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Search Publications by: Tytus Mak (Fed)

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Displaying 1 - 12 of 12

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

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

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

Gut Microbe-Targeted Choline Trimethylamine Lyase Inhibition Improves Obesity Via Rewiring of Host Circadian Rhythms

January 24, 2022
Author(s)
Rebecca Schugar, Christy Gliniak, Lucas Osborn, William Massey, Naseer Sangwan, Anthony Horak, Rakhee Banerjee, Danny Orabi, Robert Helsley, Amanda Brown, Amy Burrows, Chelsea Finney, Kevin Fung, Frederick Allen, Daniel Ferguson, Anthony Gromovsky, Chase Neumann, Kendall Cook, Amy McMillan, Jennifer Buffa, James Anderson, Margarete Mehrabian, Maryam Goudarzi, Belinda Willard, Tytus Mak, Andrew Armstrong, Garth Swanson, Ali Keshavarzian, Jose Carlos Garcia-Garcia, Zeneng Wang, Aldons Lusis, Stanley Hazen, Mark Brown
Obesity has repeatedly been linked to reorganization of the gut microbiome, yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here we show that gut microbe-targeted inhibition of the trimethylamine N-oxide (TMAO)

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)

Increasing the Coverage of a Mass Spectral Library of Milk Oligosaccharides Using a Hybrid- Search-Based Bootstrapping Method and Milks from a Wide Variety of Mammals

July 8, 2020
Author(s)
Concepcion A. Remoroza, Tytus D. Mak, Yuri A. Mirokhin, Sergey L. Sheetlin, Xiaoyu Yang, Stephen E. Stein, Power L. Michael, San Andres V. Joice, Yuxue Liang
This study significantly expands both the scope and method of identification for construction of a previously reported tandem mass spectral library of 74 human milk oligosaccharides (HMOs) derived from results of LC-MS/MS experiments. In the present work

Creating a Mass Spectral Reference Library for Oligosaccharides in Milk

July 3, 2018
Author(s)
Concepcion A. Remoroza, Tytus D. Mak, M. L. De Leoz, Yuri A. Mirokhin, Stephen E. Stein
We report the development and availability of a mass spectral reference library for oligosaccharides in human milk. This represents a new variety of spectral library that includes consensus spectra of compounds annotated through various data analysis

A serum small molecule biosignature of radiation exposure from total body irradiated patients

August 21, 2017
Author(s)
Evagelia C. Laiakis, Evan L. Pannkuk, Siddheshwar Chauthe, Yi-Wen Wang, Ming Liang, Tytus Mak, Christopher A. Barker, Giuseppe Astarita, Albert J. Fornace
The potential of radiological accidents and nuclear terrorism have increased the need for development of new rapid biodosimetry methods. In addition, in a clinical setting the issue of an individual's radiosensitivity should be taken into consideration
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