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1. Proteomics Standards Initiatives ProForma 2.0 Unifying the encoding of Proteoforms and Peptidoforms

Author

LeDuc, Richard D., Deutsch, Eric W., Binz, Pierre-Alain, Fellers, Ryan T., Cesnik, Anthony J., Klein, Joshua A., Bossche, Tim Van Den, Gabriels, Ralf, Yalavarthi, Arshika, Perez-Riverol, Yasset, Carver, Jeremy, Bittremieux, Wout, Kawano, Shin, Pullman, Benjamin, Bandeira, Nuno, Kelleher, Neil L., Thomas, Paul M., and Vizcaíno, Juan Antonio

Subjects
Quantitative Biology - Biomolecules
Abstract

There is the need to represent in a standard manner all the possible variations of a protein or peptide primary sequence, including both artefactual and post-translational modifications of peptides and proteins. With that overall aim, here, the Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has developed a notation, called ProForma 2.0, which is a substantial extension of the original ProForma notation, developed by the Consortium for Top-Down Proteomics (CTDP). ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. Therefore, this notation supports use cases needed for bottom-up and middle/topdown proteomics approaches and allows the encoding of highly modified proteins and peptides using a human and machine-readable string. ProForma 2.0 covers encoding protein modification names and accessions, cross-linking reagents including disulfides, glycans, modifications encoded using mass shifts and/or via chemical formulas, labile and C or N-terminal modifications, ambiguity in the modification position and representation of atomic isotopes, among other use cases. Notational conventions are based on public controlled vocabularies and ontologies. Detailed information about the notation and existing implementations are available at http://www.psidev.info/proforma and at the corresponding GitHub repository (https://github.com/HUPO-PSI/proforma).

Published
2021

2. Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials.

Author

Zhao, Dan, Cardona, Cesar, Gottel, Neil, Winton, Valerie J, Thomas, Paul M, Raba, Daniel A, Kelley, Scott T, Henry, Christopher, Gilbert, Jack A, and Stephens, Brent

Abstract

The impact of material chemical composition on microbial growth on building materials remains relatively poorly understood. We investigate the influence of the chemical composition of material extractives on microbial growth and community dynamics on 30 different wood species that were naturally inoculated, wetted, and held at high humidity for several weeks. Microbial growth was assessed by visual assessment and molecular sequencing. Unwetted material powders and microbial swab samples were analyzed using reverse phase liquid chromatography with tandem mass spectrometry. Different wood species demonstrated varying susceptibility to microbial growth after 3 weeks and visible coverage and fungal qPCR concentrations were correlated (R2 = 0.55). Aspergillaceae was most abundant across all samples; Meruliaceae was more prevalent on 8 materials with the highest visible microbial growth. A larger and more diverse set of compounds was detected from the wood shavings compared to the microbial swabs, indicating a complex and heterogeneous chemical composition within wood types. Several individual compounds putatively identified in wood samples showed statistically significant, near-monotonic associations with microbial growth, including C11H16O4, C18H34O4, and C6H15NO. A pilot experiment confirmed the inhibitory effects of dosing a sample of wood materials with varying concentrations of liquid C6H15NO (assuming it presented as Diethylethanolamine).

Published
2020

4. Microbial and metabolic succession on common building materials under high humidity conditions.

Author

Lax, Simon, Cardona, Cesar, Zhao, Dan, Winton, Valerie J, Goodney, Gabriel, Gao, Peng, Gottel, Neil, Hartmann, Erica M, Henry, Chris, Thomas, Paul M, Kelley, Scott T, Stephens, Brent, and Gilbert, Jack A

Subjects
Bacteria, Viruses, Fungi, RNA, Ribosomal, 16S, Humidity, Environmental Monitoring, Phylogeny, Construction Materials, RNA, Ribosomal, 16S
Abstract

Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material.

Published
2019

5. How many human proteoforms are there?

Author

Aebersold, Ruedi, Agar, Jeffrey N, Amster, I Jonathan, Baker, Mark S, Bertozzi, Carolyn R, Boja, Emily S, Costello, Catherine E, Cravatt, Benjamin F, Fenselau, Catherine, Garcia, Benjamin A, Ge, Ying, Gunawardena, Jeremy, Hendrickson, Ronald C, Hergenrother, Paul J, Huber, Christian G, Ivanov, Alexander R, Jensen, Ole N, Jewett, Michael C, Kelleher, Neil L, Kiessling, Laura L, Krogan, Nevan J, Larsen, Martin R, Loo, Joseph A, Ogorzalek Loo, Rachel R, Lundberg, Emma, MacCoss, Michael J, Mallick, Parag, Mootha, Vamsi K, Mrksich, Milan, Muir, Tom W, Patrie, Steven M, Pesavento, James J, Pitteri, Sharon J, Rodriguez, Henry, Saghatelian, Alan, Sandoval, Wendy, Schlüter, Hartmut, Sechi, Salvatore, Slavoff, Sarah A, Smith, Lloyd M, Snyder, Michael P, Thomas, Paul M, Uhlén, Mathias, Van Eyk, Jennifer E, Vidal, Marc, Walt, David R, White, Forest M, Williams, Evan R, Wohlschlager, Therese, Wysocki, Vicki H, Yates, Nathan A, Young, Nicolas L, and Zhang, Bing

Subjects
Humans, Proteins, Protein Isoforms, Proteome, Ubiquitin, Proteomics, Protein Biosynthesis, Protein Processing, Post-Translational, Phenotype, Genome, Human, Databases, Protein, Mass Spectrometry, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Biochemistry & Molecular Biology
Abstract

Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.

Published
2018

7. Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics

Author

Fornelli, Luca, Srzentić, Kristina, Toby, Timothy K., Doubleday, Peter F., Huguet, Romain, Mullen, Christopher, Melani, Rafael D., dos Santos Seckler, Henrique, DeHart, Caroline J., Weisbrod, Chad R., Durbin, Kenneth R., Greer, Joseph B., Early, Bryan P., Fellers, Ryan T., Zabrouskov, Vlad, Thomas, Paul M., Compton, Philip D., and Kelleher, Neil L.

Published
2020
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8. The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing

Author

Parsa, Sara, Ortega-Molina, Ana, Ying, Hsia-Yuan, Jiang, Man, Teater, Matt, Wang, Jiahui, Zhao, Chunying, Reznik, Ed, Pasion, Joyce P., Kuo, David, Mohan, Prathibha, Wang, Shenqiu, Camarillo, Jeannie M., Thomas, Paul M., Jain, Neeraj, Garcia-Bermudez, Javier, Cho, Byoung-kyu, Tam, Wayne, Kelleher, Neil L., Socci, Nicholas, Dogan, Ahmet, De Stanchina, Elisa, Ciriello, Giovanni, Green, Michael R., Li, Sheng, Birsoy, Kivanc, Melnick, Ari M., and Wendel, Hans-Guido

Published
2020
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13. The biosynthesis of methanobactin

Author

Kenney, Grace E., Dassama, Laura M. K., Pandelia, Maria-Eirini, Gizzi, Anthony S., Martinie, Ryan J., Gao, Peng, DeHart, Caroline J., Schachner, Luis F., Skinner, Owen S., Ro, Soo Y., Zhu, Xiao, Sadek, Monica, Thomas, Paul M., Almo, Steven C., Bollinger, J. Martin, Krebs, Carsten, Kelleher, Neil L., and Rosenzweig, Amy C.

Published
2018

14. Motivational and emotional salience effects on working memory

Author

Thomas, Paul M. J. and Raymond, Jane

Subjects
153.12
Abstract

"An object of primary memory is not thus brought back; it never was lost; its date was never cut off in consciousness from that of the immediately present moment. In fact, it comes to us as belonging to the rearward portion of the present space of time, and not to the genuine past," (James, 1890, p. 609). Since William James's seminal work on 'primary' memory, the notion that a short term memory store, now termed short term memory (STM) or working memory (WM) is a key part of human consciousness has become commonplace. This memory store is known to be subject to limitations in the amount and quality of information it can represent at any time, but is a crucial part of the cognitive toolkit humans use to navigate the physical and social world. Given these capacity limitations, there is a clear evolutionary imperative for efficient selection into and retention within WM of items of high utility over those of less importance to survival.

Published
2013

24. Supplementary Table 2 from USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia

Author

Jin, Qi, primary, Martinez, Carlos A., primary, Arcipowski, Kelly M., primary, Zhu, Yixing, primary, Gutierrez-Diaz, Blanca T., primary, Wang, Kenneth K., primary, Johnson, Megan R., primary, Volk, Andrew G., primary, Wang, Feng, primary, Wu, Jian, primary, Grove, Charles, primary, Wang, Hui, primary, Sokirniy, Ivan, primary, Thomas, Paul M., primary, Goo, Young Ah, primary, Abshiru, Nebiyu A., primary, Hijiya, Nobuko, primary, Peirs, Sofie, primary, Vandamme, Niels, primary, Berx, Geert, primary, Goosens, Steven, primary, Marshall, Stacy A., primary, Rendleman, Emily J., primary, Takahashi, Yoh-hei, primary, Wang, Lu, primary, Rawat, Radhika, primary, Bartom, Elizabeth T., primary, Collings, Clayton K., primary, Van Vlierberghe, Pieter, primary, Strikoudis, Alexandros, primary, Kelly, Stephen, primary, Ueberheide, Beatrix, primary, Mantis, Christine, primary, Kandela, Irawati, primary, Bourquin, Jean-Pierre, primary, Bornhauser, Beat, primary, Serafin, Valentina, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, Kelleher, Neil L., primary, Weinstock, Joseph, primary, Kumar, Suresh, primary, Crispino, John D., primary, Shilatifard, Ali, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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25. Figures S1-17 plus legends from USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia

Author

Jin, Qi, primary, Martinez, Carlos A., primary, Arcipowski, Kelly M., primary, Zhu, Yixing, primary, Gutierrez-Diaz, Blanca T., primary, Wang, Kenneth K., primary, Johnson, Megan R., primary, Volk, Andrew G., primary, Wang, Feng, primary, Wu, Jian, primary, Grove, Charles, primary, Wang, Hui, primary, Sokirniy, Ivan, primary, Thomas, Paul M., primary, Goo, Young Ah, primary, Abshiru, Nebiyu A., primary, Hijiya, Nobuko, primary, Peirs, Sofie, primary, Vandamme, Niels, primary, Berx, Geert, primary, Goosens, Steven, primary, Marshall, Stacy A., primary, Rendleman, Emily J., primary, Takahashi, Yoh-hei, primary, Wang, Lu, primary, Rawat, Radhika, primary, Bartom, Elizabeth T., primary, Collings, Clayton K., primary, Van Vlierberghe, Pieter, primary, Strikoudis, Alexandros, primary, Kelly, Stephen, primary, Ueberheide, Beatrix, primary, Mantis, Christine, primary, Kandela, Irawati, primary, Bourquin, Jean-Pierre, primary, Bornhauser, Beat, primary, Serafin, Valentina, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, Kelleher, Neil L., primary, Weinstock, Joseph, primary, Kumar, Suresh, primary, Crispino, John D., primary, Shilatifard, Ali, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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26. Supplementary Table 1 from USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia

Author

Jin, Qi, primary, Martinez, Carlos A., primary, Arcipowski, Kelly M., primary, Zhu, Yixing, primary, Gutierrez-Diaz, Blanca T., primary, Wang, Kenneth K., primary, Johnson, Megan R., primary, Volk, Andrew G., primary, Wang, Feng, primary, Wu, Jian, primary, Grove, Charles, primary, Wang, Hui, primary, Sokirniy, Ivan, primary, Thomas, Paul M., primary, Goo, Young Ah, primary, Abshiru, Nebiyu A., primary, Hijiya, Nobuko, primary, Peirs, Sofie, primary, Vandamme, Niels, primary, Berx, Geert, primary, Goosens, Steven, primary, Marshall, Stacy A., primary, Rendleman, Emily J., primary, Takahashi, Yoh-hei, primary, Wang, Lu, primary, Rawat, Radhika, primary, Bartom, Elizabeth T., primary, Collings, Clayton K., primary, Van Vlierberghe, Pieter, primary, Strikoudis, Alexandros, primary, Kelly, Stephen, primary, Ueberheide, Beatrix, primary, Mantis, Christine, primary, Kandela, Irawati, primary, Bourquin, Jean-Pierre, primary, Bornhauser, Beat, primary, Serafin, Valentina, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, Kelleher, Neil L., primary, Weinstock, Joseph, primary, Kumar, Suresh, primary, Crispino, John D., primary, Shilatifard, Ali, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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29. Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor

Author

Ives, Ashley N., primary, Dunn, Henry A., additional, Afsari, Hamid Samareh, additional, Seckler, Henrique dos Santos, additional, Foroutan, Max J., additional, Chavez, Erica, additional, Melani, Rafael D., additional, Fellers, Ryan T., additional, LeDuc, Richard D., additional, Thomas, Paul M., additional, Martemyanov, Kirill A., additional, Kelleher, Neil L., additional, and Vafabakhsh, Reza, additional

Published
2022
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30. A five-level classification system for proteoform identifications

Author

Smith, Lloyd M., Thomas, Paul M., Shortreed, Michael R., Schaffer, Leah V., Fellers, Ryan T., LeDuc, Richard D., Tucholski, Trisha, Ge, Ying, Agar, Jeffrey N., Anderson, Lissa C., Chamot-Rooke, Julia, Gault, Joseph, Loo, Joseph A., Paša-Tolić, Ljiljana, Robinson, Carol V., Schlüter, Hartmut, Tsybin, Yury O., Vilaseca, Marta, Vizcaíno, Juan Antonio, Danis, Paul O., and Kelleher, Neil L.

Published
2019
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35. Loss of BAP1 function leads to EZH2-dependent transformation

Author

LaFave, Lindsay M, Béguelin, Wendy, Koche, Richard, Teater, Matt, Spitzer, Barbara, Chramiec, Alan, Papalexi, Efthymia, Keller, Matthew D, Hricik, Todd, Konstantinoff, Katerina, Micol, Jean-Baptiste, Durham, Benjamin, Knutson, Sarah K, Campbell, John E, Blum, Gil, Shi, Xinxu, Doud, Emma H, Krivtsov, Andrei V, Chung, Young Rock, Khodos, Inna, de Stanchina, Elisa, Ouerfelli, Ouathek, Adusumilli, Prasad S, Thomas, Paul M, Kelleher, Neil L, Luo, Minkui, Keilhack, Heike, Abdel-Wahab, Omar, Melnick, Ari, Armstrong, Scott A, and Levine, Ross L

Subjects
Transforming growth factors -- Research, Gene mutation -- Research, Enzymes -- Research, Gene expression -- Research, Biological sciences, Health
Abstract

Author(s): Lindsay M LaFave [1, 2]; Wendy Béguelin [3]; Richard Koche [4, 5]; Matt Teater [3]; Barbara Spitzer [6]; Alan Chramiec [4]; Efthymia Papalexi [1]; Matthew D Keller [1]; Todd [...]

Published
2015
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43. The Blood Proteoform Atlas : A reference map of proteoforms in human hematopoietic cells

Author

Melani, Rafael D., Gerbasi, Vincent R., Anderson, Lissa C., Sikora, Jacek W., Toby, Timothy K., Hutton, Josiah E., Butcher, David S., Negrao, Fernanda, Seckler, Henrique S., Srzentic, Kristina, Fornelli, Luca, Camarillo, Jeannie M., LeDuc, Richard D., Cesnik, Anthony J., Lundberg, Emma, Greer, Joseph B., Fellers, Ryan T., Robey, Matthew T., DeHart, Caroline J., Forte, Eleonora, Hendrickson, Christopher L., Abbatiello, Susan E., Thomas, Paul M., Kokaji, Andy, I, Levitsky, Josh, Kelleher, Neil L., Melani, Rafael D., Gerbasi, Vincent R., Anderson, Lissa C., Sikora, Jacek W., Toby, Timothy K., Hutton, Josiah E., Butcher, David S., Negrao, Fernanda, Seckler, Henrique S., Srzentic, Kristina, Fornelli, Luca, Camarillo, Jeannie M., LeDuc, Richard D., Cesnik, Anthony J., Lundberg, Emma, Greer, Joseph B., Fellers, Ryan T., Robey, Matthew T., DeHart, Caroline J., Forte, Eleonora, Hendrickson, Christopher L., Abbatiello, Susan E., Thomas, Paul M., Kokaji, Andy, I, Levitsky, Josh, and Kelleher, Neil L.

Abstract

Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of similar to 30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma from human blood and bone marrow. The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. We demonstrate the potential for clinical application, by interrogating the BPA in the context of liver transplantation and identifying cell and proteoform signatures that distinguish normal graft function from acute rejection and other causes of graft dysfunction., QC 20220315

Published
2022
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44. Proteomics Standards Initiative's ProForma 2.0 : Unifying the Encoding of Proteoforms and Peptidoforms br

Author

LeDuc, Richard D., Deutsch, Eric W., Binz, Pierre-Alain, Fellers, Ryan T., Cesnik, Anthony J., Klein, Joshua A., Van den Bossche, Tim, Gabriels, Ralf, Yalavarthi, Arshika, Perez-Riverol, Yasset, Carver, Jeremy, Bittremieux, Wout, Kawano, Shin, Pullman, Benjamin, Bandeira, Nuno, Kelleher, Neil L., Thomas, Paul M., Vizcaino, Juan Antonio, LeDuc, Richard D., Deutsch, Eric W., Binz, Pierre-Alain, Fellers, Ryan T., Cesnik, Anthony J., Klein, Joshua A., Van den Bossche, Tim, Gabriels, Ralf, Yalavarthi, Arshika, Perez-Riverol, Yasset, Carver, Jeremy, Bittremieux, Wout, Kawano, Shin, Pullman, Benjamin, Bandeira, Nuno, Kelleher, Neil L., Thomas, Paul M., and Vizcaino, Juan Antonio

Abstract

It is important for the proteomics community to have a standardizedmanner to represent all possible variations of a protein or peptide primary sequence,including natural, chemically induced, and artifactual modifications. The HumanProteome Organization Proteomics Standards Initiative in collaboration with severalmembers of the Consortium for Top-Down Proteomics (CTDP) has developed astandard notation called ProForma 2.0, which is a substantial extension of the originalProForma notation developed by the CTDP. ProForma 2.0 aims to unify therepresentation of proteoforms and peptidoforms. ProForma 2.0 supports use casesneeded for bottom-up and middle-/top-down proteomics approaches and allows theencoding of highly modified proteins and peptides using a human- and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated bymass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical) and atomic isotopes.Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification documentand information about software implementations are available athttp://psidev.info/proforma., QC 20220516

Published
2022
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48. Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Author

LeDuc, Richard D., primary, Deutsch, Eric W., additional, Binz, Pierre-Alain, additional, Fellers, Ryan T., additional, Cesnik, Anthony J., additional, Klein, Joshua A., additional, Van Den Bossche, Tim, additional, Gabriels, Ralf, additional, Yalavarthi, Arshika, additional, Perez-Riverol, Yasset, additional, Carver, Jeremy, additional, Bittremieux, Wout, additional, Kawano, Shin, additional, Pullman, Benjamin, additional, Bandeira, Nuno, additional, Kelleher, Neil L., additional, Thomas, Paul M., additional, and Vizcaíno, Juan Antonio, additional

Published
2022
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