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Bioscience

Proteomics

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Displaying 26 - 50 of 76

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 Johnston, 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

Nanopore sensing: a physical-chemical approach

September 1, 2021
Author(s)
Joseph W. Robertson, Madhav Ghimire, Joseph Reiner
Protein nanopores have emerged as an important class of sensor, for the understanding of biophysical processes, such as molecular transport across membranes, and detection and characterization of biopolymers. We trace the development of these sensors from

Representing and Comparing Site-Specific Glycan Abundance Distributions of Glycoproteins

July 30, 2021
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Yi Liu, Yuri Mirokhin, Dmitrii V. Tchekhovskoi, Xiaoyu (Sara) Yang, Stephen E. Stein
A method for representing and comparing distributions of N-linked glycans located at specific sites in proteins is presented. The representation takes the form of a simple mass spectrum for a given peptide sequence, with each peak corresponding to a

Universal Spectrum Identifier for mass spectra

July 2, 2021
Author(s)
Eric Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremeieux, Tytus Mak, Joshua Klein, Yunping Zhu, Henry Lam, Juan Antonio Vizcaino, Nuno Bandeira
Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI)

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

April 10, 2021
Author(s)
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

Development of an LC-MS/MS Reference Method for the Standardization of Analytical Methods to Measure Lipoprotein(a) in Plasma

April 1, 2021
Author(s)
Santica Marcovina, Noemie Clouet-Foraison, Marlys Koschinsky, Mark Lowenthal, Michael Boffa, Andrew Hoofnagle, Tomas Vaisar
Background: Use of Lipoprotein(a) levels for identification of individuals at high risk for cardiovascular disease is hampered by the high size polymorphism of apolipoprotein(a) which strongly impacts immunochemical methods resulting in discordant values

Proteomics in non-model organisms: a new analytical frontier

August 9, 2020
Author(s)
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

A Single Amino Acid Substitution Alters ClpS Binding Specificity

March 27, 2020
Author(s)
Christina Bergonzo, Jennifer A. Tullman, Kunal Dharmadhikari, Emily Samuels, Makenzie Christensen
ClpS is a small protein currently under development as a probe for detecting specific N-terminal amino acids of peptides. In order for ClpS to be used in this manner, it is important to understand the structural reasons for how and why ClpS recognizes
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