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153. ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

Author

Ramos Hector, Kusebauch Ulrike, Picotti Paola, Reiter Lukas, Campbell David, Christiansen Mark, Kwok Sung-Tat, Brusniak Mi-Youn K, Deutsch Eric W, Chen Jingchun, Moritz Robert L, and Aebersold Ruedi

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM) is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology. Result We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM), which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM). ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site. This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser. Conclusions Targeted proteomics via SRM is a powerful new technique that enables the reproducible and accurate identification and quantification of sets of proteins of interest. ATAQS is the first open-source software that supports all steps of the targeted proteomics workflow. ATAQS also provides software API (Application Program Interface) documentation that enables the addition of new algorithms to each of the workflow steps. The software, installation guide and sample dataset can be found in http://tools.proteomecenter.org/ATAQS/ATAQS.html

Published
2011
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157. The SysteMHC Atlas project

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Shao, Wenguang, Pedrioli, Patrick G A, Wolski, Witold, Scurtescu, Cristian, Schmid, Emanuel, Vizcaíno, Juan Antonio, Courcelles, Mathieu, Schuster, Heiko, Kowalewski, Daniel, Marino, Fabio, Arlehamn, Cecilia S L, Vaughan, Kerrie, Peters, Bjoern, Sette, Alessandro, Ottenhoff, Tom H M, Meijgaarden, Krista E, Nieuwenhuizen, Natalie, Kaufmann, Stefan H E, Schlapbach, Ralph, Castle, John C, Nesvizhskii, Alexey I, Nielsen, Morten, Deutsch, Eric W, Campbell, David S, Moritz, Robert L, Zubarev, Roman A, Ytterberg, Anders Jimmy, Purcell, Anthony W, Marcilla, Miguel, Paradela, Alberto, Wang, Qi, Costello, Catherine E, Ternette, Nicola, van Veelen, Peter A, van Els, Cécile A C M, Heck, Albert J R, de Souza, Gustavo A, Sollid, Ludvig M, Admon, Arie, Stevanovic, Stefan, Rammensee, Hans-Georg, Thibault, Pierre, Perreault, Claude, Bassani-Sternberg, Michal, Aebersold, Ruedi, Caron, Etienne, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Shao, Wenguang, Pedrioli, Patrick G A, Wolski, Witold, Scurtescu, Cristian, Schmid, Emanuel, Vizcaíno, Juan Antonio, Courcelles, Mathieu, Schuster, Heiko, Kowalewski, Daniel, Marino, Fabio, Arlehamn, Cecilia S L, Vaughan, Kerrie, Peters, Bjoern, Sette, Alessandro, Ottenhoff, Tom H M, Meijgaarden, Krista E, Nieuwenhuizen, Natalie, Kaufmann, Stefan H E, Schlapbach, Ralph, Castle, John C, Nesvizhskii, Alexey I, Nielsen, Morten, Deutsch, Eric W, Campbell, David S, Moritz, Robert L, Zubarev, Roman A, Ytterberg, Anders Jimmy, Purcell, Anthony W, Marcilla, Miguel, Paradela, Alberto, Wang, Qi, Costello, Catherine E, Ternette, Nicola, van Veelen, Peter A, van Els, Cécile A C M, Heck, Albert J R, de Souza, Gustavo A, Sollid, Ludvig M, Admon, Arie, Stevanovic, Stefan, Rammensee, Hans-Georg, Thibault, Pierre, Perreault, Claude, Bassani-Sternberg, Michal, Aebersold, Ruedi, and Caron, Etienne

Published
2018

158. A tissue-based draft map of the murine MHC class I immunopeptidome

Author

Schuster, Heiko, Shao, Wenguang, Weiss, Tobias, Pedrioli, Patrick G A, Roth, Patrick, Weller, Michael, Campbell, David S, Deutsch, Eric W, Moritz, Robert L, Planz, Oliver, Rammensee, Hans-Georg, Aebersold, Ruedi; https://orcid.org/0000-0002-9576-3267, Caron, Etienne, Schuster, Heiko, Shao, Wenguang, Weiss, Tobias, Pedrioli, Patrick G A, Roth, Patrick, Weller, Michael, Campbell, David S, Deutsch, Eric W, Moritz, Robert L, Planz, Oliver, Rammensee, Hans-Georg, Aebersold, Ruedi; https://orcid.org/0000-0002-9576-3267, and Caron, Etienne

Abstract

The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the immune system, very little is known, in any species, about its composition across most tissues and organs in vivo. We applied mass spectrometry (MS) technologies to draft the first tissue-based atlas of the murine MHC class I immunopeptidome in health. Peptides were extracted from 19 normal tissues from C57BL/6 mice and prepared for MS injections, resulting in a total number of 28,448 high-confidence H2D/K-associated peptides identified and annotated in the atlas. This atlas provides initial qualitative data to explore the tissue-specificity of the immunopeptidome and serves as a guide to identify potential tumor-associated antigens from various cancer models. Our data were shared via PRIDE (PXD008733), SysteMHC Atlas (SYSMHC00018) and SWATH Atlas. We anticipate that this unique dataset will be expanded in the future and will find wide applications in basic and translational immunology.

Published
2018

159. Absence of full-length dystrophin impairs normal maturation and contraction of cardiomyocytes derived from human-induced pluripotent stem cells.

Author

Pioner, J Manuel, Guan, Xuan, Klaiman, Jordan M, Racca, Alice W, Pabon, Lil, Muskheli, Veronica, Macadangdang, Jesse, Ferrantini, Cecilia, Hoopmann, Michael R, Moritz, Robert L, Kim, Deok-Ho, Tesi, Chiara, Poggesi, Corrado, Murry, Charles E, Childers, Martin K, Mack, David L, and Regnier, Michael

Subjects
PLURIPOTENT stem cells, DYSTROPHIN, INDUCED pluripotent stem cells, DUCHENNE muscular dystrophy, DYSTROPHIN genes
Abstract

Aims Heart failure invariably affects patients with various forms of muscular dystrophy (MD), but the onset and molecular sequelae of altered structure and function resulting from full-length dystrophin (Dp427) deficiency in MD heart tissue are poorly understood. To better understand the role of dystrophin in cardiomyocyte development and the earliest phase of Duchenne muscular dystrophy (DMD) cardiomyopathy, we studied human cardiomyocytes differentiated from induced pluripotent stem cells (hiPSC-CMs) obtained from the urine of a DMD patient. Methods and results The contractile properties of patient-specific hiPSC-CMs, with no detectable dystrophin (DMD-CMs with a deletion of exon 50), were compared to CMs containing a CRISPR-Cas9 mediated deletion of a single G base at position 263 of the dystrophin gene (c.263delG -CMs) isogenic to the parental line of hiPSC-CMs from a healthy individual. We hypothesized that the absence of a dystrophin-actin linkage would adversely affect myofibril and cardiomyocyte structure and function. Cardiomyocyte maturation was driven by culturing long-term (80–100 days) on a nanopatterned surface, which resulted in hiPSC-CMs with adult-like dimensions and aligned myofibrils. Conclusions Our data demonstrate that lack of Dp427 results in reduced myofibril contractile tension, slower relaxation kinetics, and to Ca2+ handling abnormalities, similar to DMD cells, suggesting either retarded or altered maturation of cardiomyocyte structures associated with these functions. This study offers new insights into the functional consequences of Dp427 deficiency at an early stage of cardiomyocyte development in both patient-derived and CRISPR-generated models of dystrophin deficiency. [ABSTRACT FROM AUTHOR]

Published
2020
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162. The Micronemal Plasmodium Proteins P36 and P52 Act in Concert to Establish the Replication-Permissive Compartment Within Infected Hepatocytes

Author

Arredondo, Silvia A., primary, Swearingen, Kristian E., additional, Martinson, Thomas, additional, Steel, Ryan, additional, Dankwa, Dorender A., additional, Harupa, Anke, additional, Camargo, Nelly, additional, Betz, William, additional, Vigdorovich, Vladimir, additional, Oliver, Brian G., additional, Kangwanrangsan, Niwat, additional, Ishino, Tomoko, additional, Sather, Noah, additional, Mikolajczak, Sebastian, additional, Vaughan, Ashley M., additional, Torii, Motomi, additional, Moritz, Robert L., additional, and Kappe, Stefan H. I., additional

Published
2018
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164. Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

Author

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

Published
2018
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166. The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals

Author

Maixner, Frank, primary, Turaev, Dmitrij, additional, Cazenave-Gassiot, Amaury, additional, Janko, Marek, additional, Krause-Kyora, Ben, additional, Hoopmann, Michael R., additional, Kusebauch, Ulrike, additional, Sartain, Mark, additional, Guerriero, Gea, additional, O’Sullivan, Niall, additional, Teasdale, Matthew, additional, Cipollini, Giovanna, additional, Paladin, Alice, additional, Mattiangeli, Valeria, additional, Samadelli, Marco, additional, Tecchiati, Umberto, additional, Putzer, Andreas, additional, Palazoglu, Mine, additional, Meissen, John, additional, Lösch, Sandra, additional, Rausch, Philipp, additional, Baines, John F., additional, Kim, Bum Jin, additional, An, Hyun-Joo, additional, Gostner, Paul, additional, Egarter-Vigl, Eduard, additional, Malfertheiner, Peter, additional, Keller, Andreas, additional, Stark, Robert W., additional, Wenk, Markus, additional, Bishop, David, additional, Bradley, Daniel G., additional, Fiehn, Oliver, additional, Engstrand, Lars, additional, Moritz, Robert L., additional, Doble, Philip, additional, Franke, Andre, additional, Nebel, Almut, additional, Oeggl, Klaus, additional, Rattei, Thomas, additional, Grimm, Rudolf, additional, and Zink, Albert, additional

Published
2018
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178. A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions

Author

Michalik, Stephan, primary, Depke, Maren, additional, Murr, Annette, additional, Gesell Salazar, Manuela, additional, Kusebauch, Ulrike, additional, Sun, Zhi, additional, Meyer, Tanja C., additional, Surmann, Kristin, additional, Pförtner, Henrike, additional, Hildebrandt, Petra, additional, Weiss, Stefan, additional, Palma Medina, Laura Marcela, additional, Gutjahr, Melanie, additional, Hammer, Elke, additional, Becher, Dörte, additional, Pribyl, Thomas, additional, Hammerschmidt, Sven, additional, Deutsch, Eric W., additional, Bader, Samuel L., additional, Hecker, Michael, additional, Moritz, Robert L., additional, Mäder, Ulrike, additional, Völker, Uwe, additional, and Schmidt, Frank, additional

Published
2017
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179. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Author

Collins, Ben C., primary, Hunter, Christie L., additional, Liu, Yansheng, additional, Schilling, Birgit, additional, Rosenberger, George, additional, Bader, Samuel L., additional, Chan, Daniel W., additional, Gibson, Bradford W., additional, Gingras, Anne-Claude, additional, Held, Jason M., additional, Hirayama-Kurogi, Mio, additional, Hou, Guixue, additional, Krisp, Christoph, additional, Larsen, Brett, additional, Lin, Liang, additional, Liu, Siqi, additional, Molloy, Mark P., additional, Moritz, Robert L., additional, Ohtsuki, Sumio, additional, Schlapbach, Ralph, additional, Selevsek, Nathalie, additional, Thomas, Stefani N., additional, Tzeng, Shin-Cheng, additional, Zhang, Hui, additional, and Aebersold, Ruedi, additional

Published
2017
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180. Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites

Author

Swearingen, Kristian E., primary, Lindner, Scott E., additional, Flannery, Erika L., additional, Vaughan, Ashley M., additional, Morrison, Robert D., additional, Patrapuvich, Rapatbhorn, additional, Koepfli, Cristian, additional, Muller, Ivo, additional, Jex, Aaron, additional, Moritz, Robert L., additional, Kappe, Stefan H. I., additional, Sattabongkot, Jetsumon, additional, and Mikolajczak, Sebastian A., additional

Published
2017
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181. The SysteMHC Atlas project

Author

Shao, Wenguang, primary, Pedrioli, Patrick G A, additional, Wolski, Witold, additional, Scurtescu, Cristian, additional, Schmid, Emanuel, additional, Vizcaíno, Juan A, additional, Courcelles, Mathieu, additional, Schuster, Heiko, additional, Kowalewski, Daniel, additional, Marino, Fabio, additional, Arlehamn, Cecilia S L, additional, Vaughan, Kerrie, additional, Peters, Bjoern, additional, Sette, Alessandro, additional, Ottenhoff, Tom H M, additional, Meijgaarden, Krista E, additional, Nieuwenhuizen, Natalie, additional, Kaufmann, Stefan H E, additional, Schlapbach, Ralph, additional, Castle, John C, additional, Nesvizhskii, Alexey I, additional, Nielsen, Morten, additional, Deutsch, Eric W, additional, Campbell, David S, additional, Moritz, Robert L, additional, Zubarev, Roman A, additional, Ytterberg, Anders Jimmy, additional, Purcell, Anthony W, additional, Marcilla, Miguel, additional, Paradela, Alberto, additional, Wang, Qi, additional, Costello, Catherine E, additional, Ternette, Nicola, additional, van Veelen, Peter A, additional, van Els, Cécile A C M, additional, Heck, Albert J R, additional, de Souza, Gustavo A, additional, Sollid, Ludvig M, additional, Admon, Arie, additional, Stevanovic, Stefan, additional, Rammensee, Hans-Georg, additional, Thibault, Pierre, additional, Perreault, Claude, additional, Bassani-Sternberg, Michal, additional, Aebersold, Ruedi, additional, and Caron, Etienne, additional

Published
2017
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182. A wellness study of 108 individuals using personal, dense, dynamic data clouds

Author

Price, Nathan D, primary, Magis, Andrew T, additional, Earls, John C, additional, Glusman, Gustavo, additional, Levy, Roie, additional, Lausted, Christopher, additional, McDonald, Daniel T, additional, Kusebauch, Ulrike, additional, Moss, Christopher L, additional, Zhou, Yong, additional, Qin, Shizhen, additional, Moritz, Robert L, additional, Brogaard, Kristin, additional, Omenn, Gilbert S, additional, Lovejoy, Jennifer C, additional, and Hood, Leroy, additional

Published
2017
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184. Building ProteomeTools based on a complete synthetic human proteome

Author

Zolg, Daniel P, primary, Wilhelm, Mathias, additional, Schnatbaum, Karsten, additional, Zerweck, Johannes, additional, Knaute, Tobias, additional, Delanghe, Bernard, additional, Bailey, Derek J, additional, Gessulat, Siegfried, additional, Ehrlich, Hans-Christian, additional, Weininger, Maximilian, additional, Yu, Peng, additional, Schlegl, Judith, additional, Kramer, Karl, additional, Schmidt, Tobias, additional, Kusebauch, Ulrike, additional, Deutsch, Eric W, additional, Aebersold, Ruedi, additional, Moritz, Robert L, additional, Wenschuh, Holger, additional, Moehring, Thomas, additional, Aiche, Stephan, additional, Huhmer, Andreas, additional, Reimer, Ulf, additional, and Kuster, Bernhard, additional

Published
2017
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185. An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation

Author

Mandal, Kamal, primary, Bader, Samuel L., additional, Kumar, Pankaj, additional, Malakar, Dipankar, additional, Campbell, David S., additional, Pradhan, Bhola Shankar, additional, Sarkar, Rajesh K., additional, Wadhwa, Neerja, additional, Sensharma, Souvik, additional, Jain, Vaibhav, additional, Moritz, Robert L., additional, and Majumdar, Subeer S., additional

Published
2017
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187. Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites.

Author

Lindner, Scott E., Swearingen, Kristian E., Shears, Melanie J., Walker, Michael P., Vrana, Erin N., Hart, Kevin J., Minns, Allen M., Sinnis, Photini, Moritz, Robert L., and Kappe, Stefan H. I.

Subjects
PROTEOMICS, REPRESSION (Psychology), DEVELOPMENTAL biology, PLASMODIUM, SPOROZOITES
Abstract

Plasmodium sporozoites are transmitted from infected mosquitoes to mammals, and must navigate the host skin and vasculature to infect the liver. This journey requires distinct proteomes. Here, we report the dynamic transcriptomes and proteomes of both oocyst sporozoites and salivary gland sporozoites in both rodent-infectious Plasmodium yoelii parasites and human-infectious Plasmodium falciparum parasites. The data robustly define mRNAs and proteins that are upregulated in oocyst sporozoites (UOS) or upregulated in infectious sporozoites (UIS) within the salivary glands, including many that are essential for sporozoite functions in the vector and host. Moreover, we find that malaria parasites use two overlapping, extensive, and independent programs of translational repression across sporozoite maturation to temporally regulate protein expression. Together with gene-specific validation experiments, these data indicate that two waves of translational repression are implemented and relieved at different times during sporozoite maturation, migration and infection, thus promoting their successful development and vector-to-host transition. Here, the authors report transcriptomes and proteomes of oocyst sporozoite and salivary gland sporozoite stages in rodent-infectious Plasmodium yoelii parasites and human infectious Plasmodium falciparum parasites and define two waves of translational repression during sporozoite maturation. [ABSTRACT FROM AUTHOR]

Published
2019
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189. The 2024 Report on the Human Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., Orchard, Sandra, Lane, Lydie, Lindskog, Cecilia, Pineau, Charles, Overall, Christopher M., Budnik, Bogdan, Mudge, Jonathan M., Packer, Nicolle H., Weintraub, Susan T., Roehrl, Michael H. A., Nice, Edouard, Guo, Tiannan, Van Eyk, Jennifer E., Völker, Uwe, Zhang, Gong, Bandeira, Nuno, Aebersold, Ruedi, Moritz, Robert L., and Deutsch, Eric W.

Abstract

The Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify at least one isoform of every protein-coding gene and (2) to make proteomics an integral part of multiomics studies of human health and disease. The past year has seen major transitions for the HPP. neXtProt was retired as the official HPP knowledge base, UniProtKB became the reference proteome knowledge base, and Ensembl-GENCODE provides the reference protein target list. A function evidence FE1–5 scoring system has been developed for functional annotation of proteins, parallel to the PE1–5 UniProtKB/neXtProt scheme for evidence of protein expression. This report includes updates from neXtProt (version 2023–09) and UniProtKB release 2024_04, with protein expression detected (PE1) for 18138 of the 19411 GENCODE protein-coding genes (93%). The number of non-PE1 proteins (“missing proteins”) is now 1273. The transition to GENCODE is a net reduction of 367 proteins (19,411 PE1–5 instead of 19,778 PE1–4 last year in neXtProt). We include reports from the Biology and Disease-driven HPP, the Human Protein Atlas, and the HPP Grand Challenge Project. We expect the new Functional Evidence FE1–5 scheme to energize the Grand Challenge Project for functional annotation of human proteins throughout the global proteomics community, including π-HuB in China.

Published
2024
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190. The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends

Author

Geyer, Philipp E., Hornburg, Daniel, Pernemalm, Maria, Hauck, Stefanie M., Palaniappan, Krishnan K., Albrecht, Vincent, Dagley, Laura F., Moritz, Robert L., Yu, Xiaobo, Edfors, Fredrik, Vandenbrouck, Yves, Mueller-Reif, Johannes B., Sun, Zhi, Brun, Virginie, Ahadi, Sara, Omenn, Gilbert S., Deutsch, Eric W., and Schwenk, Jochen M.

Abstract

Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors. As representatives of HUPO’s Human Plasma Proteome Project (HPPP), we present our 2024 survey of the current progress in our community, including the latest build of the Human Plasma Proteome PeptideAtlas that now comprises 4608 proteins detected in 113 data sets. We then discuss the updates of established proteomics methods, emerging technologies, and investigations of proteoforms, protein networks, extracellualr vesicles, circulating antibodies and microsamples. Finally, we provide a prospective view of using the current and emerging proteomics tools in studies of circulating proteins.

Published
2024
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191. StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline

Author

Hoopmann, Michael R., Winget, Jason M., Mendoza, Luis, and Moritz, Robert L.

Abstract

Label-free quantification has grown in popularity as a means of obtaining relative abundance measures for proteomics experiments. However, easily accessible and integrated tools to perform label-free quantification have been lacking. We describe StPeter, an implementation of Normalized Spectral Index quantification for wide availability through integration into the widely used Trans-Proteomic Pipeline. This implementation has been specifically designed for reproducibility and ease of use. We demonstrate that StPeter outperforms other state-of-the art packages using a recently reported benchmark data set over the range of false discovery rates relevant to shotgun proteomics results. We also demonstrate that the software is computationally efficient and supports data from a variety of instrument platforms and experimental designs. Results can be viewed within the Trans-Proteomic Pipeline graphical user interfaces and exported in standard formats for downstream statistical analysis. By integrating StPeter into the freely available Trans-Proteomic Pipeline, users can now obtain high-quality label-free quantification of any data set in seconds by adding a single command to the workflow.

Published
2024
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192. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Author

Kusebauch, Ulrike, Campbell, David S., Deutsch, Eric W., Chu, Caroline S., Spicer, Douglas A., Brusniak, Mi-Youn, Slagel, Joseph, Sun, Zhi, Stevens, Jeffrey, Grimes, Barbara, Shteynberg, David, Hoopmann, Michael R., Blattmann, Peter, Ratushny, Alexander V., Rinner, Oliver, Picotti, Paola, Carapito, Christine, Huang, Chung-Ying, Kapousouz, Meghan, Lam, Henry H N, Tran, Tommy, Demir, Emek, Aitchison, John D., Sander, Chris, Hood, Leroy, Aebersold, Ruedi, Moritz, Robert L., Kusebauch, Ulrike, Campbell, David S., Deutsch, Eric W., Chu, Caroline S., Spicer, Douglas A., Brusniak, Mi-Youn, Slagel, Joseph, Sun, Zhi, Stevens, Jeffrey, Grimes, Barbara, Shteynberg, David, Hoopmann, Michael R., Blattmann, Peter, Ratushny, Alexander V., Rinner, Oliver, Picotti, Paola, Carapito, Christine, Huang, Chung-Ying, Kapousouz, Meghan, Lam, Henry H N, Tran, Tommy, Demir, Emek, Aitchison, John D., Sander, Chris, Hood, Leroy, Aebersold, Ruedi, and Moritz, Robert L.

Abstract

The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here, we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive, and robust targeted mass spectrometric method selected reaction monitoring, SRM. This human SRMAtlas provides definitive coordinates that conclusively identify the respective peptide in biological samples. We report data on 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations, and post-translational modifications. The data are freely accessible as a resource at http://www.srmatlas.org/, and we demonstrate its utility by examining the network response to inhibition of cholesterol synthesis in liver cells and to docetaxel in prostate cancer lines.

Published
2016

193. The Pig PeptideAtlas:a resource for systems biology in animal production and biomedicine

Author

Hesselager, Marianne Overgaard, Codrea, Marius C., Sun, Zhi, Deutsch, Eric W., Bennike, Tue Bjerg, Stensballe, Allan, Bundgaard, Louise, Moritz, Robert L., Bendixen, Emøke, Hesselager, Marianne Overgaard, Codrea, Marius C., Sun, Zhi, Deutsch, Eric W., Bennike, Tue Bjerg, Stensballe, Allan, Bundgaard, Louise, Moritz, Robert L., and Bendixen, Emøke

Abstract

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research.

Published
2016

194. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

Author

Deutsch, Eric W., primary, Csordas, Attila, additional, Sun, Zhi, additional, Jarnuczak, Andrew, additional, Perez-Riverol, Yasset, additional, Ternent, Tobias, additional, Campbell, David S., additional, Bernal-Llinares, Manuel, additional, Okuda, Shujiro, additional, Kawano, Shin, additional, Moritz, Robert L., additional, Carver, Jeremy J., additional, Wang, Mingxun, additional, Ishihama, Yasushi, additional, Bandeira, Nuno, additional, Hermjakob, Henning, additional, and Vizcaíno, Juan Antonio, additional

Published
2016
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195. Identification of Organ-Enriched Protein Biomarkers of Acute Liver Injury by Targeted Quantitative Proteomics of Blood in Acetaminophen- and Carbon-Tetrachloride-Treated Mouse Models and Acetaminophen Overdose Patients

Author

Qin, Shizhen, primary, Zhou, Yong, additional, Gray, Li, additional, Kusebauch, Ulrike, additional, McEvoy, Laurence, additional, Antoine, Daniel J., additional, Hampson, Lucy, additional, Park, Kevin B., additional, Campbell, David, additional, Caballero, Juan, additional, Glusman, Gustavo, additional, Yan, Xiaowei, additional, Kim, Taek-Kyun, additional, Yuan, Yue, additional, Wang, Kai, additional, Rowen, Lee, additional, Moritz, Robert L., additional, Omenn, Gilbert S., additional, Pirmohamed, Munir, additional, and Hood, Leroy, additional

Published
2016
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196. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Author

Collins, Ben C., primary, Hunter, Christie L., additional, Liu, Yansheng, additional, Schilling, Birgit, additional, Rosenberger, George, additional, Bader, Samuel L., additional, Chan, Daniel W., additional, Gibson, Bradford W., additional, Gingras, Anne-Claude, additional, Held, Jason M., additional, Hirayama-Kurogi, Mio, additional, Hou, Guixue, additional, Krisp, Christoph, additional, Larsen, Brett, additional, Lin, Liang, additional, Liu, Siqi, additional, Molloy, Mark P., additional, Moritz, Robert L., additional, Ohtsuki, Sumio, additional, Schlapbach, Ralph, additional, Selevsek, Nathalie, additional, Thomas, Stefani N., additional, Tzeng, Shin-Cheng, additional, Zhang, Hui, additional, and Aebersold, Ruedi, additional

Published
2016
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198. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

Author

Deutsch, Eric W., primary, Overall, Christopher M., additional, Van Eyk, Jennifer E., additional, Baker, Mark S., additional, Paik, Young-Ki, additional, Weintraub, Susan T., additional, Lane, Lydie, additional, Martens, Lennart, additional, Vandenbrouck, Yves, additional, Kusebauch, Ulrike, additional, Hancock, William S., additional, Hermjakob, Henning, additional, Aebersold, Ruedi, additional, Moritz, Robert L., additional, and Omenn, Gilbert S., additional

Published
2016
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199. An activated form of ADAM10 is tumor selective and regulates cancer stem-like cells and tumor growth

Author

Atapattu, Lakmali, primary, Saha, Nayanendu, additional, Chheang, Chanly, additional, Eissman, Moritz F., additional, Xu, Kai, additional, Vail, Mary E., additional, Hii, Linda, additional, Llerena, Carmen, additional, Liu, Zhanqi, additional, Horvay, Katja, additional, Abud, Helen E., additional, Kusebauch, Ulrike, additional, Moritz, Robert L., additional, Ding, Bi-Sen, additional, Cao, Zhongwei, additional, Rafii, Shahin, additional, Ernst, Matthias, additional, Scott, Andrew M., additional, Nikolov, Dimitar B., additional, Lackmann, Martin, additional, and Janes, Peter W., additional

Published
2016
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