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947 results on '"Moritz, Robert L."'

1. Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry

Author

Jiang, Yuming, Rex, Devasahayam Arokia Balaya, Schuster, Dina, Neely, Benjamin A., Rosano, Germán L., Volkmar, Norbert, Momenzadeh, Amanda, Peters-Clarke, Trenton M., Egbert, Susan B., Kreimer, Simion, Doud, Emma H., Crook, Oliver M., Yadav, Amit Kumar, Vanuopadath, Muralidharan, Mayta, Martín L., Duboff, Anna G., Riley, Nicholas M., Moritz, Robert L., and Meyer, Jesse G.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.

Published
2023

2. Structural surfaceomics reveals an AML-specific conformation of integrin β2 as a CAR T cellular therapy target

Author

Mandal, Kamal, Wicaksono, Gianina, Yu, Clinton, Adams, Jarrett J, Hoopmann, Michael R, Temple, William C, Izgutdina, Adila, Escobar, Bonell Patiño, Gorelik, Maryna, Ihling, Christian H, Nix, Matthew A, Naik, Akul, Xie, William H, Hübner, Juwita, Rollins, Lisa A, Reid, Sandy M, Ramos, Emilio, Kasap, Corynn, Steri, Veronica, Serrano, Juan Antonio Camara, Salangsang, Fernando, Phojanakong, Paul, McMillan, Melanie, Gavallos, Victor, Leavitt, Andrew D, Logan, Aaron C, Rooney, Cliona M, Eyquem, Justin, Sinz, Andrea, Huang, Benjamin J, Stieglitz, Elliot, Smith, Catherine C, Moritz, Robert L, Sidhu, Sachdev S, Huang, Lan, and Wiita, Arun P

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Pediatric, Rare Diseases, Pediatric Cancer, Immunotherapy, Orphan Drug, Hematology, Childhood Leukemia, Biotechnology, Cancer, Gene Therapy, Genetics, 5.2 Cellular and gene therapies, 5.1 Pharmaceuticals, Humans, Receptors, Chimeric Antigen, T-Lymphocytes, Integrins, Immunotherapy, Adoptive, Leukemia, Myeloid, Acute, Oncology and carcinogenesis
Abstract

Safely expanding indications for cellular therapies has been challenging given a lack of highly cancer-specific surface markers. Here we explore the hypothesis that tumor cells express cancer-specific surface protein conformations that are invisible to standard target discovery pipelines evaluating gene or protein expression, and these conformations can be identified and immunotherapeutically targeted. We term this strategy integrating cross-linking mass spectrometry with glycoprotein surface capture 'structural surfaceomics'. As a proof of principle, we apply this technology to acute myeloid leukemia (AML), a hematologic malignancy with dismal outcomes and no known optimal immunotherapy target. We identify the activated conformation of integrin β2 as a structurally defined, widely expressed AML-specific target. We develop and characterize recombinant antibodies to this protein conformation and show that chimeric antigen receptor T cells eliminate AML cells and patient-derived xenografts without notable toxicity toward normal hematopoietic cells. Our findings validate an AML conformation-specific target antigen and demonstrate a tool kit for applying these strategies more broadly.

Published
2023

3. A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

Author

Kusebauch, Ulrike, Lorenzetti, Alan PR, Campbell, David S, Pan, Min, Shteynberg, David, Kapil, Charu, Midha, Mukul K, López García de Lomana, Adrián, Baliga, Nitin S, and Moritz, Robert L

Subjects
Information and Computing Sciences, Analytical Chemistry, Biological Sciences, Chemical Sciences, Biotechnology, Generic health relevance, Halobacterium salinarum, Peptides, Proteome, Proteomics
Abstract

Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).

Published
2023

4. Proteomic changes induced by longevity-promoting interventions in mice

Author

Burns, Adam R., Wiedrick, Jack, Feryn, Alicia, Maes, Michal, Midha, Mukul K., Baxter, David H., Morrone, Seamus R., Prokop, Timothy J., Kapil, Charu, Hoopmann, Michael R., Kusebauch, Ulrike, Deutsch, Eric W., Rappaport, Noa, Watanabe, Kengo, Moritz, Robert L., Miller, Richard A., Lapidus, Jodi A., and Orwoll, Eric S.

Published
2024
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5. Standardized annotation of translated open reading frames

Author

Mudge, Jonathan M, Ruiz-Orera, Jorge, Prensner, John R, Brunet, Marie A, Calvet, Ferriol, Jungreis, Irwin, Gonzalez, Jose Manuel, Magrane, Michele, Martinez, Thomas F, Schulz, Jana Felicitas, Yang, Yucheng T, Albà, M Mar, Aspden, Julie L, Baranov, Pavel V, Bazzini, Ariel A, Bruford, Elspeth, Martin, Maria Jesus, Calviello, Lorenzo, Carvunis, Anne-Ruxandra, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W, Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T, Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L, Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S, and van Heesch, Sebastiaan

Subjects
Molecular Sequence Annotation, Open Reading Frames, Protein Biosynthesis, Ribosomes
Published
2022

7. Author Correction: Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers

Author

Watanabe, Kengo, Wilmanski, Tomasz, Baloni, Priyanka, Robinson, Max, Garcia, Gonzalo G., Hoopmann, Michael R., Midha, Mukul K., Baxter, David H., Maes, Michal, Morrone, Seamus R., Crebs, Kelly M., Kapil, Charu, Kusebauch, Ulrike, Wiedrick, Jack, Lapidus, Jodi, Pflieger, Lance, Lausted, Christopher, Roach, Jared C., Glusman, Gwênlyn, Cummings, Steven R., Schork, Nicholas J., Price, Nathan D., Hood, Leroy, Miller, Richard A., Moritz, Robert L., and Rappaport, Noa

Published
2023
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8. Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers

Author

Watanabe, Kengo, Wilmanski, Tomasz, Baloni, Priyanka, Robinson, Max, Garcia, Gonzalo G., Hoopmann, Michael R., Midha, Mukul K., Baxter, David H., Maes, Michal, Morrone, Seamus R., Crebs, Kelly M., Kapil, Charu, Kusebauch, Ulrike, Wiedrick, Jack, Lapidus, Jodi, Pflieger, Lance, Lausted, Christopher, Roach, Jared C., Glusman, Gwênlyn, Cummings, Steven R., Schork, Nicholas J., Price, Nathan D., Hood, Leroy, Miller, Richard A., Moritz, Robert L., and Rappaport, Noa

Published
2023
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9. Molecular damage in aging

Author

Gladyshev, Vadim N, Kritchevsky, Stephen B, Clarke, Steven G, Cuervo, Ana Maria, Fiehn, Oliver, de Magalhães, João Pedro, Mau, Theresa, Maes, Michal, Moritz, Robert L, Niedernhofer, Laura J, Van Schaftingen, Emile, Tranah, Gregory J, Walsh, Kenneth, Yura, Yoshimitsu, Zhang, Bohan, and Cummings, Steven R

Subjects
Aging, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Humans, DNA Damage, Organelles, DNA, Models, Biological
Abstract

Cellular metabolism generates molecular damage affecting all levels of biological organization. Accumulation of this damage over time is thought to play a central role in the aging process, but damage manifests in diverse molecular forms complicating its assessment. Insufficient attention has been paid to date to the role of molecular damage in aging-related phenotypes, particularly in humans, in part because of the difficulty in measuring its various forms. Recently, omics approaches have been developed that begin to address this challenge, because they are able to assess a sizeable proportion of age-related damage at the level of small molecules, proteins, RNA, DNA, organelles and cells. This review describes the concept of molecular damage in aging and discusses its diverse aspects from theoretical models to experimental approaches. Measurement of multiple types of damage enables studies of the role of damage in human aging outcomes and lays a foundation for testing interventions to reduce the burden of molecular damage, opening new approaches to slowing aging and reducing its consequences.

Published
2021

10. Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

Author

Leitner, Alexander, Bonvin, Alexandre M. J. J., Borchers, Christoph H., Chalkley, Robert J., Chamot-Rooke, Julia, Combe, Colin W., Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C., Heck, Albert J. R., Hoopmann, Michael R., Huang, Lan, Ishihama, Yasushi, Jones, Andrew R., Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L., Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A., Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaino, Juan A., Wilkins, Marc R., and Rappsilber, Juri

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures. Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Crosslinking MS for which guidelines should be developed as part of a Crosslinking MS standards initiative., Comment: 26 pages, 1 figure

Published
2020

11. Recent Progress in Lyme Disease and Remaining Challenges

Author

Bobe, Jason R, Jutras, Brandon L, Horn, Elizabeth J, Embers, Monica E, Bailey, Allison, Moritz, Robert L, Zhang, Ying, Soloski, Mark J, Ostfeld, Richard S, Marconi, Richard T, Aucott, John, Ma'ayan, Avi, Keesing, Felicia, Lewis, Kim, Mamoun, Choukri Ben, Rebman, Alison W, McClune, Mecaila E, Breitschwerdt, Edward B, Reddy, Panga Jaipal, Maggi, Ricardo, Yang, Frank, Nemser, Bennett, Ozcan, Aydogan, Garner, Omai, Di Carlo, Dino, Ballard, Zachary, Joung, Hyou-Arm, Garcia-Romeu, Albert, Griffiths, Roland R, Baumgarth, Nicole, and Fallon, Brian A

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Prevention, Vector-Borne Diseases, Lyme Disease, Infectious Diseases, Tickborne Diseases, Good Health and Well Being, Lyme disease, pathogenesis, diagnosis, treatment, prevention, field building, PTLD, vaccine, Biomedical and clinical sciences, Health sciences
Abstract

Lyme disease (also known as Lyme borreliosis) is the most common vector-borne disease in the United States with an estimated 476,000 cases per year. While historically, the long-term impact of Lyme disease on patients has been controversial, mounting evidence supports the idea that a substantial number of patients experience persistent symptoms following treatment. The research community has largely lacked the necessary funding to properly advance the scientific and clinical understanding of the disease, or to develop and evaluate innovative approaches for prevention, diagnosis, and treatment. Given the many outstanding questions raised into the diagnosis, clinical presentation and treatment of Lyme disease, and the underlying molecular mechanisms that trigger persistent disease, there is an urgent need for more support. This review article summarizes progress over the past 5 years in our understanding of Lyme and tick-borne diseases in the United States and highlights remaining challenges.

Published
2021

12. Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames

Author

Sandmann, Clara-L., Schulz, Jana F., Ruiz-Orera, Jorge, Kirchner, Marieluise, Ziehm, Matthias, Adami, Eleonora, Marczenke, Maike, Christ, Annabel, Liebe, Nina, Greiner, Johannes, Schoenenberger, Aaron, Muecke, Michael B., Liang, Ning, Moritz, Robert L., Sun, Zhi, Deutsch, Eric W., Gotthardt, Michael, Mudge, Jonathan M., Prensner, John R., Willnow, Thomas E., Mertins, Philipp, van Heesch, Sebastiaan, and Hubner, Norbert

Published
2023
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14. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Author

Jiang, Yuming, primary, Rex, Devasahayam Arokia Balaya, additional, Schuster, Dina, additional, Neely, Benjamin A., additional, Rosano, Germán L., additional, Volkmar, Norbert, additional, Momenzadeh, Amanda, additional, Peters-Clarke, Trenton M., additional, Egbert, Susan B., additional, Kreimer, Simion, additional, Doud, Emma H., additional, Crook, Oliver M., additional, Yadav, Amit Kumar, additional, Vanuopadath, Muralidharan, additional, Hegeman, Adrian D., additional, Mayta, Martín L., additional, Duboff, Anna G., additional, Riley, Nicholas M., additional, Moritz, Robert L., additional, and Meyer, Jesse G., additional

Published
2024
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15. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study

Author

Iacobucci, Claudio, Piotrowski, Christine, Aebersold, Ruedi, Amaral, Bruno C, Andrews, Philip, Bernfur, Katja, Borchers, Christoph, Brodie, Nicolas I, Bruce, James E, Cao, Yong, Chaignepain, Stéphane, Chavez, Juan D, Claverol, Stéphane, Cox, Jürgen, Davis, Trisha, Degliesposti, Gianluca, Dong, Meng-Qiu, Edinger, Nufar, Emanuelsson, Cecilia, Gay, Marina, Götze, Michael, Gomes-Neto, Francisco, Gozzo, Fabio C, Gutierrez, Craig, Haupt, Caroline, Heck, Albert JR, Herzog, Franz, Huang, Lan, Hoopmann, Michael R, Kalisman, Nir, Klykov, Oleg, Kukačka, Zdeněk, Liu, Fan, MacCoss, Michael J, Mechtler, Karl, Mesika, Ravit, Moritz, Robert L, Nagaraj, Nagarjuna, Nesati, Victor, Neves-Ferreira, Ana GC, Ninnis, Robert, Novák, Petr, O’Reilly, Francis J, Pelzing, Matthias, Petrotchenko, Evgeniy, Piersimoni, Lolita, Plasencia, Manolo, Pukala, Tara, Rand, Kasper D, Rappsilber, Juri, Reichmann, Dana, Sailer, Carolin, Sarnowski, Chris P, Scheltema, Richard A, Schmidt, Carla, Schriemer, David C, Shi, Yi, Skehel, J Mark, Slavin, Moriya, Sobott, Frank, Solis-Mezarino, Victor, Stephanowitz, Heike, Stengel, Florian, Stieger, Christian E, Trabjerg, Esben, Trnka, Michael, Vilaseca, Marta, Viner, Rosa, Xiang, Yufei, Yilmaz, Sule, Zelter, Alex, Ziemianowicz, Daniel, Leitner, Alexander, and Sinz, Andrea

Subjects
Generic health relevance, Cross-Linking Reagents, Laboratories, Mass Spectrometry, Reproducibility of Results, Serum Albumin, Bovine, Analytical Chemistry, Other Chemical Sciences
Abstract

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Published
2019

20. The 2023 Report on the Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Lindskog, Cecilia, Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Guo, Tiannan, Van Eyk, Jennifer E., Liu, Siqi, Bandeira, Nuno, Aebersold, Ruedi, Moritz, Robert L., Deutsch, Eric W., Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Lindskog, Cecilia, Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Guo, Tiannan, Van Eyk, Jennifer E., Liu, Siqi, Bandeira, Nuno, Aebersold, Ruedi, Moritz, Robert L., and Deutsch, Eric W.

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 2023-04-18, 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.

Published
2024
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22. The 2023 Report on the Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., primary, Lane, Lydie, additional, Overall, Christopher M., additional, Lindskog, Cecilia, additional, Pineau, Charles, additional, Packer, Nicolle H., additional, Cristea, Ileana M., additional, Weintraub, Susan T., additional, Orchard, Sandra, additional, Roehrl, Michael H. A., additional, Nice, Edouard, additional, Guo, Tiannan, additional, Van Eyk, Jennifer E., additional, Liu, Siqi, additional, Bandeira, Nuno, additional, Aebersold, Ruedi, additional, Moritz, Robert L., additional, and Deutsch, Eric W., additional

Published
2024
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23. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

Author

Martínez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura A., Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît J., Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric C., Gillece, John D., Schupp, James M., Keim, Paul S., Moritz, Robert L., Faust, Karoline, Tang, Haixu, Ye, Yuzhen, Skupin, Alexander, May, Patrick, Muller, Emilie E. L., and Wilmes, Paul

Published
2021
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24. Platelet derived growth factor receptor β (PDGFRβ) is a host receptor for the human malaria parasite adhesin TRAP

Author

Steel, Ryan W. J., Vigdorovich, Vladimir, Dambrauskas, Nicholas, Wilder, Brandon K., Arredondo, Silvia A., Goswami, Debashree, Kumar, Sudhir, Carbonetti, Sara, Swearingen, Kristian E., Nguyen, Thao, Betz, Will, Camargo, Nelly, Fisher, Bridget S., Soden, Jo, Thomas, Helen, Freeth, Jim, Moritz, Robert L., Noah Sather, D., and Kappe, Stefan H. I.

Published
2021
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26. Transcriptome and histone epigenome of Plasmodium vivax salivary-gland sporozoites point to tight regulatory control and mechanisms for liver-stage differentiation in relapsing malaria

Author

Muller, Ivo, Jex, Aaron R., Kappe, Stefan H.I., Mikolajczak, Sebastian A., Sattabongkot, Jetsumon, Patrapuvich, Rapatbhorn, Lindner, Scott, Flannery, Erika L., Koepfli, Cristian, Ansell, Brendan, Lerch, Anita, Emery-Corbin, Samantha J., Charnaud, Sarah, Smith, Jeffrey, Merrienne, Nicolas, Swearingen, Kristian E., Moritz, Robert L., Petter, Michaela, Duffy, Michael F., and Chuenchob, Vorada

Published
2019
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28. New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences

Author

Hood, Leroy E, Omenn, Gilbert S, Moritz, Robert L, Aebersold, Ruedi, Yamamoto, Keith R, Amos, Michael, Hunter‐Cevera, Jennie, Locascio, Laurie, and Participants, Workshop

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Bioengineering, Biotechnology, Agriculture, Animals, Biological Science Disciplines, Computational Biology, Ecology, Genome, Human Genome Project, Humans, Mass Spectrometry, Protein Folding, Proteins, Proteomics, Research, Systems Biology, United States, Complex systems, Democratization of proteomics, Economic growth, Grand challenges, Integration, Systems biology, Workshop Participants, Information and Computing Sciences, Medical and Health Sciences, Biochemistry & Molecular Biology, Biological sciences, Biomedical and clinical sciences
Abstract

This White Paper sets out a Life Sciences Grand Challenge for Proteomics Technologies to enhance our understanding of complex biological systems, link genomes with phenotypes, and bring broad benefits to the biosciences and the US economy. The paper is based on a workshop hosted by the National Institute of Standards and Technology (NIST) in Gaithersburg, MD, 14-15 February 2011, with participants from many federal R&D agencies and research communities, under the aegis of the US National Science and Technology Council (NSTC). Opportunities are identified for a coordinated R&D effort to achieve major technology-based goals and address societal challenges in health, agriculture, nutrition, energy, environment, national security, and economic development.

Published
2012

30. Proteomic changes induced by longevity-promoting interventions in mice

Author

Burns, Adam R., primary, Wiedrick, Jack, additional, Feryn, Alicia, additional, Maes, Michal, additional, Midha, Mukul K., additional, Baxter, David H., additional, Morrone, Seamus R., additional, Prokop, Timothy J., additional, Kapil, Charu, additional, Hoopmann, Michael R., additional, Kusebauch, Ulrike, additional, Deutsch, Eric W., additional, Rappaport, Noa, additional, Watanabe, Kengo, additional, Moritz, Robert L., additional, Miller, Richard A., additional, Lapidus, Jodi A., additional, and Orwoll, Eric S., additional

Published
2023
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31. Borrelia PeptideAtlas: A proteome resource of commonBorrelia burgdorferiisolates for Lyme research

Author

Reddy, Panga Jaipal., primary, Sun, Zhi, additional, Wippel, Helisa H., additional, Baxter, David, additional, Swearingen, Kristian, additional, Shteynberg, David D., additional, Midha, Mukul K., additional, Caimano, Melissa J., additional, Strle, Klemen, additional, Choi, Yongwook, additional, Chan, Agnes P., additional, Schork, Nicholas J., additional, and Moritz, Robert L., additional

Published
2023
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34. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

Author

Herold, Malte, Martínez Arbas, Susana, Narayanasamy, Shaman, Sheik, Abdul R., Kleine-Borgmann, Luise A. K., Lebrun, Laura A., Kunath, Benoît J., Roume, Hugo, Bessarab, Irina, Williams, Rohan B. H., Gillece, John D., Schupp, James M., Keim, Paul S., Jäger, Christian, Hoopmann, Michael R., Moritz, Robert L., Ye, Yuzhen, Li, Sujun, Tang, Haixu, Heintz-Buschart, Anna, May, Patrick, Muller, Emilie E. L., Laczny, Cedric C., and Wilmes, Paul

Published
2020
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36. A high-stringency blueprint of the human proteome

Author

Adhikari, Subash, Nice, Edouard C., Deutsch, Eric W., Lane, Lydie, Omenn, Gilbert S., Pennington, Stephen R., Paik, Young-Ki, Overall, Christopher M., Corrales, Fernando J., Cristea, Ileana M., Van Eyk, Jennifer E., Uhlén, Mathias, Lindskog, Cecilia, Chan, Daniel W., Bairoch, Amos, Waddington, James C., Justice, Joshua L., LaBaer, Joshua, Rodriguez, Henry, He, Fuchu, Kostrzewa, Markus, Ping, Peipei, Gundry, Rebekah L., Stewart, Peter, Srivastava, Sanjeeva, Srivastava, Sudhir, Nogueira, Fabio C. S., Domont, Gilberto B., Vandenbrouck, Yves, Lam, Maggie P. Y., Wennersten, Sara, Vizcaino, Juan Antonio, Wilkins, Marc, Schwenk, Jochen M., Lundberg, Emma, Bandeira, Nuno, Marko-Varga, Gyorgy, Weintraub, Susan T., Pineau, Charles, Kusebauch, Ulrike, Moritz, Robert L., Ahn, Seong Beom, Palmblad, Magnus, Snyder, Michael P., Aebersold, Ruedi, and Baker, Mark S.

Published
2020
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39. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

Author

Lorenzetti, Alan P. R., primary, Kusebauch, Ulrike, additional, Zaramela, Lívia S., additional, Wu, Wei-Ju, additional, de Almeida, João P. P., additional, Turkarslan, Serdar, additional, L. G. de Lomana, Adrián, additional, Gomes-Filho, José V., additional, Vêncio, Ricardo Z. N., additional, Moritz, Robert L., additional, Koide, Tie, additional, and Baliga, Nitin S., additional

Published
2023
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41. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Lindskog, Cecilia, Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Liu, Siqi, Bandeira, Nuno, Chen, Yu-Ju, Guo, Tiannan, Aebersold, Ruedi, Moritz, Robert L., Deutsch, Eric W., Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Lindskog, Cecilia, Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Liu, Siqi, Bandeira, Nuno, Chen, Yu-Ju, Guo, Tiannan, Aebersold, Ruedi, Moritz, Robert L., and Deutsch, Eric W.

Abstract

The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, “A Function for Each Protein”.

Published
2023
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44. The 5300-year-old Helicobacter pylori genome of the Iceman

Author

Maixner, Frank, Krause-Kyora, Ben, Turaev, Dmitrij, Herbig, Alexander, Hoopmann, Michael R., Hallows, Janice L., Kusebauch, Ulrike, Vigl, Eduard Egarter, Malfertheiner, Peter, Megraud, Francis, O'Sullivan, Niall, Cipollini, Giovanna, Coia, Valentina, Samadelli, Marco, Engstrand, Lars, Linz, Bodo, Moritz, Robert L., Grimm, Rudolf, Krause, Johannes, Nebel, Almut, Moodley, Yoshan, Rattei, Thomas, and Zink, Albert

Published
2016

48. Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline

Author

Hoopmann, Michael R., primary, Shteynberg, David D., additional, Zelter, Alex, additional, Riffle, Michael, additional, Lyon, Andrew S., additional, Agard, David A., additional, Luan, Qing, additional, Nolen, Brad J., additional, MacCoss, Michael J., additional, Davis, Trisha N., additional, and Moritz, Robert L., additional

Published
2023
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49. The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data

Author

Kertesz-Farkas, Attila, primary, Nii Adoquaye Acquaye, Frank Lawrence, additional, Bhimani, Kishankumar, additional, Eng, Jimmy K., additional, Fondrie, William E., additional, Grant, Charles, additional, Hoopmann, Michael R., additional, Lin, Andy, additional, Lu, Yang Y., additional, Moritz, Robert L., additional, MacCoss, Michael J., additional, and Noble, William Stafford, additional

Published
2023
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