Browsing by Subject "Tandem mass spectrometry"

Now showing 1 - 6 of 6
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    A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer's disease
    (Springer Nature, 2023-04-14) Merrihew, Gennifer E.; Park, Jea; Plubell, Deanna; Searle, Brian C.; Keene, C. Dirk; Larson, Eric B.; Bateman, Randall; Perrin, Richard J.; Chhatwal, Jasmeer P.; Farlow, Martin R.; McLean, Catriona A.; Ghetti, Bernardino; Newell, Kathy L.; Frosch, Matthew P.; Montine, Thomas J.; MacCoss, Michael J.; Neurology, School of Medicine
    Alzheimer's disease (AD) is a looming public health disaster with limited interventions. Alzheimer's is a complex disease that can present with or without causative mutations and can be accompanied by a range of age-related comorbidities. This diverse presentation makes it difficult to study molecular changes specific to AD. To better understand the molecular signatures of disease we constructed a unique human brain sample cohort inclusive of autosomal dominant AD dementia (ADD), sporadic ADD, and those without dementia but with high AD histopathologic burden, and cognitively normal individuals with no/minimal AD histopathologic burden. All samples are clinically well characterized, and brain tissue was preserved postmortem by rapid autopsy. Samples from four brain regions were processed and analyzed by data-independent acquisition LC-MS/MS. Here we present a high-quality quantitative dataset at the peptide and protein level for each brain region. Multiple internal and external control strategies were included in this experiment to ensure data quality. All data are deposited in the ProteomeXchange repositories and available from each step of our processing.
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    dbRUSP: An Interactive Database to Investigate Inborn Metabolic Differences for Improved Genetic Disease Screening
    (MDPI, 2022-08-29) Peng, Gang; Zhang, Yunxuan; Zhao, Hongyu; Scharfe, Curt; Medical and Molecular Genetics, School of Medicine
    The Recommended Uniform Screening Panel (RUSP) contains more than forty metabolic disorders recommended for inclusion in universal newborn screening (NBS). Tandem-mass-spectrometry-based screening of metabolic analytes in dried blood spot samples identifies most affected newborns, along with a number of false positive results. Due to their influence on blood metabolite levels, continuous and categorical covariates such as gestational age, birth weight, age at blood collection, sex, parent-reported ethnicity, and parenteral nutrition status have been shown to reduce the accuracy of screening. Here, we developed a database and web-based tools (dbRUSP) for the analysis of 41 NBS metabolites and six variables for a cohort of 500,539 screen-negative newborns reported by the California NBS program. The interactive database, built using the R shiny package, contains separate modules to study the influence of single variables and joint effects of multiple variables on metabolite levels. Users can input an individual's variables to obtain metabolite level reference ranges and utilize dbRUSP to select new candidate markers for the detection of metabolic conditions. The open-source format facilitates the development of data mining algorithms that incorporate the influence of covariates on metabolism to increase accuracy in genetic disease screening.
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    Harmonization of Newborn Screening Results for Pompe Disease and Mucopolysaccharidosis Type I
    (MDPI, 2023-02-27) Dorley, M. Christine; Dizikes, George J.; Pickens, Charles Austin; Cuthbert, Carla; Basheeruddin, Khaja; Gulamali-Majid, Fizza; Hetterich, Paul; Hietala, Amy; Kelsey, Ashley; Klug, Tracy; Lesko, Barbara; Mills, Michelle; Moloney, Shawn; Neogi, Partha; Orsini, Joseph; Singer, Douglas; Petritis, Konstantinos; Pathology and Laboratory Medicine, School of Medicine
    In newborn screening, false-negative results can be disastrous, leading to disability and death, while false-positive results contribute to parental anxiety and unnecessary follow-ups. Cutoffs are set conservatively to prevent missed cases for Pompe and MPS I, resulting in increased falsepositive results and lower positive predictive values. Harmonization has been proposed as a way to minimize false-negative and false-positive results and correct for method differences, so we harmonized enzyme activities for Pompe and MPS I across laboratories and testing methods (Tandem Mass Spectrometry (MS/MS) or Digital Microfluidics (DMF)). Participating states analyzed proofof- concept calibrators, blanks, and contrived specimens and reported enzyme activities, cutoffs, and other testing parameters to Tennessee. Regression and multiples of the median were used to harmonize the data. We observed varied cutoffs and results. Six of seven MS/MS labs reported enzyme activities for one specimen for MPS I marginally above their respective cutoffs with results classified as negative, whereas all DMF labs reported this specimen’s enzyme activity below their respective cutoffs with results classified as positive. Reasonable agreement in enzyme activities and cutoffs was achieved with harmonization; however, harmonization does not change how a value would be reported as this is dependent on the placement of cutoffs.
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    Oxylipins in Breast Implant–Associated Systemic Symptoms
    (Oxford University Press, 2024) Khan, Imran; Timsina, Lava; Chauhan, Ruvi; Ingersol, Christopher; Wang, David R.; Rinne, Ethan; Muraru, Rodica; Mohan, Ganesh; Minto, Robert E.; Van Natta, Bruce W.; Hassanein, Aladdin H.; Kelley-Patteson, Christine; Sinha, Mithun; Surgery, School of Medicine
    Background: A subset of females with breast implants have reported a myriad of nonspecific systemic symptoms collectively termed systemic symptoms associated with breast implants (SSBI). SSBI symptoms are similar to manifestations associated with autoimmune and connective tissue disorders. Breast tissue is rich in adipose cells, comprised of lipids. Insertion of an implant creates an oxidative environment leading to lipid oxidation. Oxylipins can influence immune responses and inflammatory processes. Objectives: In this study we explored the abundance of a spectrum of oxylipins in the periprosthetic tissue surrounding the breast implant. Because oxylipins are immunogenic, we sought to determine if they were associated with the SSBI patients. We have also attempted to determine if the common manifestations exhibited by such patients have any association with oxylipin abundance. Methods: The study included 120 patients divided into 3 cohorts. We analyzed 46 patients with breast implants exhibiting manifestations associated with SSBI; 29 patients with breast implants not exhibiting manifestations associated with SSBI (control cohort I, non-SSBI); and 45 patients without implants (control cohort II, no-implant tissue). Lipid extraction and oxylipin quantification were performed with liquid chromatography mass spectrometry (LC-MS/MS). LC-MS/MS targeted analysis of the breast adipose tissue was performed. Results: Of the 15 oxylipins analyzed, 5 exhibited increased abundance in the SSBI cohort when compared to the non-SSBI and no-implant cohorts. Conclusions: The study documents the association of the oxylipins with each manifestation reported by the patient. This study provides an objective assessment of the subjective questionnaire, highlighting which symptoms may be more relevant than the others.
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    Rapid measurement of tacrolimus in whole blood by paper spray-tandem mass spectrometry (PS-MS/MS)
    (Elsevier, 2015-02) Shi, Run-Zhang; El Gierari, El Taher M.; Manicke, Nicholas E.; Faix, James D.; Department of Chemistry & Chemical Biology, IU School of Science
    Background Liquid chromatography-tandem mass spectrometry (LC-MS/MS) provides sensitivity and specificity for monitoring tacrolimus drug level in blood, but it requires an LC system and sample preparation, which is not amenable to random access testing typical of immunoassays. Paper spray (PS) ionization generates gas phase analyte ions directly from dried blood spots without sample preparation and LC. We evaluated a PS-MS/MS method for tacrolimus drug monitoring in a clinical diagnostic laboratory. Methods Whole blood sample was mixed with stable isotope labeled internal standard ([13C, 2H2]-FK506) and spotted onto a cartridge containing triangular shaped card paper. After drying, samples were analyzed by PS MS/MS in the selected reaction monitoring (SRM) mode, with a run time of 3 min/sample. Results Analytical measurement range was 1.5–30 ng/ml. Assay inter-day imprecision was 13%, 8%, and 5% at tacrolimus concentrations of 4.5, 10.5, and 24.5 ng/ml, respectively. Accuracy was determined by pure tacrolimus solution and was confirmed by result correlation to an immunoassay (slope = 1.0, intercept = − 0.02; r2 = 0.99), and to a conventional LC-MS/MS method (slope = 0.90, intercept = 0.4; r2 = 0.94). Conclusions PS-MS/MS provides accurate results for tacrolimus with rapid turnaround time amenable to random access testing protocols.
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    The role of solvation on the conformational landscape of α-synuclein
    (Royal Society of Chemistry, 2023-12-18) Cheung See Kit, Melanie; Cropley, Tyler C.; Bleiholder, Christian; Chouinard, Christopher D.; Sobott, Frank; Webb, Ian K.; Chemistry and Chemical Biology, School of Science
    Native ion mobility mass spectrometry has been used extensively to characterize ensembles of intrinsically disordered protein (IDP) conformers, but the extent to which the gaseous measurements provide realistic pictures of the solution conformations for such flexible proteins remains unclear. Therefore, we systematically studied the relationship between the solution and gaseous structural ensembles by measuring electrospray charge state and collision cross section (CCS) distributions for cationic and anionic forms of α-synuclein (αSN), an anionic protein in solution, as well as directly probed gas phase residue to residue distances via ion/ion reactions between gaseous α-synuclein cations and disulfonic acid linkers that form strong electrostatic bonds. We also combined results from in-solution protein crosslinking identified from native tandem mass spectrometry (MS/MS) with an initial αSN ensemble generated computationally by IDPConformerGenerator to generate an experimentally restrained solution ensemble of αSN. CCS distributions were directly calculated for the solution ensembles determined by NMR and compared to predicted gaseous conformers. While charge state and collision cross section distributions are useful for qualitatively describing the relative structural dynamics of proteins and major conformational changes induced by changes to solution states, the predicted and measured gas phase conformers include subpopulations that are significantly different than those expected from completely "freezing" solution conformations and preserving them in the gas phase. However, insights were gained on the various roles of solvent in stabilizing various conformers for extremely dynamic proteins like α-synuclein.