A5007273329- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Analytical Chemistry and Chromatography
- Biotin and Related Studies
- Amyotrophic Lateral Sclerosis Research
- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- RNA Research and Splicing
- Insect symbiosis and bacterial influences
- Nanoparticles: synthesis and applications
- Bioinformatics and Genomic Networks
- Birth, Development, and Health
- Carbohydrate Chemistry and Synthesis
- Graphene and Nanomaterials Applications
- Ubiquitin and proteasome pathways
- Alzheimer's disease research and treatments
- Plant Virus Research Studies
- Insect-Plant Interactions and Control
- Neurogenetic and Muscular Disorders Research
- Advanced Biosensing Techniques and Applications
- Spinal Cord Injury Research
- Advanced Chemical Sensor Technologies
- RNA modifications and cancer
North Carolina State University
2014-2024
Duke University Hospital
2022
Duke Medical Center
2022
University of Washington
2011-2017
Seattle University
2013
Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need improved label-free approaches. This is particularly pressing workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as tags relative absolute quantitation tandem mass may prove problematic or stable isotope with amino acids cell culture cannot be readily applied. Skyline freely available, open source software tool data...
Abstract Background Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The command, implemented as part the Crux software toolkit, implements four previously reported spectral methods, index (SI N ), exponentially modified protein abundance (emPAI), normalized factor (NSAF), and distributed (dNSAF). Results We compared reproducibility linearity relative to each protein’s metrics. Our...
TDP-43 pathology marks a spectrum of multisystem proteinopathies including amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and sporadic inclusion body myositis. Surprisingly, it has been challenging to recapitulate this pathology, highlighting an incomplete understanding regulatory mechanisms. Here we provide evidence supporting acetylation as trigger for disease pathology. Using cultured cells mouse skeletal muscle, show that acetylation-mimics promote phosphorylation...
Reversed-phase liquid chromatography is the most commonly used separation method for shotgun proteomics. Nanoflow has emerged as preferred its increased sensitivity and separation. Despite common use, there are a wide range of parameters conditions across research groups. These have an effect on quality chromatographic separation, which critical to maximizing number peptide identifications minimizing ion suppression. Here we examined relationship between column lengths, gradient...
We report the development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments. LC–MS/MS runs are automatically imported into Skyline and multiple identification-free metrics extracted from targeted peptides. These data then uploaded Panorama document repository where can be viewed web-based interface using powerful process control techniques, including Levey–Jennings Pareto plots. The is versatile takes user input, which allows significant over...
A thorough evaluation of the quality, reproducibility, and variability bottom-up proteomics data is necessary at every stage a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures assess sample preparation, system function, quantitative System suitability samples are repeatedly measured longitudinally with targeted methods, we examples where they used on three instrument platforms identify severe failures track function over months years....
We report the first coupling of a desorption electrospray ionization (DESI) ion source to Fourier transform cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) for high-resolution protein analysis. The DESI FT-ICR-MS design is described in detail along with preliminary data obtained on peptides and proteins ranging from 1 5.7 kDa.
We report the development of split-less nano-flow liquid chromatography mass spectrometric analysis glycans chemically cleaved from glycoproteins in plasma. Porous graphitized carbon operating under reverse-phase conditions and an amide-based stationary phase hydrophilic interaction are quantitatively compared for glycan separation. Both phases demonstrated similar column efficiencies excellent retention time reproducibility without internal standard to correct shift. The 95% confidence...
Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification genes proteins mediating transmission is critical to develop agriculturally sustainable management practices understand viral strategies for circulative movement in all insect Two cyclophilin B proteins, S28 S29, were identified previously populations Schizaphis graminum that differed their ability transmit RPV strain Cereal yellow...
A thorough evaluation of the quality, reproducibility, and variability bottom-up proteomics data is necessary at every stage a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures assess sample preparation, system function, quantitative System suitability samples are repeatedly measured longitudinally with targeted methods, we examples where they used on three instrument platforms identify severe failures track function over months years....
Filter-aided sample preparation (FASP) and a new method using modified commercial SDS removal spin column are quantitatively compared in terms of their performance for shotgun proteomic experiments three complex samples: Saccharomyces cerevisiae lysate (insoluble fraction), Caenorhabditis elegans (soluble human embryonic kidney cell line (HEK293T). The characteristics total number peptides proteins identified between the two procedures. procedure affords conservative fourfold improvement...
Novel tags are used to increase the hydrophobicity of glycans and impart a permanent charge yielding as great approximately 5-fold in electrospray response from both standard complex mixture.
Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification assignable causes variation any creates products, services, or information. A tool has been developed termed Process Control Proteomics (SProCoP) which implements aspects SPC (e.g., charts Pareto analysis) into Skyline proteomics software. It monitors five quality metrics shotgun targeted proteomic workflow. None these require peptide identification. The source code,...
Abstract We use shotgun proteomics to identify biomarkers of diagnostic and prognostic value in individuals diagnosed with amyotrophic lateral sclerosis. Matched cerebrospinal plasma fluids were subjected abundant protein depletion analyzed by nano-flow liquid chromatography high resolution tandem mass spectrometry. Label free quantitation was used differential proteins between ALS (n = 33) healthy controls 30) both fluids. In CSF, 118 (p-value < 0.05) 27 (q-value identified as...
We report the use of fluorescence spectroscopy to investigate amount material removed from a PTFE surface and detected during desorption electrospray ionization (DESI) mass spectrometry measurements. The intensity before after DESI analysis rhodamine 6G is used determine per spectrum. Calculations indicate low attomole amounts are linear ion trap
The goal of this study is to investigate the molecular pathways perturbed by in vitro exposure beta-methylamino-L-alanine (BMAA) NSC-34 cells via contemporary proteomics. Our analysis differentially regulated proteins reveals significant enrichment (p < 0.01) related ER stress, protein ubiquitination, unfolded response, and mitochondrial dysfunction. Upstream regulator indicates that BMAA induces activation transcription factors (X-box binding 1; nuclear factor 2 erythroid like 2;...
Exposure to toxins produced by cyanobacteria (ie, cyanotoxins) is an emerging health concern due their increasing prevalence and previous associations with neurodegenerative diseases including amyotrophic lateral sclerosis. The objective of this study was evaluate the neurotoxic effects a mixture two co-occurring cyanotoxins, β-methylamino-l-alanine (BMAA) microcystin leucine arginine (MCLR), using larval zebrafish model. We combined high-throughput behavior-based toxicity assays discovery...
Exposure to cyanotoxins has been linked neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer's, and Parkinson's disease. While the cyanotoxin β-methylamino-L-alanine (BMAA) received much attention, cyanobacteria produce many cyanotoxic compounds, several of which have detected in nature alongside BMAA, 2,4-diaminobutyric acid (2,4-DAB) N-(2-aminoethyl)glycine (AEG). Thus, question whether 2,4-DAB AEG also cause neurotoxic effects vivo is great interest, as they...
Recent investigations continue to emphasize the importance of glycosylation in various diseases including cancer. In this work, we present a step-by-step protocol describing method for N-linked glycan profiling plasma glycoproteins by nanoflow liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (FTICR−MS). A large experimental space was initially explored and is described herein. Three internal standards were spiked into sample provided normalization abundance...
Circulative transmission of viruses in the Luteoviridae, such as cereal yellow dwarf virus (CYDV), requires a series precisely orchestrated interactions between virus, plant, and aphid proteins. Natural selection has favored these to be retained phloem facilitate acquisition by aphids. We show that treatment infected oat tissue homogenate with sodium sulfite reduces purified Transmission electron microscopy data indicated no gross change virion morphology due treatments. However, treated...
We report the use of desorption electrospray ionization hybrid Fourier transform ion cyclotron resonance mass spectrometry (DESI-FT-ICR-MS) for analysis carbohydrates. Spectra neat carbohydrates are presented along with their measurement accuracies and limits detection. Furthermore, a comparison is made between analyses O-linked glycans from mucin by DESI-FT-ICR-MS matrix-assisted laser desorption/ionization spectrometry. Finally, identified using high accuracy tandem MS capabilities...
Selected Reaction Monitoring (SRM) is a powerful tool for targeted detection and quantification of peptides in complex matrices. An important objective SRM to obtain peptide quantifications that are (1) suitable the investigation, (2) reproducible across laboratories runs. The first achieved by system suitability tests (SST), which verify mass spectrometric instrumentation performs as specified. second quality control (QC), provides in-process assurance sample profile. A common aspect SST QC...