Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Search Publications by: Ben Neely (Fed)

Search Title, Abstract, Conference, Citation, Keyword or Author
Displaying 1 - 24 of 24

Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry

June 4, 2024
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
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

A multipathway phosphopeptide standard for rapid phosphoproteomics assay development

August 30, 2023
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
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

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

June 2, 2023
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
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

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

January 24, 2023
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

Glycosylation and the global virome

October 10, 2022
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
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

The science of the host-virus network

November 24, 2021
Gregory Albery, Daniel J. Becker, Liam Brierley, Cara Brook, Rebecca Christofferson, Lily Cohen, Tad Dallas, Evan Eskew, Anna Fagre, Maxwell Farrell, Emma Glennon, Sarah Guth, Maxwell Joseph, Nardus Mollentze, Ben Neely, Timothee Poisot, Angela Rasmussen, Sadie Ryan, Anna Siodin, Stephanie Seifert, Erin Sorrell, Colin Carlson
Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral

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

October 6, 2021
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

Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

June 7, 2021
Claire R. Peart, Christina Williams, Saurabh Pophaly, Jeremy Johnson, Ben Neely, Frances Gulland, David Adams, Bee Ng, William Cheng, Joseph Hoffman, Matthew Breen, Jochen Wolf
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome

Surveying the vampire bat (Desmodus rotundus) serum proteome: a resource for identifying immunological proteins and detecting pathogens

April 10, 2021
Ben Neely, Michael G. Janech, Alison Bland, Brock Fenton, Nancy B. Simmons, Daniel J. Becker
Bats (Order: Chiroptera) are increasingly studied as model systems for longevity and for their ability to seemingly tolerate typically virulent viruses without showing clinical disease. Yet our ability to characterize immune mechanisms of viral tolerance

Proteomics in non-model organisms: a new analytical frontier

August 9, 2020
Michelle Heck, Ben Neely
For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly and annotation, non-model organisms may be studied with the same advanced bioanalytical

Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing

January 31, 2019
Mak Saito, Erin Bertrand, Megan Duffy, David Gaylord, Noelle Held, Judson Harvey, Robert Hettich, Pratik Jagtap, Michael G. Janech, Danie Kinkade, Dasha Leary, Matt McIlvin, Eli Moore, Robert Morris, Ben Neely, Brook Nunn, Jaclyn Sanders, Adam Shepherd, Nick Symmonds, David Walsh
Ocean metaproteomics is an emerging field that provides an exciting new datatype with potential to enable discoveries regarding marine microbial communities and their underlying impact on global biogeochemical processes. For example, recent ocean

C3a receptor antagonism as a novel therapeutic target for chronic rhinosinusitis

June 15, 2018
Jennifer K. Mulligan, Tucker Williamson, Nicholas Reaves, William Carroll, Sarah Stephenson, Peng Gao, Richard R. Drake, Ben Neely, Rodney J. Schlosser, Carl Atkinson
Background: Innate immune factors, including the complement system, have been implicated in the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP). Here we examine complement activity within the respiratory mucosa of CRSwNP patients, and a