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Bioscience

Proteomics

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Displaying 1 - 25 of 131

Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions

November 24, 2024
Author(s)
Amie Solosky, Iliana Claudio, Kaylie Kirkwood, Jessie Chappel, Michael Janech, Alison Bland, Frances Gulland, Benjamin Neely, Erin Baker
Domoic acid is a neurotoxin secreted by the marine diatom genus Pseudo-nitzschia during toxic algal bloom events. California sea lions (Zalophus californianus) are exposed to domoic acid through the ingestion of fish that feed on toxic diatoms, resulting

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

November 8, 2024
Author(s)
Mak Saito, Jaclyn Saunders, Matthew McIlvin, Erin Bertrand, John Breier, Margaret Brisbin, Sophie Colston, Jaimee Compton, Tim Griffin, Judson Harvey, Robert Hettich, Pratik Jagtap, Michael Janech, Rod Johnson, Rick Keil, Hugo Kleikamp, Dasha Leary, Scott McCain, Eli Moore, Subina Mehta, Dawn Moran, Jacqui Neibauer, Benjamin Neely, Michael Jakuba, Jim Johnson, Megan Duffy, Gerhard Herndl, Richard Giannone, Ryan Mueller, Brook Nunn, Martin Pabst, Samantha Peters, Andrew Rajczewski, Elden Rowland, Brian Searle, Tim Van Den Bossche, Gary Vora, Jacob Waldbauer, Haiyan Zheng, Zihao Zhao
Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory

Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer

September 11, 2024
Author(s)
Ben Neely, Yasset Perez-Riverol, Magnus Palmblad
The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry–based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically

Variation of Site-Specific Glycosylation Profiles of Recombinant Influenza Glycoproteins

August 9, 2024
Author(s)
Zachary Goecker, Meghan Burke Harris, Concepcion Remoroza, Yi Liu, Yuri Mirokhin, Sergey Sheetlin, Dmitrii V. Tchekhovskoi, Xiaoyu (Sara) Yang, Stephen E. Stein
This work presents a detailed determination of site-specific N-glycan distributions of the recombinant influenza glycoproteins hemagglutinin (HA) and neuraminidase. Variation in glycosylation among recombinant glycoproteins is not predictable and can

The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF

August 5, 2024
Author(s)
Joshua Klein, Henry Lam, Tytus Mak, Wout Bittremieux, Yasset Perez-Riverol, Ralf Gabriels, Jim Shofstahl, Helge Hecht, Pierre-Alain Binz, Shin Kawano, Tim Van Den Bossche, Jeremy Carver, Ben Neely, Luis Mendoza, Tomi Suomi, Tine Claeys, Thomas Payne, Douwe Schulte, Zhi Sun, Nils Hoffmann, Yunping Zhu, Steffen Neumann, Andrew Jones, Nuno Bandeira, Juan Antonio Vizcaino, Eric Deutsch
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding

Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry

June 4, 2024
Author(s)
Yuming Jiang, Devasahayam Rex, Dina Schuster, Ben Neely, German Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton Peters-Clarke, Susan Egbert, Simion Kreimer, Emma Doud, Oliver Cook, Amit Yadav, Muralidharan Vanuopadath, Martin Mayta, Anna Duboff, Nicholas Riley, Robert Moritz, Jesse Meyer
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

Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (Zalophus californianus)

May 28, 2024
Author(s)
Gautam Ghosh, Ben Neely, Alison Bland, Emily Whitmer, Cara Field, Padraig Duignan, Michael Janech
Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis have consistently increased. Currently there are no practical non-lethal clinical tests for the diagnosis of domoic acid toxicosis (DAT) that

Comparison of N-glycopeptide to released N-glycan abundances and the influence of glycopeptide mass and charge state on N-linked glycosylation of IgG antibodies

March 7, 2024
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Tytus Mak, Sergey Sheetlin, Yuri Mirokhin, Zachary Goecker, Brian T. Cooper, Mark Lowenthal, Xiaoyu (Sara) Yang, Guanghui Wang, Dmitrii V. Tchekhovskoi, Stephen E. Stein
We report the comparison of mass-spectral-based abundances of tryptic glycopeptides to fluorescence abundances of released labeled glycans and the effects of mass and charge state and in-source fragmentation on glycopeptide abundances. The primary

A multipathway phosphopeptide standard for rapid phosphoproteomics assay development

August 30, 2023
Author(s)
Brian Searle, Allis Chien, Antonius Koller, David Hawke, Anthony Herren, Jenny Kim, Kimberly Lee, Ryan Leib, Alissa Nelson, Jian Min Ren, Paul Stemmer, Yiying Zhu, Ben Neely, Bhavin Patel
Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive

The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)

August 7, 2023
Author(s)
Pratik Jagtap, Michael Hoopmann, Ben Neely, Anthony Harvey, Lukas Kall, Yasset Perez-Riverol, Milky Abajorga, Julie Thomas, Susan Weintraub, Magnus Palmblad
Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation

Engineering Nanopore Approaches toward Protein Sequencing

July 25, 2023
Author(s)
Xiaojun Wei, Tadas Penkauskas, Joseph Reiner, Mark Uline, Qian Wang, Sheng Li, Aleksei Aksimentiev, Joseph Robertson, Chang Liu
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have of identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule

2019 Association of Biomolecular Resource Facilities Multi-laboratory Data-Independent Acquisition Study

June 2, 2023
Author(s)
Ben Neely, Paul Stemmer, Brian Searle, Laura Herring, LeRoy Martin, Mukul Midha, Brett Phinney, Baozhen Shan, Magnus Palmblad, Yan Wang, Pratik Jagtap, Joanna Kirkpatrick
Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in proteomics core facility settings has been slow

Toward an Integrated Machine Learning Model of a Proteomics Experiment

February 6, 2023
Author(s)
Ben Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric Deutsch, Siegfried Gessulat, Tobias Rehfeldt, Lukas Kall, Veit Schwammle, Samuel Payne, Tobias Schmidt, Pawel Palczynski, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals to evaluate and
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