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  • 01 Nov 2022 6:22 PM | Anonymous member (Administrator)

    Authors:

    Yun-En Chung1 and Mathieu Lavallée-Adam1

    1Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada

    Mass spectrometry-based proteomics data analysis has never been more exciting. The combination of computational hardware improvements and a wide diversity of instruments and experimental techniques has created a gigantic playground for computational researchers and software developers. In recent years, one attraction at this playground has gained a lot of attention from both academia and industry: real-time analysis of proteomics data.

    In a traditional mass spectrometry-based proteomics experiment, tens of thousands of mass spectra are collected for a biological sample. After the conclusion of the experiment these mass spectra are then inputted into software packages for peptide and protein identification and quantification. Hence, since biological information is inferred solely through post-hoc analysis, the mass spectrometry experiment is mostly running blind and does not adapt in real-time based on the biological data that is being acquired.

    Improvements in computational hardware and the recent availability of Application Programming Interfaces (APIs) enabling mass spectrometry data analysis during proteomics experiments have paved the way to the design of a new family of algorithms and software packages performing the real-time analysis of mass spectrometry data. Tools such as the Thermo Fisher Scientific Instrument API (IAPI)1 and the Bruker Parallel database Search Engine in Real-time (PaSER)2 are enabling the design of analyses that accelerate data processing, help diagnose problems with instrumentation and enhance the characterization capabilities of mass spectrometry.

    One of the early modern applications of real-time mass spectrometry data analysis is the on-the-fly quality assessment of mass spectrometry experiments. Instrument performance drop or malfunction are often only identified after post-hoc data analysis. Such a late discovery results in a waste of time and resources that are used to acquire unusable or subpar data. The QC-ART approach3 has been developed to evaluate instrument performance in near real-time and allow for immediate intervention. QC-ART ensures consistent high-quality data collection and the rapid detection of instrumentation problems.

    Since the early beginnings of mass spectrometry-based proteomics, data acquisition remained an extremely active research topic. Still today, new acquisition techniques are being developed to supplement the current families of approaches including data-dependent acquisition4, data-independent acquisition5 and targeted methods6,7. Traditionally, an instrument would apply the same acquisition strategy (precursor ion selection algorithm, scan window size, …) for the entirety of an experiment. This standard acquisition method works reasonably well in common proteomics use cases. However, since the instrument does not consider the biological relevance of the data it is acquiring, a significant proportion of this data does not translate into meaningful biological discoveries.

    An excellent example of this is how real-time database search for peptide identification can support the selection of peptides for quantification with isobaric labeling. It was previously shown that MS3 spectra lead to more accurate quantification using tandem mass tag reporter ions than MS2 spectra8. However, acquiring MS3 spectra is resource intensive. It is therefore important to acquire MS3 spectra for data that is biologically relevant. Orbiter was therefore developed to identify peptides in real-time from MS2 spectra with a database search method9. Orbiter then only acquires MS3 spectra from MS2 spectra that yield a confident peptide identification and therefore optimizes resource usage for protein quantification.

    Other groups developed software packages to identify peptides in real-time10,11, while McQueen et al. presented a pseudo real-time approach that paused the experiment to adjust future data acquisition based on such peptide identifications. Inspired by these methods, our team proposed that the real-time identification of peptides and proteins can be used to guide mass spectrometry data acquisition in order to optimize resource usage and maximize protein identifications. Indeed, our computational approach, named MealTime-MS12, uses real-time database search to identify peptides and supervised learning to assess the confidence of protein identifications. MealTime-MS then uses confident protein identifications to generate an exclusion list preventing the acquisition of tandem mass spectra for peptide ions that are expected to belong to proteins that were already identified in the mass spectrometry run. MealTime-MS showed that up to 33% of the mass spectra collected in traditional experiments could be safely ignored with minimal losses of proteins identified compared to standard experiments and that these mass spectra could be repurposed for the identification of additional proteins.

    Alternatively, real-time analysis of mass spectrometry data has demonstrated its utility in targeted proteomics. In a typical targeted proteomics experiment, specific elution time windows need to be determined for targeted peptides. Due to run-to-run technical variation, the size of these scheduled windows must be kept relatively large to ensure the instrument encounters these peptides, thereby limiting the number of possible targets. MaxQuant.Live presented a solution via real-time recognition of precursor ions13. The algorithm uses the retention time, mass-to-charge ratio, and intensity of the precursor ions encountered to predict and therefore select those that should be targeted for quantification. This approach enabled the targeting of over 25,000 peptides in a single mass spectrometry run.

    Real-time analysis of mass spectrometry-based proteomics data has also demonstrated its clinical applications. Devices such as the MasSpec Pen demonstrated how a small handheld device can be used to rapidly detect features including lipids, metabolites and proteins in human tissue. Such features can be used as biomarkers to diagnose in real-time whether tissues are cancerous or healthy.

    After reading about these applications, we would like you to join the conversation on Twitter by answering our poll question here and letting us know where the future of real-time proteomics data analysis sits:  

    Twitter Poll:

    In which area do you think real-time analysis of mass spectrometry-based proteomics data will have the greatest impact in the future:

    1. Protein ID
    2. Protein Quantification
    3. Clinical Applications
    4. Other (write in replies)

    Figure 1. Graphical representation of the traditional mass spectrometry-based proteomics pipeline, where acquired data is analyzed after the completion of the experiment and of a pipeline integrating real-time data analysis to adjust mass spectrometry data acquisition during the experiment.


    Computer Icon created by Freepik - Flaticon: https://www.flaticon.com/free-icons/course.

    Bios:

    Yun-En Chung:

    Yun-En Chung is an undergraduate student in Translational and Molecular Medicine and researcher in Dr. Mathieu Lavallée-Adam’s lab at the University of Ottawa. His research focuses on the development of software packages to guide mass spectrometry experiments in real-time to improve data acquisition efficiency. His publication on the real-time identification of proteins in mass spectrometry data was recognized as the best paper from a Master’s or Undergraduate student at the Ottawa Institute of Systems Biology in 2020. He also received several awards for his presentations, including a 2nd place for his oral presentation at the Undergraduate Research Opportunities Program Seminar day at the University of Ottawa and an honorable mention for his poster at the American Society for Mass Spectrometry annual conference in 2022. Yun-En’s research is funded by awards from the Natural Sciences and Engineering Research Council of Canada and Mitacs.

    Mathieu Lavallée-Adam:

    Mathieu Lavallée-Adam is an Associate Professor at the University of Ottawa in the Department of Biochemistry, Microbiology and Immunology and is affiliated to the Ottawa Institute of Systems Biology. He obtained a B.Sc. in Computer Science and a Ph.D. in Computer Science, Bioinformatics option, from McGill University and performed his postdoctoral research at The Scripps Research Institute. His research focuses on the development of statistical and machine learning algorithms for the analysis of mass spectrometry-based proteomics data and protein-protein interaction networks. Dr. Lavallée-Adam is a recipient of the John Charles Polanyi Prize in Chemistry, rewarding the impact of his bioinformatics algorithms on the mass spectrometry community and was named Early Career Researcher of the Year by the Ottawa Institute for Systems Biology in 2021. He is also Co-Chair of the HUPO Early Career Researcher Initiative and a member of the HUPO Executive Committee, in which he develops training activities and advocates for junior investigators in proteomics and organize events highlighting their research on the international stage.

    References:

    1.        Scientific, T. F. Thermo Fisher Scientific IAPI GitHub. (2022). Available at: https://github.com/thermofisherlsms/iapi.

    2.        Bruker. PaSER 2022. (2022).

    3.        Stanfill, B. A., Nakayasu, E. S., Bramer, L. M., Thompson, A. M., Ansong, C. K., Clauss, T. R., Gritsenko, M. A., Monroe, M. E., Moore, R. J., Orton, D. J., Piehowski, P. D., Schepmoes, A. A., Smith, R. D., Webb-Robertson, B.-J. M., Metz, T. O. & TEDDY Study Group. Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data. Mol. Cell. Proteomics 17, 1824–1836 (2018).

    4.        Liu, H., Sadygov, R. G. & Yates, J. R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193–201 (2004).

    5.        Venable, J. D., Dong, M.-Q., Wohlschlegel, J., Dillin, A. & Yates, J. R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39–45 (2004).

    6.        Kuhn, E., Wu, J., Karl, J., Liao, H., Zolg, W. & Guild, B. Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics 4, 1175–86 (2004).

    7.        Anderson, L. & Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5, 573–88 (2006).

    8.        Ting, L., Rad, R., Gygi, S. P. & Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 8, 937–40 (2011).

    9.        Schweppe, D. K., Eng, J. K., Yu, Q., Bailey, D., Rad, R., Navarrete-Perea, J., Huttlin, E. L., Erickson, B. K., Paulo, J. A. & Gygi, S. P. Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics. J. Proteome Res. 19, 2026–2034 (2020).

    10.      Bailey, D. J., Rose, C. M., McAlister, G. C., Brumbaugh, J., Yu, P., Wenger, C. D., Westphall, M. S., Thomson, J. A. & Coon, J. J. Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 109, 8411–6 (2012).

    11.      Graumann, J., Scheltema, R. A., Zhang, Y., Cox, J. & Mann, M. A framework for intelligent data acquisition and real-time database searching for shotgun proteomics. Mol. Cell. Proteomics 11, M111.013185 (2012).

    12.      Pelletier, A. R., Chung, Y.-E., Ning, Z., Wong, N., Figeys, D. & Lavallée-Adam, M. MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion. J. Am. Soc. Mass Spectrom. 31, 1459–1472 (2020).

    13.      Wichmann, C., Meier, F., Winter, S. V., Brunner, A.-D., Cox, J. & Mann, M. MaxQuant.Live enables global targeting of more than 25,000 peptides. bioRxiv 443838 (2018). doi:10.1101/443838

  • 01 Nov 2022 10:28 AM | Anonymous member (Administrator)

    Join the next online panel hosted by the HUPO Early Career Researcher (ECR) Initiative on November 16th at 4PM GMT for a discussion on 'Science communication - who, how, where, and why?'.  We have three wonderful panelists:

    • Dr. David Tabb, Institut Pasteur
    • Dr. Ann Van der Jeugd, Leuven Brain Institute
    • Dr. Ben Orsburn, Johns Hopkins University

    Effective science communication has ripple effects through all aspects of society. But how do you convey clear and concise messages? What is the best way to get these messages across a wide range of platforms? Get the answers to all these questions and more!

    REGISTER HERE in advance for this webinar.

    After registering, you will receive a confirmation email containing information about joining the webinar.

  • 26 Oct 2022 12:53 AM | Anonymous member (Administrator)

    The HUPO Education and Training Committee (ETC) webinar series is intended to help you organize and write a quality academic research paper. We will present how to polish academic style, how to manage data presentation, and how to learn from critical reading. Our mission is to provide academic support to strengthen student learning and empower every student to develop as self-academic writer whose work is admire.

    Date: November 2, 2022
    Time: 8:00 am PST

    WEBINAR LINK:  https://us06web.zoom.us/j/84142263041

    Speaker: John Yates III, PhD, Professor, Department of Molecular Medicine, Editor of Journal of Proteome Research. Dr. Yates research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and biological studies involving proteomics. Additional to thousands of publications, international and national awards, and recognitions, Dr. Yates served as an Associate Editor at Analytical Chemistry for 15 years and is currently the Editor in Chief at the Journal of Proteome Research.


  • 15 Oct 2022 1:30 PM | Anonymous member (Administrator)

    See our exciting program information below.  REGISTER TODAY!

    All times are US Eastern Time. 

    10:00 am Matthias Mann, "Ultra-high sensitivity for precision oncology"

    10:30 am Erwin Schoof, "Leveraging advanced latest-generation acquisition and MS instrument architecture for improving single cell proteomics experiments"

    11:00 am Roman Zubarev, "Since cell proteomics - some considerations from the chemical proteomics point of view"

    11:30 am Claudia Ctortecka, "Variations of the proteoCHIP - a high-throughput sample preparation approach for single-cell proteomics"

    12:00 pm Ying Zhu, "Enhancing single cell proteomics and tissue proteome mapping with ion mobility filtering"

    12:30 pm Ryan Kelly, "Advanced separations and data acquisitions strategies for in-depth single-cell proteomics"

    13:00 pm Closing remarks

    REGISTER HERE!

    Organized by the B/D-HPP Single Cell Initiative. Please contact Initiative Chair Dr. Bogdan Budnik (Bogdan.Budnik@wyss.harvard.edu) with any questions or if you want more info!  

  • 12 Oct 2022 12:31 PM | Anonymous member (Administrator)

    Check out the October issue of HUPOST here, full of the latest news and updates, including HUPO's Strategic Plan!

  • 03 Oct 2022 4:23 PM | Anonymous member (Administrator)

    Dr. Seyedmohammad started off his career in immunology where he Investigated Inhibitory signals at the T-cell Immune Synapse. During his master’s degree at Imperial College London, he developed important immune assays that helped in the identification of prominent signaling molecules involved in T-cell activation. He then obtained his doctoral degree in biochemistry at the University of Cambridge, where he studied the characterization of a bacterial iron transport protein from Pseudomonas aeruginosa. In that thesis, Dr. Seyedmohammad successfully proved the trimeric conformation of the protein and identified key binding motifs driving the acquisition of iron into the bacterial cell. After venturing into several start-ups, he began a post-doctoral fellowship under the supervision of Dr. Van Eyk at the Advanced Clinical Biosciences Research Institute in Cedars Sinai Medical Research Division, where he is currently using novel proteomic approaches to study heart failure. Dr. Seyedmohammad is responsible for identifying newly synthesized proteins in human cardiomyocytes using AHA-labeling and is applying this approach to characterize important protein pathways involved in heart disease as a consequence of ischemia and reperfusion. He is also responsible for developing high-throughput assays, using a COVARIS sonication system to scale-up sample processing for a robust workflow.

  • 06 Sep 2022 1:14 PM | Anonymous member (Administrator)

    The September HUPOST is now available!  Lots of exciting and interesting info - Congress updates, EC Elections, ECR News, B/D HPP info and more!

  • 06 Sep 2022 11:12 AM | Anonymous member (Administrator)

    See our exciting program information below.  All times are US Eastern Time. 

    10:00 am Matthias Mann, "Ultra-high sensitivity for precision oncology"

    10:30 am Erwin Schoof, "Leveraging advanced latest-generation acquisition and MS instrument architecture for improving single cell proteomics experiments"

    11:00 am Roman Zubarev, "Since cell proteomics - some considerations from the chemical proteomics point of view"

    11:30 am Claudia Ctortecka, "Variations of the proteoCHIP - a high-throughput sample preparation approach for single-cell proteomics"

    12:00 pm Ying Zhu, "Enhancing single cell proteomics and tissue proteome mapping with ion mobility filtering"

    12:30 pm Ryan Kelly, "Advanced separations and data acquisitions strategies for in-depth single-cell proteomics"

    13:00 pm Closing remarks

    REGISTER HERE!

    Organized by the B/D-HPP Single Cell Initiative. Please contact Initiative Chair Dr. Bogdan Budnik (Bogdan.Budnik@wyss.harvard.edu) with any questions or if you want more info!  

  • 01 Sep 2022 6:28 PM | Anonymous member (Administrator)

    Livia Rosa-Fernandes is part of Prof. Marinho’s research team at The Institute of Biomedical Sciences of the University of São Paulo and a Research Fellow in Neuroproteomics at Macquarie University Centre for Motor Neuron Disease Research. She received her Ph.D. in Medical Sciences from USP Medical School (2015). During her Ph.D., she had the opportunity to work at Brigham and Women´s Hospital-Harvard Medical School (USA), as part of the Postgraduate Research Exchange Program. In 2016, Livia moved to Denmark, where she worked as a post-doctoral researcher both at the Department of Biochemistry and Molecular Biology and the Institute of Molecular Medicine, at the University of Southern Denmark. From 2019, she was enrolled as a post-doctoral fellow at the Institute of Biomedical Sciences, USP (Brazil).

    Over time, Livia has gathered experience using in vivo and in vitro models together with molecular tools to study biological processes focusing on disease progression, cellular communication, and its microenvironment. MS-based proteomics and data analytics play a key role in her research as powerful tools to better understand a biological event. Her scientific production reflects an effort to engage in multidisciplinary fields and strengthen a collaborative approach to science. She is also part of the Brazilian Proteomics Society council and is engaged in several initiatives to promote knowledge transfer and increase access to scientific education.

  • 01 Sep 2022 6:19 PM | Anonymous member (Administrator)

    With the recent refresh of the HUPO Biology/Disease-driven Human Proteome Project (B/D-HPP) Executive Committee, we took the opportunity to get the thoughts of several members of the committee who completed their tenure. Drs. Corrales, Deutsch, Omenn, and Schmidt have all given their valuable time and leadership to the HUPO mission and have been critical to the continued growth of the B/D-HPP initiatives and the continued adoption of proteomics advances toward understanding pressing questions in health and life sciences. We asked them what they would like to share with the HUPO community on this occasion.

    Dr. Fernando Corrales served as co-chair, chair, and past-chair of the B/D-HPP from 2015–2021. As the Human Liver Proteome Project (HLPP) chair, he also has led the HLPP since 2014. Regarding what he sees as the importance of the B/D-HPP at large, the former chair said that it has represented to him an “opportunity to translate the essence of proteomics” and particularly into “functional understanding of biological systems.” Dr. Corrales, who is Professor at the Spanish National Centre for Biotechnology, sees the B/D-HPP as the masterpiece of the upcoming Grand Project once it is integrated with the other resources of the HPP. The experience sharing the coordination of the B/D-HPP with Drs. Jenny van Eyk and Ileana Cristea has been outstanding and the efforts of all persons on board during these years have been generous, says Dr. Corrales.

    “Defining protein function is something clearly dependent on the biological environment where proteins develop their activity and B/D Teams integrate an ideal research network to dissect so far hidden functionalities and place them into the adequate physiological and/or pathological framework." – Fernando Corrales

    Dr. Eric Deutsch, who served on the executive committee for five years, agrees on the importance of ensuring B/D-HPP initiatives receive continued community support. “I wish the new committee well in working to increase active participation of all B/D-HPP initiatives”, adds the longtime HUPO leader and Principal Scientist at the Institute of Systems Biology.

    Dr. Gil Omenn is the Harold T. Shapiro Distinguished University Professor at University of Michigan and a longtime chair of the HUPO Human Proteome Project (HPP). He served on the B/D-HPP executive committee for a decade alongside Drs. Ruedi Aebersold, Jenny van Eyk, Fernando Corrales, Ileana Cristea, and now Nicki Packer as chairs, and chaired the Human Plasma Proteome Project from the launch of HUPO in 2002. Under his leadership, the Plasma, Brain, Liver, Cancer, and Cardiovascular Proteome Projects were brought together with many emerging projects to form the B/D-HPP in 2011 and join the Chromosome-centric C-HPP in the HUPO HPP. This year, Dr. Omenn has rotated off the B/D-HPP executive committee after a successful term that saw him continue to lead the executive committee with his vision, which culminated in an HPP Metrics of the Human Proteome paper in the annual special issues of the Journal of Proteome Research[1] and a special perspective article in Molecular & Cellular Proteomics[2].

    “The B/D-HPP teams have made important contributions to the global explosion of research utilizing proteomics to reveal pathways, networks, mechanisms, and biomarkers underlying a great range of biological processes and diseases,” – Gil Omenn

    Dr. Frank Schmidt is an active leader in the B/D-HPP community and served on the executive committee. As his term concludes, Dr. Schmidt said he will remember his time with the committee “very positively”. The transition to the digital age during the COVID-19 pandemic was especially memorable, "when we successfully held our first professional webinars and were able to push new ideas under the excellent leadership of Ileana [Cristea] and Fernando [Corrales]”, reminisces Dr. Schmidt, who is Professor at Weill Cornell Medicine-Qatar. He wishes the new committee good luck as a new crop of members from the proteomics community continue the initiative missions.

    We look forward to continuing the work of the HUPO B/D-HPP in engaging the proteomics community and promoting the adaption of proteomics advances toward life and medical sciences. We welcome the new and continuing HUPO B/D-HPP Executive Committee members for 2022–2023:

    • Dr. Michal Bassani, Immunopeptidomics, continuing
    • Dr. Bogdan Budnik, Single cell proteomics, new
    • Dr. Ferdinando Cerciello, Cancer, continuing
    • Dr. Ileana Cristea (Co-chair/Past Chair), Infectious disease, continuing
    • Dr. Ruth Huttenhain, Signaling and protein networks & ECR, new
    • Dr. Maggie Lam, Cardiovascular, continuing
    • Dr. Ed Nice, Cancer, new
    • Dr. Aleksandra Nita-lazar, Infectious disease, continuing
    • Dr. Nicki Packer (Chair), Glycoproteomics, continuing
    • Dr. Uwe Völker, Clinical proteomics, new

    Footnotes:

    [1] Omenn GS et al. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res. 2020 Dec 4; 19(12): 4735–4746. PMID: 32931287

    [2] Omenn GS. Reflections on the HUPO Human Proteome Project, the flagship project of the Human Proteome Organization, at 10 years. Mol Cell Proteomics. 2021 Feb 26;20:100062. PMID: 33640492.



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