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Bioscience

Proteomics

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Displaying 26 - 50 of 131

ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics

January 24, 2023
Author(s)
Tobias Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Magnus Palmblad, Ben Neely, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaino, Eric Deutsch
Dataset acquisition and curation are often the hardest and most time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based LC-IM-MS datasets, due to the high-throughput data structure with high levels of noise and

The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

January 10, 2023
Author(s)
Eric Deutsch, Juan Antonio Vizcaino, Andrew Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremeieux, Yasset Perez-Riverol, David Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffman, Jim Shofstahl, Yunping Zhu, Federica Quaglia, Silvio Tosatto, Sandra Orchard
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its

Glycosylation and the global virome

October 10, 2022
Author(s)
Cassandra Pegg, Benjamin Schulz, Ben Neely, Gregory Albery, Colin Carlson
The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harnessing it for

compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets

September 29, 2022
Author(s)
Rob Marissen, Jeroen Laros, Josef Rasinger, Madhushri Varunjikar, Ben Neely, Magnus Palmblad
It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected

Mass Spectral Library Methods for Analysis of Site-Specific N-Glycosylation: Application to Human Milk Proteins

September 16, 2022
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Xiaoyu (Sara) Yang, Sergey Sheetlin, Yuri Mirokhin, Sanford Markey, Dmitrii V. Tchekhovskoi, Stephen E. Stein
We present a mass-spectral library-based method for analyzing site-specific N-linked protein glycosylation. Its operation and utility are illustrated by applying it to both newly measured and available proteomics data of human milk glycoproteins. It

Reference Materials for MS-based Untargeted Metabolomics and Lipidomics: A Review by the Metabolomics Quality Assurance and Quality Control Consortium (mQACC)

April 9, 2022
Author(s)
Katrice Lippa, William Davis, Christina Jones, Tracey Schock, Juan Aristizabal-Henao, Richard Beger, John Bowden, Corey Broeckling, Chris Beecher, Warwick Dunn, Roberto Flores, Goncalo Gouveia, Thomas Hartung, Matthew Lewis, Ioanna Ntai, Andrew Percy, Dan Raftery, Jinchun Sun, Georgios Theodoridis, Fariba Tayyari, Federico Torta, Candice Ulmer, Baljit Ubhi
Introduction The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control

HDX-MS and MD simulations provide evidence for stabilization of the IgG1- FcgRIa (CD64a) immune complex through intermolecular glycoprotein bonds

December 8, 2021
Author(s)
Kyle Anderson, Kerry Scott, Christina Bergonzo, Ioannis Karageorgos, Elyssia Gallagher, Venkata Tayi, Michael Butler, Jeffrey W. Hudgens
Previous reports present different models for the stabilization of the Fc—FcγRI immune complex. Although accord exists on the importance of L235 in IgG1 and some hydrophobic contacts for complex stabilization, discord exists regarding the existence of

Liver proteome response to torpor in a basoendothermic mammal, Tenrec ecaudatus, provides insights into the evolution of homeothermy

October 6, 2021
Author(s)
Jane Khudyakov, Michael Treat, Mikayla Shanafelt, Jared Deyarmin, Ben Neely, Frank van Breukelen
Many mammals use adaptive heterothermy (e.g., torpor, hibernation) to reduce metabolic demands of maintaining high body temperature (Tb). Torpor is typically characterized by coordinated declines in Tb and metabolic rate (MR) followed by active rewarming
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