Michael S. Bereman

Works (51)

Updated: April 25th, 2025 17:35

2024 article

A Framework for Quality Control in Quantitative Proteomics

Tsantilas, K. A., Merrihew, G. E., Robbins, J. E., Johnson, R. S., Park, J., Plubell, D. L., … MacCoss, M. J. (2024, September 9). Journal of Proteome Research.

By: K. Tsantilas *, G. Merrihew *, J. Robbins *, R. Johnson *, J. Park*, D. Plubell *, J. Canterbury*, E. Huang * ...

author keywords: quality control; proteomics; mass spectrometry; liquid chromatography; sample preparation; system suitability; quantitative results; PRM; DIA; DDA
MeSH headings : Proteomics / methods; Proteomics / standards; Quality Control; Reproducibility of Results; Humans; Workflow; Peptides / analysis; Peptides / standards
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Bioinformatics and Genomic Networks; Gene expression and cancer classification
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Source: Web Of Science
Added: September 23, 2024

2022 article

An experimental evaluation of the efficacy of perinatal sulforaphane supplementation to decrease the incidence and severity of vinclozolin-induced hypospadias in the mouse model

Amato, C. M., Fricke, A., Marella, S., Mogus, J. P., Bereman, M., & McCoy, K. A. (2022, July 26). Toxicology and Applied Pharmacology.

By: C. Amato *, A. Fricke*, S. Marella *, J. Mogus *, M. Bereman n & K. McCoy *

author keywords: Birth defects prevention; Hypospadias; Mechanisms of resilience; Preventive toxicology; Sulforaphane; Vinclozolin
MeSH headings : Animals; Dietary Supplements; Disease Models, Animal; Environmental Pollutants / adverse effects; Female; Humans; Hypospadias / chemically induced; Hypospadias / prevention & control; Incidence; Isothiocyanates / pharmacology; Male; Mice; NF-E2-Related Factor 2 / genetics; Oxazoles; Pregnancy; Sulfoxides
topics (OpenAlex): Urological Disorders and Treatments; Birth, Development, and Health; Neonatal Respiratory Health Research
TL;DR: Pregnant mice were exposed to the demasculinizing toxicant, vinclozolin, in combination with increasing doses of the NRF2 activator, sulforaphane, to test the hypothesis that pollutant-induced birth defects can be prevented and reduced in severity by augmenting natural mechanisms of resilience. (via Semantic Scholar)
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Source: Web Of Science
Added: January 3, 2023

2022 article

The Cyanotoxin 2,4-DAB Reduces Viability and Causes Behavioral and Molecular Dysfunctions Associated with Neurodegeneration in Larval Zebrafish

Martin, R. M., Bereman, M. S., & Marsden, K. C. (2022, January 14). Neurotoxicity Research, Vol. 40, pp. 347–364.

By: R. Martin n, M. Bereman n & K. Marsden n 

author keywords: Cyanotoxins; Mixtures; 2,4-DAB; Zebrafish; Behavior; Proteomics
MeSH headings : Amino Acids, Diamino / toxicity; Animals; Cyanobacteria; Cyanobacteria Toxins; Isomerism; Larva; Neurotoxicity Syndromes; Neurotoxins / toxicity; Zebrafish
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Spinal Cord Injury Research; Spinal Dysraphism and Malformations
TL;DR: Together, the data demonstrate that BMAA and its isomers AEG and 2,4-DAB cause neurotoxic effects in vivo, with 2, 4- DAB as the most potent of the three in the zebrafish model. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: January 15, 2022

2021 article

ALSUntangled #60: light therapy

Bedlack, R., Barkhaus, P., Barnes, B., Bereman, M., Bertorini, T., Carter, G., … Wicks, P. (2021, March 8). Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration.

By: R. Bedlack *, P. Barkhaus *, B. Barnes*, M. Bereman n, T. Bertorini *, G. Carter, J. Crayle *, S. Kihuwa-Mani* ...

author keywords: Light; energy; alternative therapy; epidemiology; ethics; therapy
MeSH headings : Amyotrophic Lateral Sclerosis / drug therapy; Humans; Phototherapy
topics (OpenAlex): Laser Applications in Dentistry and Medicine; Planarian Biology and Electrostimulation; Migraine and Headache Studies
TL;DR: Light therapy has theoretically plausible mechanisms, three flawed pre-clinical data, studies, and one incompletely documented case report supporting its use, and it is explained why further studies are needed to determine whether any specific light therapy protocol can help people with ALS. (via Semantic Scholar)
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Added: April 26, 2021

2021 article

ALSUntangled 59: Tamoxifen

Bedlack, R., Kihuwa-mani, S., Barkhaus, P. E., Bereman, M., Caress, J. B., Crayle, J., … Salmon, K. (2021, January 21). Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration.

By: R. Bedlack *, S. Kihuwa-mani*, P. Barkhaus *, M. Bereman n, J. Caress *, J. Crayle *, G. Pattee *, T. Patterson* ...

author keywords: Tamoxifen; ALSUntangled; off-label treatment; trials; ethics; therapy; clinical trials
MeSH headings : Amyotrophic Lateral Sclerosis / drug therapy; Humans; Tamoxifen / therapeutic use
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Histone Deacetylase Inhibitors Research; Synthetic Organic Chemistry Methods
TL;DR: While Tamoxifen cannot yet endorse this as an ALS treatment, there is enough evidence to warrant another larger ALS trial, and it appears reasonably safe, though there is a small risk of developing cancer with long term use. (via Semantic Scholar)
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Source: Web Of Science
Added: March 15, 2021

2021 article

Toxicant exposure during pregnancy increases protective proteins in the dam and a sexually dimorphic response in the fetus

Rister, A. L., Amato, C. M., Nash, T., McCoy, M. W., Bereman, M., & McCoy, K. A. (2021, January 10). Toxicology and Applied Pharmacology.

By: A. Rister *, C. Amato *, T. Nash n, M. McCoy *, M. Bereman n & K. McCoy *

author keywords: Vinclozolin; Endocrine Disrupting Compounds; Proteomics; Detoxification; Liver
MeSH headings : Adenosine Triphosphate / metabolism; Androgen Antagonists / metabolism; Androgen Antagonists / toxicity; Animals; Endocrine Disruptors / metabolism; Endocrine Disruptors / toxicity; Female; Liver / drug effects; Liver / embryology; Liver / metabolism; Male; Maternal Exposure; Metabolic Detoxication, Phase I; Metabolic Detoxication, Phase II; Mice; Oxazoles / metabolism; Oxazoles / toxicity; Oxidative Phosphorylation; Pregnancy; Proteome; Proteomics; Sex Characteristics; Sex Factors
topics (OpenAlex): Birth, Development, and Health; Effects and risks of endocrine disrupting chemicals; Prenatal Substance Exposure Effects
TL;DR: Proteomic alterations in the livers of mouse dams and their male and female fetuses induced by vinclozolin, a model antiandrogenic EDC, suggest that female Fetuses increase protective mechanisms, whereas male fetuses increase ATP production and upregulate several disease pathways that are indicative of oxidative damage. (via Semantic Scholar)
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Source: Web Of Science
Added: March 15, 2021

2020 article

BMAA and MCLR Interact to Modulate Behavior and Exacerbate Molecular Changes Related to Neurodegeneration in Larval Zebrafish

Martin, R. M., Bereman, M. S., & Marsden, K. C. (2020, November 20). Toxicological Sciences, Vol. 179, pp. 251–261.

By: R. Martin n, M. Bereman n & K. Marsden n 

author keywords: cyanotoxins; mixtures; zebrafish; behavior; proteomics
MeSH headings : Amino Acids, Diamino / toxicity; Animals; Cyanobacteria Toxins; Larva; Proteomics; Zebrafish
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Alzheimer's disease research and treatments; Neuroinflammation and Neurodegeneration Mechanisms
TL;DR: This study evaluates the neurotoxic effects of a mixture of two co-occurring cyanotoxins, β-methylamino-L-alanine (BMAA) and microcystin leucine and arginine (MCLR), using the larval zebrafish model to reveal that BMAA and MCLR interact in vivo to enhance neurotoxicity. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 15, 2020

2020 article

Metabolite Profiling Reveals Predictive Biomarkers and the Absence of β-Methyl Amino-l-alanine in Plasma from Individuals Diagnosed with Amyotrophic Lateral Sclerosis

Bereman, M. S., Kirkwood, K. I., Sabaretnam, T., Furlong, S., Rowe, D. B., Guillemin, G. J., … Muddiman, D. C. (2020, May 18). Journal of Proteome Research, Vol. 19, pp. 3276–3285.

By: M. Bereman n, K. Kirkwood n, T. Sabaretnam *, S. Furlong *, D. Rowe *, G. Guillemin *, A. Mellinger n, D. Muddiman n 

author keywords: amyotrophic lateral sclerosis; biomarkers; BMAA; CZE-MS/MS; metabolites; plasma
MeSH headings : Alanine; Amyotrophic Lateral Sclerosis / diagnosis; Biomarkers; Female; Humans; Male; Mass Spectrometry; Metabolome
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Cholinesterase and Neurodegenerative Diseases; Neurological diseases and metabolism
TL;DR: The plasma metabolome of 134 patients diagnosed with sporadic amyotrophic lateral sclerosis and 118 individuals deemed healthy was profiled, and two models using the metabolite abundances were developed for the separation of ALS and healthy samples and the prediction of disease progression based on the ALS functional rating score. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: September 14, 2020

2020 article

Peptide variability and signatures associated with disease progression in CSF collected longitudinally from ALS patients

Mellinger, A. L., Griffith, E. H., & Bereman, M. S. (2020, June 26). Analytical and Bioanalytical Chemistry, Vol. 412, pp. 5465–5475.

By: A. Mellinger n, E. Griffith n  & M. Bereman n

author keywords: Amyotrophic lateral sclerosis; Cerebrospinal fluid; Longitudinal modeling; Proteomics; Biomarker
MeSH headings : Aged; Amyotrophic Lateral Sclerosis / cerebrospinal fluid; Chromatography, Liquid / methods; Disease Progression; Female; Humans; Longitudinal Studies; Male; Middle Aged; Peptides / cerebrospinal fluid; Proteomics; Tandem Mass Spectrometry / methods
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Alzheimer's disease research and treatments; Cholinesterase and Neurodegenerative Diseases
TL;DR: Overall, the CSF protein abundances are tightly regulated with the intra-individual variability contributing just 4% to the overall variance and the association of inflammation with rate of disease progression is explored. (via Semantic Scholar)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: July 13, 2020

2019 article

Maternal vitamin D deficiency and developmental origins of health and disease (DOHaD)

Ideraabdullah, F. Y., Belenchia, A. M., Rosenfeld, C. S., Kullman, S. W., Knuth, M., Mahapatra, D., … Peterson, C. A. (2019, March 25). Journal of Endocrinology.

By: F. Ideraabdullah *, A. Belenchia *, C. Rosenfeld *, S. Kullman n , M. Knuth  n, D. Mahapatra  n, M. Bereman n, E. Levin *, C. Peterson*

author keywords: vitamin D deficiency; DOHAD; metabolic disorders; autism; neurobehavioral disorders; animal models
topics (OpenAlex): Vitamin D Research Studies; Birth, Development, and Health; Health, Environment, Cognitive Aging
TL;DR: A detailed review and perspective of evidence for the role of maternal VDD in offspring long term health, particularly as it relates to Developmental Origins of Health and Disease (DOHaD), and evidence implicating epigenetic mechanisms as a mediator of this link is explored. (via Semantic Scholar)
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2. Zero Hunger (OpenAlex)
Source: Web Of Science
Added: June 17, 2019

2019 journal article

Mixture designs to investigate adverse effects upon co-exposure to environmental cyanotoxins

Toxicology, 421, 74–83.

By: R. Martin n, J. Stallrich n  & M. Bereman n

Contributors: R. Martin n, J. Stallrich n  & M. Bereman n

author keywords: Cyanotoxins; Mixture design; Interaction; Environmental exposure; Proteomics
MeSH headings : Animals; Bacterial Toxins / toxicity; Cell Line; Cell Survival / drug effects; Cyanobacteria; Drug Interactions; Mice; No-Observed-Adverse-Effect Level; Proteome / drug effects; Risk Assessment / methods; Toxicity Tests / methods
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Alcoholism and Thiamine Deficiency; Prion Diseases and Protein Misfolding
TL;DR: The results highlight the need to study combinations of cyanotoxins when investigating the link between cyanobacteria and neurodegenerative pathologies and the application of design of experiment (DoE) as an efficient methodology to study mixtures of relevant environmental toxins. (via Semantic Scholar)
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6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: April 20, 2020

2018 article

A novel integrated strategy for the detection and quantification of the neurotoxin β-N-methylamino-l-alanine in environmental samples

Beri, J., Kirkwood, K. I., Muddiman, D. C., & Bereman, M. S. (2018, February 17). Analytical and Bioanalytical Chemistry, Vol. 410, pp. 2597–2605.

By: J. Beri n, K. Kirkwood n, D. Muddiman n  & M. Bereman n

author keywords: BMAA; CZE; Isomer separation; Quantification; HRAM MS/MS; Seafood
MeSH headings : Amino Acids, Diamino / analysis; Animals; Cyanobacteria Toxins; Environmental Monitoring / methods; Environmental Pollutants / analysis; Fishes / metabolism; Food Analysis / methods; Humans; Limit of Detection; Neurotoxins / analysis; Seafood / analysis; Tandem Mass Spectrometry / methods
topics (OpenAlex): Amino Acid Enzymes and Metabolism; Metabolomics and Mass Spectrometry Studies; Polyamine Metabolism and Applications
TL;DR: Interestingly, BMAA was not identified in the free protein fraction but only detected after protein hydrolysis which suggests that BMAA is tightly bound by and/or incorporated into proteins. (via Semantic Scholar)
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14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2018 article

Leveraging proteomics to compare submerged versus air-liquid interface carbon nanotube exposure to a 3D lung cell model

Hilton, G., Barosova, H., Petri-Fink, A., Rothen-Rutishauser, B., & Bereman, M. (2018, September 20). Toxicology in Vitro.

By: G. Hilton n, H. Barosova *, A. Petri-Fink *, B. Rothen-Rutishauser * & M. Bereman n

author keywords: Carbon nanotubes; Lung cell co-cultures; Air-liquid interface; In vitro assay development; Label-free proteomics; Toxicoproteomics
MeSH headings : Cell Line; Coculture Techniques; Epithelial Cells / drug effects; Epithelial Cells / metabolism; Fibroblasts / drug effects; Fibroblasts / metabolism; Humans; Lung / cytology; Macrophages / drug effects; Macrophages / metabolism; Nanotubes, Carbon / toxicity; Proteomics; Toxicity Tests
topics (OpenAlex): Nanoparticles: synthesis and applications; Graphene and Nanomaterials Applications; Air Quality and Health Impacts
TL;DR: Comparison of MWCNT exposure methods yielded protein enrichment in pathways known to be associated with carbon nanotube exposure stress response, such as acute phase response signaling and NRF2-mediated oxidative stress response. (via Semantic Scholar)
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Added: January 14, 2019

2018 article

Machine Learning Reveals Protein Signatures in CSF and Plasma Fluids of Clinical Value for ALS

Bereman, M. S., Beri, J., Enders, J. R., & Nash, T. (2018, October 30). Scientific Reports, Vol. 8.

By: M. Bereman n, J. Beri n, J. Enders n  & T. Nash n

Contributors: M. Bereman n, J. Beri n, J. Enders n  & T. Nash n

MeSH headings : Amyotrophic Lateral Sclerosis / blood; Amyotrophic Lateral Sclerosis / cerebrospinal fluid; Amyotrophic Lateral Sclerosis / metabolism; Humans; Machine Learning; Multivariate Analysis; Proteomics
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Studies on Chitinases and Chitosanases; Cystic Fibrosis Research Advances
TL;DR: The potential of a panel of targeted proteins for objective measurements of clinical value in ALS is demonstrated, and three proteins composed a prognostic model that explained 49% of the variation in the ALS-FRS scores. (via Semantic Scholar)
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10. Reduced Inequalities (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 19, 2018

2017 journal article

Acetylation-induced TDP-43 pathology is suppressed by an HSF1-dependent chaperone program

Nature Communications, 8(1).

By: P. Wang *, C. Wander *, C. Yuan*, M. Bereman n & T. Cohen *

MeSH headings : Acetylation; Animals; DNA-Binding Proteins / metabolism; Heat Shock Transcription Factors / genetics; Heat Shock Transcription Factors / metabolism; Humans; Mice; Molecular Chaperones; Muscle, Skeletal / metabolism; Protein Processing, Post-Translational; Protein Refolding; TDP-43 Proteinopathies / metabolism
topics (OpenAlex): Amyotrophic Lateral Sclerosis Research; Neurogenetic and Muscular Disorders Research; Parkinson's Disease Mechanisms and Treatments
TL;DR: It is shown that acetylation of the protein triggers TDP-43 pathology in cultured cells and mouse skeletal muscle, which can be cleared through an HSF1-dependent chaperone mechanism that disaggregates the protein. (via Semantic Scholar)
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Sources: Crossref, NC State University Libraries
Added: August 6, 2018

2017 journal article

Development of selected reaction monitoring methods to systematically quantify kinase abundance and phosphorylation stoichiometry in human samples

Kinase Signaling Networks, 1636, 353–369.

By: K. Beck, N. Camp, M. Bereman, J. Bollinger, J. Egertson, M. MacCoss, A. Wolf-Yadlin

Source: NC State University Libraries
Added: August 6, 2018

2017 journal article

Exposure to BMAA mirrors molecular processes linked to neurodegenerative disease

PROTEOMICS, 17(17-18), 1700161.

By: J. Beri n, T. Nash n, R. Martin n & M. Bereman n

author keywords: Amyotrophic lateral sclerosis; BMAA; Exposures; LC-MS; MS; Neurodegeneration
MeSH headings : Amino Acids, Diamino / toxicity; Amyotrophic Lateral Sclerosis / chemically induced; Amyotrophic Lateral Sclerosis / metabolism; Amyotrophic Lateral Sclerosis / pathology; Animals; Cell Line; Cyanobacteria Toxins; Diet / adverse effects; Excitatory Amino Acid Agonists / toxicity; Gene Expression Regulation / drug effects; Mice; Motor Neurons / metabolism; Motor Neurons / pathology; Neuroblastoma / metabolism; Neuroblastoma / pathology
topics (OpenAlex): Endoplasmic Reticulum Stress and Disease; Amyotrophic Lateral Sclerosis Research; Folate and B Vitamins Research
TL;DR: Analysis of differentially regulated proteins reveals significant enrichment of pathways related to ER stress, protein ubiquitination, the unfolded protein response, and mitochondrial dysfunction, and the hypothesis that BMAA causes protein damage via misincorporation in place of L‐Serine is examined. (via Semantic Scholar)
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Sources: Crossref, NC State University Libraries
Added: August 6, 2018

2017 article

MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments

Dogu, E., Mohammad-Taheri, S., Abbatiello, S. E., Bereman, M. S., MacLean, B., Schilling, B., & Vitek, O. (2017, May 8). Molecular & Cellular Proteomics.

By: E. Dogu *, S. Mohammad-Taheri *, S. Abbatiello *, M. Bereman n, B. MacLean *, B. Schilling *, O. Vitek *

MeSH headings : Humans; Internet; Mass Spectrometry; Peptides / analysis; Proteomics / standards; Quality Control; Software
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Advanced Biosensing Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: Evaluations on simulated data sets, and on data sets from the Clinical Proteomics Technology Assessment for Cancer consortium, demonstrated that these methods substantially improve the ability of real time monitoring, early detection and prevention of chromatographic and instrumental problems. (via Semantic Scholar)
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Added: August 6, 2018

2017 article

Mapping differential cellular protein response of mouse alveolar epithelial cells to multi-walled carbon nanotubes as a function of atomic layer deposition coating

Hilton, G. M., Taylor, A. J., Hussain, S., Dandley, E. C., Griffith, E. H., Garantziotis, S., … Bereman, M. S. (2017, February 23). Nanotoxicology, Vol. 11, pp. 313–326.

By: G. Hilton n, A. Taylor n, S. Hussain *, E. Dandley n, E. Griffith n , S. Garantziotis *, G. Parsons n , J. Bonner n , M. Bereman n

author keywords: Carbon nanotube; label-free proteomics; pulmonary fibrosis; toxicoproteomics
MeSH headings : Aluminum Oxide / toxicity; Alveolar Epithelial Cells / chemistry; Alveolar Epithelial Cells / drug effects; Animals; Cells, Cultured; Mice; Nanotubes, Carbon / toxicity; Proteomics / methods; Pulmonary Fibrosis / etiology; Zinc Oxide / toxicity
topics (OpenAlex): Graphene and Nanomaterials Applications; Air Quality and Health Impacts; Nanoparticles: synthesis and applications
TL;DR: It is demonstrated that specific types of metal oxide thin film coatings applied by ALD produce distinct cellular and biochemical responses related to lung inflammation and fibrosis compared to uncoated MWCNT exposure in vitro. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2016 article

An Automated Pipeline to Monitor System Performance in Liquid Chromatography–Tandem Mass Spectrometry Proteomic Experiments

Bereman, M. S., Beri, J., Sharma, V., Nathe, C., Eckels, J., MacLean, B., & MacCoss, M. J. (2016, September 26). Journal of Proteome Research.

By: M. Bereman*, J. Beri*, V. Sharma *, C. Nathe, J. Eckels, B. MacLean *, M. MacCoss *

author keywords: system suitability; process control; proteomics; tandem mass spectrometry; control charts
MeSH headings : Automation; Chromatography, Liquid / methods; Chromatography, Liquid / standards; Information Dissemination; Internet; Proteomics / methods; Tandem Mass Spectrometry / methods; Tandem Mass Spectrometry / standards; Workflow
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Advanced Biosensing Techniques and Applications
TL;DR: The development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments, termed Panorama AutoQC, is reported, to evaluate LC-MS/MS performance in a range of scenarios including identification of suboptimal instrument performance, evaluation of ultrahigh pressure chromatography, and identification of the major sources of variation throughout years of peptide data collection. (via Semantic Scholar)
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Added: August 6, 2018

2016 article

Improving the analytical performance and versatility of paper spray mass spectrometry via paper microfluidics

Murray, I., Walker, G., & Bereman, M. S. (2016, January 1). The Analyst.

By: I. Murray n, G. Walker n & M. Bereman n

topics (OpenAlex): Biosensors and Analytical Detection; Mass Spectrometry Techniques and Applications; Advanced Chemical Sensor Technologies
TL;DR: Two paper-based microfluidic techniques, photolithography and wax patterning, were investigated for their potential to improve upon the sensitivity, reproducibility, and versatility of paper spray mass spectrometry. (via Semantic Scholar)
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Added: August 6, 2018

2016 article

Nuclear Localized LSR: A Novel Regulator of Breast Cancer Behavior and Tumorigenesis

Reaves, D. K., Hoadley, K. A., Fagan-Solis, K. D., Jima, D. D., Bereman, M., Thorpe, L., … Fleming, J. M. (2016, November 17). Molecular Cancer Research.

By: D. Reaves*, K. Hoadley *, K. Fagan-Solis*, D. Jima n, M. Bereman n, L. Thorpe*, J. Hicks*, D. McDonald * ...

MeSH headings : Animals; Breast Neoplasms / genetics; Breast Neoplasms / metabolism; Breast Neoplasms / pathology; Carcinogenesis / genetics; Carcinogenesis / metabolism; Carcinogenesis / pathology; Cell Transformation, Neoplastic / genetics; Cell Transformation, Neoplastic / metabolism; Cell Transformation, Neoplastic / pathology; Female; Heterografts; Humans; Mice; Receptors, LDL / biosynthesis; Receptors, LDL / genetics; Receptors, LDL / metabolism
topics (OpenAlex): RNA Research and Splicing; RNA and protein synthesis mechanisms; RNA Interference and Gene Delivery
TL;DR: Results show that nuclear LSR alters gene expression and may promote aggressive cancer phenotypes through differential subcellular localization to alter cell signaling, bioenergetics, and gene expression. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2015 article

Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications

Porter, C. J., & Bereman, M. S. (2015, June 23). Analytical and Bioanalytical Chemistry.

By: C. Porter n & M. Bereman n

author keywords: Protein adducts; Toxicoproteomics; Mass spectrometry; Data-independent acquisition; Exposome
MeSH headings : Algorithms; Amino Acids / analysis; Amino Acids / chemistry; Binding Sites; Chromatography, Liquid / methods; Data Mining / methods; Databases, Protein; Peptides / analysis; Peptides / chemistry; Protein Binding; Protein Interaction Mapping / methods; Reproducibility of Results; Sensitivity and Specificity; Spectrometry, Mass, Electrospray Ionization / methods
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: A novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner and an application in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species. (via Semantic Scholar)
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Added: August 6, 2018

2015 article

Reagent for Evaluating Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS) Performance in Bottom-Up Proteomic Experiments

Beri, J., Rosenblatt, M. M., Strauss, E., Urh, M., & Bereman, M. S. (2015, November 5). Analytical Chemistry.

By: J. Beri n, M. Rosenblatt*, E. Strauss*, M. Urh * & M. Bereman n

MeSH headings : Amino Acids / chemistry; Chromatography, Liquid / methods; HEK293 Cells; Humans; Hydrophobic and Hydrophilic Interactions; Indicators and Reagents / chemistry; Peptides / chemical synthesis; Peptides / chemistry; Proteomics / methods; Tandem Mass Spectrometry / methods
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: A novel proteomic standard for assessing liquid chromatography-tandem mass spectrometry (LC-MS/MS) instrument performance, in terms of chromatographic reproducibility and dynamic range within a single LC- MS/MS injection, is presented. (via Semantic Scholar)
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Added: August 6, 2018

2015 article

Toxicoproteomic analysis of pulmonary carbon nanotube exposure using LC-MS/MS

Hilton, G. M., Taylor, A. J., McClure, C. D., Parsons, G. N., Bonner, J. C., & Bereman, M. S. (2015, January 15). Toxicology, Vol. 329, pp. 80–87.

By: G. Hilton n, A. Taylor n, C. McClure n, G. Parsons n , J. Bonner n  & M. Bereman n

Contributors: G. Hilton n, A. Taylor n, C. McClure n, G. Parsons n , J. Bonner n  & M. Bereman n

author keywords: Carbon nanotube; Label-free proteomics; Pulmonary fibrosis; Toxicoproteomics
MeSH headings : Acute-Phase Proteins / genetics; Acute-Phase Proteins / metabolism; Animals; Bronchoalveolar Lavage Fluid / chemistry; Chromatography, Liquid; Complement C3 / genetics; Complement C3 / metabolism; Complement C4b / genetics; Complement C4b / metabolism; Complement C9 / genetics; Complement C9 / metabolism; Histones / genetics; Histones / metabolism; Lactoferrin / genetics; Lactoferrin / metabolism; Lipocalin-2; Lipocalins / genetics; Lipocalins / metabolism; Lung / drug effects; Lung / metabolism; Mice; Mice, Inbred C57BL; Nanotubes, Carbon / chemistry; Nanotubes, Carbon / toxicity; Oncogene Proteins / genetics; Oncogene Proteins / metabolism; Peroxidase / genetics; Peroxidase / metabolism; Proteome / metabolism; Pulmonary Surfactant-Associated Protein B / genetics; Pulmonary Surfactant-Associated Protein B / metabolism; Tandem Mass Spectrometry; Toxicity Tests
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications; Nanoparticles: synthesis and applications
TL;DR: The protein secretion profile in lung bronchoalveolar lavage fluid from mice exposed to non-functionalized multi-walled carbon nanotubes or MWCNTs functionalized by nanoscale Al2O3 coatings formed using atomic layer deposition (ALD) was compared. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2014 journal article

C/EBPα regulates CRL4Cdt2-mediated degradation of p21 in response to UVB-induced DNA damage to control the G1/S checkpoint

Cell Cycle, 13(22), 3602–3610.

By: J. Hall n , M. Bereman n, A. Nepomuceno n, E. Thompson n, D. Muddiman n  & R. Smart n 

author keywords: C/EBP alpha; CRL4(Cdt2); G(1)/S DNA damage checkpoint; keratinocytes; p21
MeSH headings : Animals; CCAAT-Enhancer-Binding Protein-alpha / genetics; CCAAT-Enhancer-Binding Protein-alpha / metabolism; Cell Cycle Checkpoints / genetics; Cell Cycle Checkpoints / radiation effects; Cyclin-Dependent Kinase Inhibitor p21 / metabolism; DNA Damage / genetics; DNA Damage / radiation effects; G1 Phase Cell Cycle Checkpoints / genetics; Keratinocytes / metabolism; Keratinocytes / radiation effects; Mice; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Proteolysis; Ubiquitin-Protein Ligases / genetics; Ubiquitin-Protein Ligases / metabolism; Ultraviolet Rays; p21-Activated Kinases / genetics; p21-Activated Kinases / metabolism
topics (OpenAlex): Cancer-related Molecular Pathways; Ubiquitin and proteasome pathways; DNA Repair Mechanisms
TL;DR: Findings reveal C/EBPα regulates G1/S cell cycle arrest in response to DNA damage via the control of CRL4Cdt2 mediated degradation of p21. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2014 journal article

Evidence of the Biochemical Basis of Host Virulence in the Greenbug Aphid,Schizaphis graminum(Homoptera: Aphididae)

Journal of Proteome Research, 13(4), 2094–2108.

By: P. Pinheiro *, M. Bereman*, J. Burd, M. Pals, S. Armstrong, K. Howe *, T. Thannhauser *, M. MacCoss *, S. Gray *, M. Cilia*

author keywords: aphid; biotype; vector biology; insect-plant interactions; host virulence; Schizaphis graminum; greenbug; DIGE; LC-MS/MS
MeSH headings : Animals; Aphids / genetics; Aphids / microbiology; Aphids / pathogenicity; Aphids / physiology; Buchnera; Host-Parasite Interactions; Insect Proteins / analysis; Insect Proteins / classification; Insect Proteins / genetics; Insect Proteins / metabolism; Poaceae / parasitology; Proteome / analysis; Proteome / genetics; Proteome / metabolism; Proteome / physiology; Symbiosis
topics (OpenAlex): Insect symbiosis and bacterial influences; Insect-Plant Interactions and Control; Insect Resistance and Genetics
Source: Crossref
Added: August 28, 2020

2014 article

Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS

Bereman, M. S., Johnson, R., Bollinger, J., Boss, Y., Shulman, N., MacLean, B., … MacCoss, M. J. (2014, February 4). Journal of the American Society for Mass Spectrometry.

By: M. Bereman n, R. Johnson *, J. Bollinger*, Y. Boss*, N. Shulman*, B. MacLean *, A. Hoofnagle *, M. MacCoss *

author keywords: Quality control; Statistical process control; Proteomics; Mass spectrometry; Shewhart control charts
MeSH headings : Chromatography, Liquid / methods; Models, Statistical; Peptides / analysis; Peptides / chemistry; Proteomics / methods; Tandem Mass Spectrometry / methods
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software, which monitors five quality control metrics in a shotgun or targeted proteomic workflow. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2014 article

Tools for monitoring system suitability in LC MS/MS centric proteomic experiments

Bereman, M. S. (2014, October 18). PROTEOMICS.

By: M. Bereman n

author keywords: Mass spectrometry; Quality control; Shewhart control charts; Statistical process control; System suitability; Technology
MeSH headings : Chromatography, Liquid / methods; Chromatography, Liquid / standards; Peptides / analysis; Peptides / chemistry; Proteins / analysis; Proteins / chemistry; Proteomics / methods; Proteomics / standards; Quality Control; Tandem Mass Spectrometry / methods; Tandem Mass Spectrometry / standards
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: The implementation of a robust system suitability workflow is discussed in terms of metrics, type of standard, and frequency of evaluation along with the obstacles to overcome prior to incorporating a more proactive approach to overall quality control in liquid chromatography coupled to tandem mass spectrometry based proteomic workflows. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2013 journal article

Development and Characterization of a Novel Plug and Play Liquid Chromatography-Mass Spectrometry (LC-MS) Source That Automates Connections between the Capillary Trap, Column, and Emitter

Molecular & Cellular Proteomics, 12(6), 1701–1708.

By: M. Bereman*, E. Hsieh*, T. Corso*, C. Van Pelt* & M. MacCoss *

MeSH headings : Animals; Caenorhabditis elegans / chemistry; Caenorhabditis elegans Proteins / chemistry; Caenorhabditis elegans Proteins / isolation & purification; Chromatography, Liquid / instrumentation; Chromatography, Liquid / methods; Mass Spectrometry / instrumentation; Mass Spectrometry / methods; Peptides / analysis; Proteomics / instrumentation; Proteomics / methods
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications; Analytical Chemistry and Chromatography
TL;DR: This device is the first to make automated connections with user-packed capillary traps, columns, and capillary emitters and exchange of the individual trap and emitter cartridges was found to have an insignificant effect on the abundance of various peptides. (via Semantic Scholar)
Source: Crossref
Added: January 5, 2021

2012 journal article

A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome

Analytical and Bioanalytical Chemistry, 403(8), 2397–2402.

By: M. Bereman*, D. Tomazela*, H. Heins *, M. Simonato *, P. Cogo *, A. Hamvas *, B. Patterson, F. Cole *, M. MacCoss *

author keywords: Protein turnover; Respiratory distress syndrome; Selected reaction monitoring; SRM; Protein kinetics; Protein metabolism
MeSH headings : Amino Acid Sequence; Complement Factor B / analysis; Complement Factor B / metabolism; Humans; Infant, Newborn; Kinetics; Mass Spectrometry / methods; Molecular Sequence Data; Protein Precursors / analysis; Protein Precursors / metabolism; Proteins / analysis; Proteins / metabolism; Proteolipids / analysis; Proteolipids / metabolism; Proteomics / methods; Pulmonary Surfactant-Associated Protein B / analysis; Pulmonary Surfactant-Associated Protein B / metabolism; Respiratory Distress Syndrome, Newborn / metabolism; Trachea / metabolism
topics (OpenAlex): Neonatal Respiratory Health Research; Infant Nutrition and Health; Neonatal Health and Biochemistry
TL;DR: In vivo turnover of four proteins from sequential tracheal aspirates obtained from human newborn infants with respiratory distress syndrome using targeted proteomics is measured and complement factor B, a component of the alternative pathway of complement activation, had an approximately twofold-longer half-life than the other three proteins. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2012 journal article

De Novo Correction of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics

Journal of The American Society for Mass Spectrometry, 23(12), 2075–2082.

By: J. Egertson *, J. Eng *, M. Bereman*, E. Hsieh*, G. Merrihew * & M. MacCoss *

author keywords: Mass spectrometry; Proteomics; Tandem mass spectrometry; Calibration; Mass measurement accuracy; Shotgun proteomics; Resolution
MeSH headings : Algorithms; Calibration; Models, Molecular; Peptide Fragments / chemistry; Peptide Mapping / methods; Proteomics / methods; Saccharomyces cerevisiae Proteins / chemistry; Sensitivity and Specificity; Tandem Mass Spectrometry / methods; Tandem Mass Spectrometry / standards
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: The algorithm is implemented in a program called FineTune, which corrects systematic mass measurement error in 1 min, with no input required besides the mass spectra themselves, and the precision in mass measurement was improved due to the correction of non-linear variation inmass measurement accuracy across the m/z range. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2012 journal article

Effects of Column and Gradient Lengths on Peak Capacity and Peptide Identification in Nanoflow LC-MS/MS of Complex Proteomic Samples

Journal of The American Society for Mass Spectrometry, 24(1), 148–153.

By: E. Hsieh*, M. Bereman*, S. Durand, G. Valaskovic & M. MacCoss *

author keywords: Shotgun proteomics; Nanoflow liquid chromatography; Peak capacity
MeSH headings : Caenorhabditis elegans Proteins / analysis; Caenorhabditis elegans Proteins / chemistry; Chromatography, Liquid / instrumentation; Chromatography, Liquid / methods; Nanotechnology / instrumentation; Peptide Mapping / instrumentation; Peptide Mapping / methods; Proteome / analysis; Proteome / chemistry; Proteomics / instrumentation; Proteomics / methods; Tandem Mass Spectrometry / methods
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications; Analytical Chemistry and Chromatography
TL;DR: It is found that while longer column and gradient lengths generally increase peptide identifications, the degree of improvement is dependent on both parameters and is diminished at longer column, gradient, and gradients. (via Semantic Scholar)
Source: Crossref
Added: January 5, 2021

2012 journal article

Homopteran Vector Biomarkers for Efficient Circulative Plant Virus Transmission are Conserved in Multiple Aphid Species and the Whitefly Bemisia tabaci

Journal of Integrative Agriculture, 11(2), 249–262.

By: M. Cilia*, M. Bereman*, T. Fish *, M. MacCoss * & S. Gray *

author keywords: aphid; whitefly; Schizaphis graminum; Bemisia tabaci; Acyrthosiphon pisum; Toxoptera citricida; Myzus persicae; proteomics; biomarker; circulative transmission; begomovirus; luteovirus; geminivirus; leafhopper; selected reaction monitoring; SRM; mass spectrometry; targeted proteomics; Skyline
topics (OpenAlex): Plant Virus Research Studies; Insect-Plant Interactions and Control; Insect symbiosis and bacterial influences
TL;DR: The conservation of these proteins in multiple insect taxa that transmit plant viruses along the circulative transmission pathway creates the opportunity to use these biomarkers to rapidly identify insect populations that are the most efficient vectors and allow them to be targeted for control prior to the spread of virus within a crop. (via Semantic Scholar)
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15. Life on Land (OpenAlex)
Source: Crossref
Added: February 24, 2020

2012 journal article

Learning Score Function Parameters for Improved Spectrum Identification in Tandem Mass Spectrometry Experiments

Journal of Proteome Research, 11(9), 4499–4508.

By: M. Spivak*, M. Bereman*, M. MacCoss * & W. Noble *

author keywords: machine learning; spectrum identification; shotgun proteomics
MeSH headings : Algorithms; Artificial Intelligence; Caenorhabditis elegans Proteins / chemistry; Peptide Fragments / chemistry; Peptide Mapping / methods; Reproducibility of Results; Saccharomyces cerevisiae Proteins / chemistry; Software; Tandem Mass Spectrometry / methods
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Machine Learning in Bioinformatics
TL;DR: The present work addresses algorithms to rank peptide-spectrum matches with a richer and more flexible feature set representation that is based on the parametrization of the SEQUEST XCorr score and that can be used by all of these algorithms. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2012 journal article

Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline

Molecular & Cellular Proteomics, 11(5), 202–214.

By: B. Schilling *, M. Rardin *, B. MacLean *, A. Zawadzka *, B. Frewen*, M. Cusack*, D. Sorensen*, M. Bereman* ...

MeSH headings : Acetylation; Amino Acid Sequence; Animals; Breast Neoplasms; Calibration / standards; Cell Line, Tumor; Chromatography, High Pressure Liquid; Culture Media, Conditioned / chemistry; Female; Fourier Analysis; Humans; Mice; Mice, Knockout; Mitochondria, Liver / enzymology; Mitochondria, Muscle / metabolism; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Mapping / methods; Phosphorylation; Protein Processing, Post-Translational; Proteome / chemistry; Proteome / isolation & purification; Proteome / metabolism; Proteomics; Pyruvate Dehydrogenase Complex / chemistry; Pyruvate Dehydrogenase Complex / isolation & purification; Pyruvate Dehydrogenase Complex / metabolism; Reference Standards; Software; Tandem Mass Spectrometry / standards
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: The capabilities of Skyline were expanded to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments and the utility of the MS1 filtering approach was examined. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2012 journal article

The development of selected reaction monitoring methods for targeted proteomics via empirical refinement

PROTEOMICS, 12(8), 1134–1141.

By: M. Bereman*, B. MacLean *, D. Tomazela*, D. Liebler * & M. MacCoss *

author keywords: Selected reaction monitoring; Skyline; SRM assays; Targeted proteomics; Technology
MeSH headings : Amino Acid Sequence; Calibration; Humans; Infant, Newborn; Lung / physiopathology; Mass Spectrometry / methods; Mass Spectrometry / standards; Molecular Sequence Data; Peptides / analysis; Peptides / chemical synthesis; Proteomics / methods; Proteomics / standards; Pulmonary Surfactant-Associated Protein B / analysis; Reference Standards; Reproducibility of Results; Respiratory Distress Syndrome, Newborn / diagnosis; Respiratory Distress Syndrome, Newborn / physiopathology; Sensitivity and Specificity; Software
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications; Metabolomics and Mass Spectrometry Studies
TL;DR: A method, which uses the in‐house developed software tool termed Skyline, for empirical refinement of candidate peptides from targeted proteins to identify the best performing peptide in terms of ionization efficiency, reproducibility, specificity, and chromatographic characteristics to monitor as a proxy for protein abundance. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2011 journal article

Comparison between procedures using SDS for shotgun proteomic analyses of complex samples

PROTEOMICS, 11(14), 2931–2935.

By: M. Bereman*, J. Egertson * & M. MacCoss *

author keywords: Bottom-up proteomics; Protein identifications; Sample preparation protocols; Shotgun proteomics; Sodium dodecyl sulfate; Technology
MeSH headings : Animals; Caenorhabditis elegans Proteins / analysis; HEK293 Cells / chemistry; Humans; Mass Spectrometry / methods; Peptides / analysis; Proteins / analysis; Proteomics / methods; Saccharomyces cerevisiae Proteins / analysis; Sodium Dodecyl Sulfate / chemistry; Surface-Active Agents / chemistry
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Identification and Quantification in Food
TL;DR: Filter‐aided sample preparation (FASP) and a new sample preparation method using a modified commercial SDS removal spin column are quantitatively compared in terms of their performance for shotgun proteomic experiments in three complex proteomic samples. (via Semantic Scholar)
Source: Crossref
Added: February 24, 2020

2011 journal article

Evaluation of Front-End Higher Energy Collision-Induced Dissociation on a Benchtop Dual-Pressure Linear Ion Trap Mass Spectrometer for Shotgun Proteomics

Analytical Chemistry, 84(3), 1533–1539.

By: M. Bereman*, J. Canterbury*, J. Egertson *, J. Horner*, P. Remes *, J. Schwartz*, V. Zabrouskov *, M. MacCoss *

MeSH headings : Animals; Caenorhabditis elegans / metabolism; Glycopeptides / analysis; Mass Spectrometry / instrumentation; Mass Spectrometry / methods; Phosphopeptides / analysis; Pressure; Proteomics / instrumentation; Software
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications; Analytical Chemistry and Chromatography
TL;DR: Front-end higher energy collision-induced dissociation (fHCD) on a benchtop dual-pressure linear ion trap offers a clear advantage for the analysis of phosphorylated and glycosylated (O-GlcNAc) peptides as the average cross-correlation score (XCorr) for spectra using fHCD was statistically greater than for specta collected using RE-CID. (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Source: Crossref
Added: February 24, 2020

2011 journal article

Garrod's fourth inborn error of metabolism solved by the identification of mutations causing pentosuria

Proceedings of the National Academy of Sciences, 108(45), 18313–18317.

By: S. Pierce *, C. Spurrell *, J. Mandell *, M. Lee *, S. Zeligson*, M. Bereman*, S. Stray*, S. Fokstuen * ...

author keywords: dicarbonyl reductase; exome sequencing; glucuronic acid; history of genetics
MeSH headings : Blotting, Western; Carbohydrate Metabolism, Inborn Errors / ethnology; Carbohydrate Metabolism, Inborn Errors / genetics; DNA / genetics; Female; Humans; Jews; Male; Mutation; Pedigree; RNA, Messenger / genetics; Sugar Alcohol Dehydrogenases / deficiency; Sugar Alcohol Dehydrogenases / genetics; Xylulose / genetics
topics (OpenAlex): Metabolism and Genetic Disorders; Biomedical Research and Pathophysiology; Amino Acid Enzymes and Metabolism
TL;DR: Pentosuria, which affects almost exclusively individuals of Ashkenazi Jewish ancestry, is characterized by high levels of the pentose sugar l-xylulose in blood and urine and deficiency of the enzyme l-Xylulosing reductase, and the relationship between the DCXR genotypes and the pentosuric phenotype was confirmed. (via Semantic Scholar)
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3. Good Health and Well-being (OpenAlex)
Source: Crossref
Added: February 24, 2020

2010 article

One-year plasma N-linked glycome intra-individual and inter-individual variability in the chicken model of spontaneous ovarian adenocarcinoma

Dixon, R. B., Bereman, M. S., Petitte, J. N., Hawkridge, A. M., & Muddiman, D. C. (2010, May 28). International Journal of Mass Spectrometry, Vol. 305, pp. 79–86.

By: R. Dixon n, M. Bereman n, J. Petitte n , A. Hawkridge n & D. Muddiman n 

author keywords: N-linked glycans; HILIC; FTMS; Longitudinal sampling
topics (OpenAlex): Glycosylation and Glycoproteins Research; Cancer, Hypoxia, and Metabolism; Viral Infectious Diseases and Gene Expression in Insects
TL;DR: The initial interrogation of longitudinally-procured samples provides evidence that supports the value of this strategy in the search for glycomic biomarkers, and identifies 35 N-linked glycans identified in this study. (via Semantic Scholar)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018

2010 article

The effects of abundant plasma protein depletion on global glycan profiling using NanoLC FT-ICR mass spectrometry

Bereman, M. S., & Muddiman, D. C. (2010, January 19). Analytical and Bioanalytical Chemistry, Vol. 396, pp. 1473–1479.

By: M. Bereman n & D. Muddiman n 

author keywords: HILIC; NanoLCFT-ICRMS; Glycan profiling; N-linked glycans; Protein depletion
MeSH headings : Blood Proteins / chemistry; Blood Proteins / standards; Chromatography, Liquid; Nanotechnology; Polysaccharides / chemistry; Polysaccharides / standards; Proteomics / instrumentation; Proteomics / methods; Reproducibility of Results; Spectroscopy, Fourier Transform Infrared
topics (OpenAlex): Glycosylation and Glycoproteins Research; Carbohydrate Chemistry and Synthesis; Genomics and Phylogenetic Studies
TL;DR: Protein depletion was found to marginally effect the abundance of high mannose, hybrid, and large highly sialylated complex species and small fucosylated non-sialylation complex glycans were found to decrease in abundance in the depleted samples. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2009 article

Development of a Robust and High Throughput Method for Profiling N-Linked Glycans Derived from Plasma Glycoproteins by NanoLC−FTICR Mass Spectrometry

Bereman, M. S., Young, D. D., Deiters, A., & Muddiman, D. C. (2009, May 12). Journal of Proteome Research, Vol. 8, pp. 3764–3770.

By: M. Bereman n, D. Young n, A. Deiters n & D. Muddiman n 

MeSH headings : Biomarkers, Tumor / metabolism; Blood Proteins / chemistry; Chromatography, Liquid / methods; Detergents / pharmacology; Glycoproteins / chemistry; Humans; Mass Spectrometry / methods; Microwaves; Peptides / chemistry; Polysaccharides / chemistry; Proteome; Proteomics / methods; Spectroscopy, Fourier Transform Infrared / methods; Time Factors
topics (OpenAlex): Glycosylation and Glycoproteins Research; Carbohydrate Chemistry and Synthesis; Enzyme Structure and Function
TL;DR: A step-by-step protocol describing a method for N-linked glycan profiling of plasma glycoproteins by nanoflow liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is presented. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2009 article

Increasing the hydrophobicity and electrospray response of glycans through derivatization with novel cationic hydrazides

Bereman, M. S., Comins, D. L., & Muddiman, D. C. (2009, November 18). Chemical Communications, Vol. 46, pp. 237–239.

By: M. Bereman n, D. Comins n & D. Muddiman n 

topics (OpenAlex): Mass Spectrometry Techniques and Applications; Enzyme Catalysis and Immobilization; Electrohydrodynamics and Fluid Dynamics
TL;DR: Novel tags are used to increase the hydrophobicity of glycans and impart a permanent charge yielding as great as a approximately 5-fold increase in electrospray response from both a standard and complex mixture. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2008 article

Development of a nanoLC LTQ Orbitrap Mass Spectrometric Method for Profiling Glycans Derived from Plasma from Healthy, Benign Tumor Control, and Epithelial Ovarian Cancer Patients

Bereman, M. S., Williams, T. I., & Muddiman, D. C. (2008, December 29). Analytical Chemistry, Vol. 2, pp. 1130–1136.

By: M. Bereman n, T. Williams n  & D. Muddiman n 

Contributors: M. Bereman n, T. Williams n  & D. Muddiman n 

MeSH headings : Biomarkers, Tumor / blood; Biomarkers, Tumor / chemistry; Carcinoma / diagnosis; Chromatography, Liquid / methods; Female; Genital Neoplasms, Female / chemistry; Genital Neoplasms, Female / diagnosis; Glycoproteins / blood; Glycoproteins / chemistry; Humans; Hydrophobic and Hydrophilic Interactions; Lectins / blood; Lectins / chemistry; Male; Ovarian Neoplasms / diagnosis; Polysaccharides / blood; Polysaccharides / chemistry; ROC Curve; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods
topics (OpenAlex): Glycosylation and Glycoproteins Research; Analytical Chemistry and Chromatography; Mass Spectrometry Techniques and Applications
TL;DR: A split-less nano-flow liquid chromatography mass spectrometric analysis of glycans chemically cleaved from glycoproteins in plasma shows similar column efficiencies and excellent retention time reproducibility without an internal standard to correct for retention time shift. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018

2008 article

Mass measurement accuracy comparisons between a double‐focusing magnetic sector and a time‐of‐flight mass analyzer

Bereman, M. S., Lyndon, M. M., Dixon, R. B., & Muddiman, D. C. (2008, April 17). Rapid Communications in Mass Spectrometry, Vol. 22, pp. 1563–1566.

By: M. Bereman n, M. Lyndon n, R. Dixon n & D. Muddiman n 

MeSH headings : Equipment Design; Equipment Failure Analysis; Magnetics / instrumentation; Reproducibility of Results; Sensitivity and Specificity; Spectrometry, Mass, Electrospray Ionization / instrumentation; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / instrumentation
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Analytical Chemistry and Chromatography; Advanced Proteomics Techniques and Applications
TL;DR: A direct comparison of the mass measurement accuracies (MMAs) obtained on different mass spectrometry instrument types; a magnetic sector as the 'gold standard' and an electrospray ionization time-of-flight (ESI-TOF) instrument. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2007 article

Carbohydrate Analysis by Desorption Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Bereman, M. S., Williams, T. I., & Muddiman, D. C. (2007, October 6). Analytical Chemistry, Vol. 11, pp. 8812–8815.

By: M. Bereman n, T. Williams n  & D. Muddiman n 

Contributors: M. Bereman n, T. Williams n  & D. Muddiman n 

MeSH headings : Carbohydrates / analysis; Cyclotrons; Fourier Analysis; Spectrometry, Mass, Electrospray Ionization / methods
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Analytical Chemistry and Chromatography; Metabolomics and Mass Spectrometry Studies
TL;DR: G glycans from mucin are identified by using the high mass measurement accuracy and tandem MS capabilities afforded by the hybrid FT-ICR-MS platform. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018

2007 article

Detection of Attomole Amounts of Analyte by Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) Determined Using Fluorescence Spectroscopy

Bereman, M. S., & Muddiman, D. C. (2007, March 22). Journal of the American Society for Mass Spectrometry, Vol. 18, pp. 1093–1096.

By: M. Bereman n & D. Muddiman n 

MeSH headings : Microchemistry / methods; Nanotechnology / methods; Rhodamines / chemistry; Spectrometry, Fluorescence / methods; Spectrometry, Mass, Electrospray Ionization / methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Analytical Chemistry and Chromatography; Analytical chemistry methods development
TL;DR: The use of fluorescence spectroscopy is reported to investigate the amount of material removed from a PTFE surface and detected during desorption electrospray ionization (DESI) mass spectrometry measurements. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2007 article

Remote mass spectrometric sampling of electrospray- and desorption electrospra-generated ions using an air ejector

Journal of the American Society for Mass Spectrometry, Vol. 18, pp. 1844–1847.

By: R. Dixon, M. Bereman, D. Muddiman  & A. Hawkridge

topics (OpenAlex):
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018

2007 journal article

Remote mass spectrometric sampling of electrospray- and desorption electrospray-generated ions using an air ejector

Journal of the American Society for Mass Spectrometry, 18(10), 1844–1847.

By: R. Dixon n, M. Bereman n, D. Muddiman n  & A. Hawkridge  n

MeSH headings : Air; Environmental Monitoring / instrumentation; Equipment Design; Equipment Failure Analysis; Flow Injection Analysis / instrumentation; Flow Injection Analysis / methods; Rheology / instrumentation; Rheology / methods; Robotics / instrumentation; Specimen Handling / instrumentation; Spectrometry, Mass, Electrospray Ionization / instrumentation; Spectrometry, Mass, Electrospray Ionization / methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / instrumentation
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Analytical Chemistry and Chromatography; Microfluidic and Capillary Electrophoresis Applications
TL;DR: This work demonstrates the remote analysis of a series of analyte ions that range from small molecules and polymers to polypeptides using the AE-LTQ interface and presents preliminary mass spectrometric data. (via Semantic Scholar)
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Sources: Crossref, NC State University Libraries
Added: February 24, 2020

2006 journal article

Direct high-resolution peptide and protein analysis by desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Rapid Communications in Mass Spectrometry, 20(22), 3409–3411.

By: M. Bereman n, L. Nyadong *, F. Fernandez * & D. Muddiman n 

MeSH headings : Bradykinin / analysis; Formates / analysis; Glucagon / analysis; Insulin / analysis; Melitten / analysis; Peptides / analysis; Proteins / analysis; Spectrometry, Mass, Electrospray Ionization / methods; Spectroscopy, Fourier Transform Infrared; Vasodilator Agents / analysis
topics (OpenAlex): Mass Spectrometry Techniques and Applications; Advanced Proteomics Techniques and Applications; Analytical Chemistry and Chromatography
TL;DR: The first coupling of a desorption electrospray ionization (DESI) ion source to Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) for high-resolution protein analysis is reported. (via Semantic Scholar)
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Sources: Crossref, Web Of Science, NC State University Libraries
Added: August 6, 2018

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