Michael R Shortreed
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Explore the profile of Michael R Shortreed including associated specialties, affiliations and a list of published articles.
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83
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1594
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Recent Articles
11.
Schaffer L, Shortreed M, Smith L
Methods Mol Biol
. 2022 Jun;
2500:67-81.
PMID: 35657588
Proteoform Suite is an interactive software program for the identification and quantification of intact proteoforms from mass spectrometry data. Proteoform Suite identifies proteoforms observed by intact-mass (MS1) analysis. In intact-mass...
12.
Miller R, Jordan B, Mehlferber M, Jeffery E, Chatzipantsiou C, Kaur S, et al.
Genome Biol
. 2022 Mar;
23(1):69.
PMID: 35241129
Background: The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved...
13.
Miller R, Knoener R, Benner B, Frey B, Scalf M, Shortreed M, et al.
J Proteome Res
. 2022 Feb;
21(4):993-1001.
PMID: 35192358
Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits...
14.
Carr A, Frey B, Scalf M, Cesnik A, Rolfs Z, Pike K, et al.
J Proteome Res
. 2022 Jan;
21(2):410-419.
PMID: 35073098
Interpreting proteomics data remains challenging due to the large number of proteins that are quantified by modern mass spectrometry methods. Weighted gene correlation network analysis (WGCNA) can identify groups of...
15.
Yau B, Naghiloo S, Diaz-Vegas A, Carr A, van Gerwen J, Needham E, et al.
iScience
. 2021 Oct;
24(10):103099.
PMID: 34622154
Pancreatic islets are essential for maintaining physiological blood glucose levels, and declining islet function is a hallmark of type 2 diabetes. We employ mass spectrometry-based proteomics to systematically analyze islets...
16.
Weisbrod C, Anderson L, Hendrickson C, Schaffer L, Shortreed M, Smith L, et al.
Anal Chem
. 2021 Jun;
93(26):9119-9128.
PMID: 34165955
Proton-transfer reactions (PTRs) have emerged as a powerful tool for the study of intact proteins. When coupled with /-selective kinetic excitation, such as parallel ion parking (PIP), one can exert...
17.
Lu L, Scalf M, Shortreed M, Smith L
J Am Soc Mass Spectrom
. 2021 Mar;
32(6):1319-1325.
PMID: 33754701
Top-down proteomics is a key mass spectrometry-based technology for comprehensive analysis of proteoforms. Proteoforms exhibit multiple high charge states and isotopic forms in full MS scans. The dissociation behavior of...
18.
Shortreed M, Millikin R, Liu L, Rolfs Z, Miller R, Schaffer L, et al.
J Proteome Res
. 2021 Mar;
20(4):1997-2004.
PMID: 33683901
MetaMorpheus is a free, open-source software program for the identification of peptides and proteoforms from data-dependent acquisition tandem MS experiments. There is inherent uncertainty in these assignments for several reasons,...
19.
Lu L, Riley N, Shortreed M, Bertozzi C, Smith L
Nat Methods
. 2020 Oct;
17(11):1133-1138.
PMID: 33106676
We report O-Pair Search, an approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides via an ion-indexed open modification search and...
20.
Schaffer L, Anderson L, Butcher D, Shortreed M, Miller R, Pavelec C, et al.
J Proteome Res
. 2020 Oct;
20(1):317-325.
PMID: 33074679
Identification of proteoforms, the different forms of a protein, is important to understand biological processes. A proteoform family is the set of different proteoforms from the same gene. We previously...