Search results for: Michael S. Westphall

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article

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation

Nicholas M. Riley, Michael S. Westphall, Joshua J. Coon

Journal of The American Society for Mass Spectrometry > 2018 > 29 > 1 > 140-149

The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (<30 kDa). Recent studies have focused on improving the analysis of larger intact proteins (up to ~75 kDa), but they have also highlighted several challenges to be addressed. One major hurdle...

article

Gender Diversity in a STEM Subfield – Analysis of a Large Scientific Society and Its Annual Conferences

Evgenia Shishkova, Nicholas W. Kwiecien, Alexander S. Hebert, Michael S. Westphall, more

Journal of The American Society for Mass Spectrometry > 2017 > 28 > 12 > 2523-2531

Speaking engagements, serving as session chairs, and receiving awards at national meetings are essential stepping stones towards professional success for scientific researchers. Studies of gender parity in meetings of national scientific societies repeatedly uncover bias in speaker selection, engendering underrepresentation of women among featured presenters. To continue this dialogue, we analyzed...

article

A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions

Gregory K. Potts, Rachel M. McNally, Rocky Blanco, Jae‐Sung You, more

The Journal of Physiology > 595 > 15 > 5209 - 5226

Key points Mechanical signals play a critical role in the regulation of muscle mass, but the molecules that sense mechanical signals and convert this stimulus into the biochemical events that regulate muscle mass remain ill‐defined. Here we report a mass spectrometry‐based workflow to study the changes in protein phosphorylation that occur in mouse skeletal muscle 1 h after a bout of electrically...

article

Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer

Franklin E. Leach, Nicholas M. Riley, Michael S. Westphall, Joshua J. Coon, more

Journal of The American Society for Mass Spectrometry > 2017 > 28 > 9 > 1844-1854

The structural characterization of sulfated glycosaminoglycan (GAG) carbohydrates remains an important target for analytical chemists attributable to challenges introduced by the natural complexity of these mixtures and the defined need for molecular-level details to elucidate biological structure–function relationships. Tandem mass spectrometry has proven to be the most powerful technique for this...

article

Identification of the phosphorylation targets of symbiotic receptor‐like kinases using a high‐throughput multiplexed assay for kinase specificity

Dhileepkumar Jayaraman, Alicia L. Richards, Michael S. Westphall, Joshua J. Coon, more

The Plant Journal > 90 > 6 > 1196 - 1207

Detecting the phosphorylation substrates of multiple kinases in a single experiment is a challenge, and new techniques are being developed to overcome this challenge. Here, we used a multiplexed assay for kinase specificity (MAKS) to identify the substrates directly and to map the phosphorylation site(s) of plant symbiotic receptor‐like kinases. The symbiotic receptor‐like kinases nodulation receptor‐like...

article

Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Matthew J. P. Rush, Nicholas M. Riley, Michael S. Westphall, John E. P. Syka, more

Journal of The American Society for Mass Spectrometry > 2017 > 28 > 7 > 1324-1332

Negative mode proteome analysis offers access to unique portions of the proteome and several acidic post-translational modifications; however, traditional collision-based fragmentation methods fail to reliably provide sequence information for peptide anions. Negative electron transfer dissociation (NETD), on the other hand, can sequence precursor anions in a high-throughput manner. Similar to other...

article

Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity

Jonathan A. Stefely, Floriana Licitra, Leila Laredj, Andrew G. Reidenbach, more

Molecular Cell > 2016 > 63 > 4 > 608-620

The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosynthesis and an ataxia (ARCA2) through unclear means. We show that mice lacking COQ8A develop a slowly progressive cerebellar ataxia linked to Purkinje...

article

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function

Brendan J. Floyd, Emily M. Wilkerson, Mike T. Veling, Catie E. Minogue, more

Molecular Cell > 2016 > 63 > 4 > 621-632

Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory...

article

NeuCode Proteomics Reveals Bap1 Regulation of Metabolism

Joshua M. Baughman, Christopher M. Rose, Ganesh Kolumam, Joshua D. Webster, more

Cell Reports > 2016 > 16 > 2 > 583-595

We introduce neutron-encoded (NeuCode) amino acid labeling of mice as a strategy for multiplexed proteomic analysis in vivo. Using NeuCode, we characterize an inducible knockout mouse model of Bap1, a tumor suppressor and deubiquitinase whose in vivo roles outside of cancer are not well established. NeuCode proteomics revealed altered metabolic pathways following Bap1 deletion, including profound...

article

Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation

Nicholas M. Riley, Christopher Mullen, Chad R. Weisbrod, Seema Sharma, more

Journal of The American Society for Mass Spectrometry > 2016 > 27 > 3 > 520-531

Electron transfer dissociation (ETD) is a valuable tool for protein sequence analysis, especially for the fragmentation of intact proteins. However, low product ion signal-to-noise often requires some degree of signal averaging to achieve high quality MS/MS spectra of intact proteins. Here we describe a new implementation of ETD on the newest generation of quadrupole-Orbitrap-linear ion trap Tribrid,...

article

Potential regulatory phosphorylation sites in a Medicago truncatula plasma membrane proton pump implicated during early symbiotic signaling in roots

Thao T. Nguyen, Jeremy D. Volkening, Christopher M. Rose, Muthusubramanian Venkateshwaran, more

FEBS Letters > 2015 > 589 > 17 > 2186-2193

In plants and fungi the plasma membrane proton pump generates a large proton-motive force that performs essential functions in many processes, including solute transport and the control of cell elongation. Previous studies in yeast and higher plants have indicated that phosphorylation of an auto-inhibitory domain is involved in regulating pump activity. In this report we examine the Medicago truncatula...

article

A Calibration Routine for Efficient ETD in Large-Scale Proteomics

Christopher M. Rose, Matthew J. P. Rush, Nicholas M. Riley, Anna E. Merrill, more

Journal of The American Society for Mass Spectrometry > 2015 > 26 > 11 > 1848-1857

Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine...

article

Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single‐Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

Liangliang Sun, Alexander S. Hebert, Xiaojing Yan, Yimeng Zhao, more

Angewandte Chemie > 126 > 50 > 14151 - 14153

Capillary zone electrophoresis (CZE)–tandem mass spectrometry (MS/MS) has recently attracted attention as a tool for shotgun proteomics. However, its performance for this analysis has so far fallen far below that of reversed‐phase liquid chromatography (RPLC)–MS/MS. The use of a CZE method with a wide separation window (up to 90 min) and high peak capacity (ca. 300) is reported. This method was coupled...

article

Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single‐Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

Liangliang Sun, Alexander S. Hebert, Xiaojing Yan, Yimeng Zhao, more

Angewandte Chemie International Edition > 53 > 50 > 13931 - 13933

article

NANOG Is Multiply Phosphorylated and Directly Modified by ERK2 and CDK1 In Vitro

Justin Brumbaugh, Jason D. Russell, Pengzhi Yu, Michael S. Westphall, more

Stem Cell Reports > 2014 > 2 > 1 > 18-25

NANOG is a divergent homeobox protein and a core component of the transcriptional circuitry that sustains pluripotency and self-renewal. Although NANOG has been extensively studied on the transcriptional level, little is known regarding its posttranslational regulation, likely due to its low abundance and challenging physical properties. Here, we identify eleven phosphorylation sites on endogenous...

article

Neutron-Encoded Protein Quantification by Peptide Carbamylation

Arne Ulbrich, Anna E. Merrill, Alexander S. Hebert, Michael S. Westphall, more

Journal of The American Society for Mass Spectrometry > 2014 > 25 > 1 > 6-9

We describe a chemical tag for duplex proteome quantification using neutron encoding (NeuCode). The method utilizes the straightforward, efficient, and inexpensive carbamylation reaction. We demonstrate the utility of NeuCode carbamylation by accurately measuring quantitative ratios from tagged yeast lysates mixed in known ratios and by applying this method to quantify differential protein expression...

article

Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome

Alexander S. Hebert, Kristin E. Dittenhafer-Reed, Wei Yu, Derek J. Bailey, more

Molecular Cell > 2013 > 49 > 1 > 186-199

Calorie restriction (CR) extends life span in diverse species. Mitochondria play a key role in CR adaptation; however, the molecular details remain elusive. We developed and applied a quantitative mass spectrometry method to probe the liver mitochondrial acetyl-proteome during CR versus control diet in mice that were wild-type or lacked the protein deacetylase SIRT3. Quantification of 3,285 acetylation...

article

Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer

Aaron R. Ledvina, Christopher M. Rose, Graeme C. McAlister, John E. P. Syka, more

Journal of The American Society for Mass Spectrometry > 2013 > 24 > 11 > 1623-1633

We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons...

article

Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species

Christopher M. Rose, Jason D. Russell, Aaron R. Ledvina, Graeme C. McAlister, more

Journal of The American Society for Mass Spectrometry > 2013 > 24 > 6 > 816-827

We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section rf ion storage and transfer device to enable injection and simultaneous separate storage...

article

A Quantitative Map of the Liver Mitochondrial Phosphoproteome Reveals Posttranslational Control of Ketogenesis

Paul A. Grimsrud, Joshua J. Carson, Alex S. Hebert, Shane L. Hubler, more

Cell Metabolism > 2012 > 16 > 5 > 672-683

Mitochondria are dynamic organelles that play a central role in a diverse array of metabolic processes. Elucidating mitochondrial adaptations to changing metabolic demands and the pathogenic alterations that underlie metabolic disorders represent principal challenges in cell biology. Here, we performed multiplexed quantitative mass spectrometry-based proteomics to chart the remodeling of the mouse...

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Search results for: Michael S. Westphall

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation

Gender Diversity in a STEM Subfield – Analysis of a Large Scientific Society and Its Annual Conferences

A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions

Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer

Identification of the phosphorylation targets of symbiotic receptor‐like kinases using a high‐throughput multiplexed assay for kinase specificity

Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function

NeuCode Proteomics Reveals Bap1 Regulation of Metabolism

Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation

Potential regulatory phosphorylation sites in a Medicago truncatula plasma membrane proton pump implicated during early symbiotic signaling in roots

A Calibration Routine for Efficient ETD in Large-Scale Proteomics

Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single‐Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single‐Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

NANOG Is Multiply Phosphorylated and Directly Modified by ERK2 and CDK1 In Vitro

Neutron-Encoded Protein Quantification by Peptide Carbamylation

Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome

Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer

Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species

A Quantitative Map of the Liver Mitochondrial Phosphoproteome Reveals Posttranslational Control of Ketogenesis

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