MS/MS data to this study.

  • 04 May 2018 11:01 AM | Anonymous member (Administrator)

    The 7th newsletter of the Chromosome-centric Human Proteome Project is now available online, read it here.

    In this issue:

    • The New Release of neXtProt
    • Highlights of C-HPP Consortium News
    • Summary of Discussion on the C_HPP Progress
    • 2018 JPR PSecial Issue Call for Papers
    • 19th C-HPP Workshop in Santiago, Spain
    • Future C-HPP Scientific Workshops
    • C-HPP Leadership
    • C-HPP PIC Members
  • 29 Mar 2018 9:40 AM | Anonymous member (Administrator)

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

    The last decades saw a steady increase in the incidence of rheumatic and autoimmune diseases such as osteoarthritis (OA) rheumatoid arthritis (RA), multiple sclerosis (MS), inflammatory bowel diseases (IBD) and systemic lupus erythematosus (SLE). Rheumatic and autoimmune diseases (RAD) are characterised by inflammation of joints, muscles, and connective tissues around joints and bones. Apart from the debilitating mobility and pain, RAD patients are also at increased risk of cardiovascular and neurodegenerative diseases. Given the huge socioeconomic impact of RAD, broad research efforts have been dedicated these diseases worldwide.

    The RAD B/D-HPP initiative was launched in 2017 by Francisco J. Blanco (Rheumatology Department, INIBIC-Complejo Hospitalario Universitario A Coruña in Spain) with co-chair Paul J. Utz from Stanford Department of Medicine, USA). Currently, 6 research groups from 5 countries participate in RAD-HPP, but the collaborative network has already extended to Cardiovascular-HPP and Chromosome 16-HPP .

    After establishing the networks and promoting visibility of the new initiative, the immediate scientific goals of RAD-HPP are to define the proteome of human joint tissues (cartilage, synovial membrane, subchondral bone), and to assemble prioritized lists of proteins clinically relevant in RAD using the ‘popular proteins’ strategy with text mining tools. Collaborations within the RAD-HPP have already resulted in several publications in 2017, including circulating biomarkers for knee radiographic osteoarthritis , use of protein array to discover and validate biomarkers for Osteoarticular Pathologies , and anti-citrullinated protein antibodies in rheumatoid arthritis.

    To spread the word outside of proteomics research circles, RAD-HPP members presented their proteomics work at key RAD clinical meetings around the globe in 2017. These included Osteoarthritis Research Society International (OARSI) World Congress in Las Vegas (USA), the Annual European Congress of Rheumatology-EULAR in Madrid (Spain), Annual Meeting of the American College of Rheumatology in San Diego (USA), and XLIII Congress of the Spanish Rheumatology Society in Bilbao (Spain).

    To boost the development and utility of quantitative proteomics assays, RAD-HPP members conducted focused proteomics training sessions in 2017, with highlights being sessions at “Cutting Edge Osteoarthritis” Symposium at Pembroke College, Oxford, and “Proteomics in rheumatic diseases” lecture at a Summer School on Platform Technologies and Big Data applications in Precision Medicine, in Santander, Spain.

    With the synergistic international effort and strong clinical translational focus, the RAD-HPP initiative is poised to realise the utility of proteomics in RAD diagnosis and management.

  • 06 Dec 2017 1:14 PM | Anonymous member (Administrator)

    Submit your manuscript to Journal of Proteome Research for the 2018 HUPO Human Proteome Project Special Issue. Submission deadline May 31, 2018 

    The JPR Special Issue on the HPP will now consider short definitive reports, submitted in the Letters format, on the discovery of a Missing Protein(s). 

    To be considered for publication, the missing protein(s) must meet the Guidelines v 2.1 and be cast in the context of both the HPP and biological setting in which they were discovered. We anticipate this format will encourage many teams, particularly of the B/D-HPP, to highlight such protein discoveries in a disease and biological context.

    Click here for more info.

  • 20 Nov 2017 5:00 PM | Anonymous member (Administrator)

    AMSTERDAM, NOVEMBER 20 2017 – While colorectal cancer screening already saves many thousands of lives, there is still room for improvement. By looking at a combination of specific proteins rather than at a single blood protein alone, substantially more patients with colorectal cancer and advanced adenomas could be detected. The study describing these findings, conducted by researchers from the Netherlands Cancer Institute and VU University Medical Center, is published in the Annals of Internal Medicine.

    Click here to read the full article. 

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