scholarly journals A generic normalization method for proper quantification in untargeted proteomics screening

2018 ◽  
Author(s):  
Sandra Isabel Anjo ◽  
Isaura Simões ◽  
Pedro Castanheira ◽  
Mário Grãos ◽  
Bruno Manadas

ABSTRACTThe label-free quantitative mass spectrometry methods, in particular, the SWATH-MS approach, have gained popularity and became a powerful technique for comparison of large datasets. In the present work, it is introduced the use of recombinant proteins as internal standards for untargeted label-free methods. The proposed internal standard strategy reveals a similar intragroup normalization capacity when compared with the most common normalization methods, with the additional advantage of maintaining the overall proteome changes between groups (which are lost using other methods). Therefore, the proposed strategy is able to maintain a good performance even when large qualitative and quantitative differences in sample composition are observed, such as the ones induced by biological regulation (as observed in secretome and other biofluids’ analyses) or by enrichment approaches (such as immunopurifications). Moreover, this approach corresponds to a cost-effective alternative, easier to implement than the current stable-isotope labeling internal standards, therefore being an appealing strategy for large quantitative screening, as clinical cohorts for biomarker discovery.

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 26 ◽  
Author(s):  
Kayla Borland ◽  
Jan Diesend ◽  
Taku Ito-Kureha ◽  
Vigo Heissmeyer ◽  
Christian Hammann ◽  
...  

Post-transcriptional RNA modifications have been found to be present in a wide variety of organisms and in different types of RNA. Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. In addition, the abundance of modified nucleosides fluctuates based on growth phase, external stress, or possibly other factors not yet explored. With modifications ever changing, a method to determine absolute quantities for multiple nucleoside modifications is required. Here, we report metabolic isotope labeling to produce isotopically labeled internal standards in bacteria and yeast. These can be used for the quantification of 26 different modified nucleosides. We explain in detail how these internal standards are produced and show their mass spectrometric characterization. We apply our internal standards and quantify the modification content of transfer RNA (tRNA) from bacteria and various eukaryotes. We can show that the origin of the internal standard has no impact on the quantification result. Furthermore, we use our internal standard for the quantification of modified nucleosides in mouse tissue messenger RNA (mRNA), where we find different modification profiles in liver and brain tissue.


Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 967-967
Author(s):  
Xionghao Lin ◽  
Santosh L. Saraf ◽  
Simran Soni ◽  
Nowah Kokou Apeadoufia Afangbedji ◽  
Victor R. Gordeuk ◽  
...  

Abstract BACKGROUND: Chronic kidney disease (CKD) is common in patients with sickle cell disease (SCD). However, the progression of CKD in SCD and factors associated with such progression remain poorly defined. Liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics has become a highly potent method for biomarker discovery due to growing capabilities for broad proteome coverage and good accuracy and precision in quantification. OBJECTIVES: The purpose of this study was to identify the potential markers associated with CKD progression in patients with SCD using quantitative proteomics. METHODS: Urine samples were collected from healthy controls and SCD patients with different CKD stages from University of Illinois at Chicago (UIC). Mass-spectrometry analysis was performed on an LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific) coupled to a Prominence Nano LC (Shimadzu) using the Xcalibur version 2.7.0 (Thermo Scientific). Proteome Discoverer 1.4 and SIEVE 2.1 programs were used for protein identification and label-free quantification. Heavy isotope labeled peptide EDQTSPAPGLR(13C6, 15N) was used as an internal standard for high resolution/selected ion monitoring (HR/SIM) analysis of HGFL. Urinary HGFL protein together wiht creatinine and albumin were also measured by ELISA. RESULTS: Since glomerular hyperfiltration is an early stage of renal dysfunction. We performed label-free quantitative proteomic analysis for urine samples collected from SCD patients with hyperfiltration (N=3) and normal (N=3). Hepatocyte growth factor-like (HGFL) protein was found to be significantly downregulated (5.52-fold, p=8.05 × 10-5) in samples with glomerular hyperfiltration compared to normal group. Next, we developed a high resolution/selected ion monitoring (HR/SIM) method by measuring the HGFL peptide (m/z 585.79) with isotope labeled-HGFL peptide (m/z 590.80) as internal standard (IS). HR/SIM quantification was performed for 19 urine samples from SCD patients and 12 urine samples from healthy controls. HGFL levels were found to be significantly downregulated (p=0.0084) in the SCD urine samples compared to samples from healthy controls (Figure 1). To further assess the correlation between HGFL level and CDK stage, we expanded the analysis to SCD patients with different CKD stage ranging from 0 to 5 and 19 healthy individuals by ELISA. The result confirmed the finding of HR/SIM quantification, moreover, showed that urinary HGFL level highly correlated with CKD stage (r= ̶ 0.4106, p=0.002, Figure 1) and showed high sensitivity and specificity by Receiver Operating Characteristic (ROC) curve analysis (AUC=0.78). CONCLUSIONS: HGFL protein has been identified as a negative regulator of phosphatidylinositol 3-kinase (PI3K), and PI3K/Akt pathway was found to be activated in the progress of CKD. Therefore, the decrease of HGFL level in urines from SCD patients may indicate the development of CKD. Combination of LC-MS based quantitative proteomics and ELISA validation is an useful approach for biomarker discovery. ACKNOWLEDGMENTS: This work was supported by NIH Research Grants 1P50HL118006, 1R01HL125005, 5G12MD007597 and K23HL125984. The content is solely the responsibility of the authors and does not necessarily represent the official view of NHLBI, NIMHD or NIH. Disclosures Gordeuk: Emmaus Life Sciences: Consultancy.


2020 ◽  
pp. 1192-1198
Author(s):  
M.S. Mohammad ◽  
Tibebe Tesfaye ◽  
Kim Ki-Seong

Ultrasonic thickness gauges are easy to operate and reliable, and can be used to measure a wide range of thicknesses and inspect all engineering materials. Supplementing the simple ultrasonic thickness gauges that present results in either a digital readout or as an A-scan with systems that enable correlating the measured values to their positions on the inspected surface to produce a two-dimensional (2D) thickness representation can extend their benefits and provide a cost-effective alternative to expensive advanced C-scan machines. In previous work, the authors introduced a system for the positioning and mapping of the values measured by the ultrasonic thickness gauges and flaw detectors (Tesfaye et al. 2019). The system is an alternative to the systems that use mechanical scanners, encoders, and sophisticated UT machines. It used a camera to record the probe’s movement and a projected laser grid obtained by a laser pattern generator to locate the probe on the inspected surface. In this paper, a novel system is proposed to be applied to flat surfaces, in addition to overcoming the other limitations posed due to the use of the laser projection. The proposed system uses two video cameras, one to monitor the probe’s movement on the inspected surface and the other to capture the corresponding digital readout of the thickness gauge. The acquired images of the probe’s position and thickness gauge readout are processed to plot the measured data in a 2D color-coded map. The system is meant to be simpler and more effective than the previous development.


Alloy Digest ◽  
1980 ◽  
Vol 29 (11) ◽  

Abstract JS777 is a high-alloy, fully austenitic stainless steel developed for applications where corrosive conditions are too severe for the standard grades of stainless steel. It also provides a cost-effective alternative to more expensive nickel-base and titanium-base alloys. It has relatively high resistance to stress-corrosion cracking and to intergranular corrosion. This datasheet provides information on composition, physical properties, hardness, elasticity, and tensile properties. It also includes information on corrosion resistance as well as forming, heat treating, machining, joining, and surface treatment. Filing Code: SS-377. Producer or source: Jessop Steel Company.


Alloy Digest ◽  
2009 ◽  
Vol 58 (11) ◽  

Abstract Ancorsteel 4300 alloy ferrous powder simulates wrought steel compositions and is a cost-effective alternative to alloys requiring secondary processing. This datasheet provides information on composition, physical properties, hardness, and tensile properties as well as fracture toughness. It also includes information on heat treating and powder metal forms. Filing Code: SA-611. Producer or source: Hoeganaes Corporation.


2016 ◽  
Vol 5 (03) ◽  
pp. 4862 ◽  
Author(s):  
Mathew George* ◽  
Lincy Joseph ◽  
Arpit Kumar Jain ◽  
Anju V.

A simple, sensitive, rapid and economic high performance thin layer chromatographic method and a mass spectroscopic assay method has been developed for the quantification of telmisartan and hydrochlorthiazide combination in human plasma. The internal standards and analytes were extracted from human plasma by solid-phase extraction with HLB Oasis1cc (30mg) catridges. The scanning and optimization for the samples are done using methanol: water (50:50). The samples were chromatographed using reverse phase chromatography with C-18 column of different manufacturers like Ascentis C18 (150×4. 6, 5µ) using the buffer system Acetonitrile: Buffer (80:20%v/v) which consist of 2±0. 1Mm ammonium format at a flow rate of 0. 7ml/min at a column oven temperature 35±10c. The internal standard used was hydrochlorthiazide13c1, d2 and telmisartand3. The extraction techniques include conditioning, loading, washing and elution, drying followed by reconstitution of the dried samples. The volume injected was 10µl with the retention time of 3-4 min for telmisartan, 1-2 min for hydrochlorthiazide and for the internal standards the retention time was 3-4 min for telmisartand3 and 1-2 min for hydrochlorthiazide c13d2. The rinsing solution was Acetonitrile: HPLC grade water in the ratio (50:50). The above developed method was validated using various parameters like selectivity and sensitivity, accuracy and precision, matrix effects, % recovery and various stability studies. The method was proved to be sensitive, accurate, precise and reproducible. The preparation showed high recovery for the quantitative determination of telmisartan and hydrochlorthiazide in human plasma.


2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 119-120
Author(s):  
N. Østerås ◽  
E. Aas ◽  
T. Moseng ◽  
L. Van Bodegom-Vos ◽  
K. Dziedzic ◽  
...  

Background:To improve quality of care for patients with hip and knee osteoarthritis (OA), a structured model for integrated OA care was developed based on international treatment recommendations. A previous analysis of a cluster RCT (cRCT) showed that compared to usual care, the intervention group reported higher quality of care and greater satisfaction with care. Also, more patients were treated according to international guidelines and fulfilled recommendations for physical activity at the 6-month follow-up.Objectives:To assess the cost-utility of a structured model for hip or knee OA care.Methods:A cRCT with stepped-wedge cohort design was conducted in 6 Norwegian municipalities (clusters) in 2015-17. The OA care model was implemented in one cluster at the time by switching from “usual care” to the structured model. The implementation of the model was facilitated by interactive workshops for general practitioners (GPs) and physiotherapists (PTs) with an update on OA treatment recommendations. The GPs explained the OA diagnosis and treatment alternatives, provided pharmacological treatment when appropriate, and suggested referral to physiotherapy. The PT-led patient OA education programme was group-based and lasted 3 hours followed by an 8–12-week individually tailored resistance exercise programme with twice weekly 1-hour supervised group sessions (5–10 patients per PT). An optional 10-hours Healthy Eating Program was available. Participants were ≥45 years with symptomatic hip or knee OA.Costs were measured from the healthcare perspective and collected from several sources. Patients self-reported visits in primary healthcare at 3, 6, 9 and 12 months. Secondary healthcare visits and joint surgery data were extracted from the Norwegian Patient Register. The health outcome, quality-adjusted life-year (QALY), was estimated based on the EQ-5D-5L scores at baseline, 3, 6, 9 and 12 months. The result of the cost-utility analysis was reported using the incremental cost-effectiveness ratio (ICER), defined as the incremental costs relative to incremental QALYs (QALYs gained). Based on Norwegian guidelines, the threshold is €27500. Sensitivity analyses were performed using bootstrapping to assess the robustness of reported results and presented in a cost-effectiveness plane (Figure 1).Results:The 393 patients’ mean age was 63 years (SD 9.6) and 74% were women. 109 patients were recruited during control periods (control group), and 284 patients were recruited during interventions periods (intervention group). Only the intervention group had a significant increase in EQ-5D-5L utility scores from baseline to 12 months follow-up (mean change 0.03; 95% CI 0.01, 0.05) with QALYs gained: 0.02 (95% CI -0.08, 0.12). The structured OA model cost approx. €301 p.p. with an additional €50 for the Healthy Eating Program. Total 12 months healthcare cost p.p. was €1281 in the intervention and €3147 in the control group, resulting in an incremental cost of -€1866 (95% CI -3147, -584) p.p. Costs related to surgical procedures had the largest impact on total healthcare costs in both groups. During the 12-months follow-up period, 5% (n=14) in the intervention compared to 12% (n=13) in the control group underwent joint surgery; resulting in a mean surgical procedure cost of €553 p.p. in the intervention as compared to €1624 p.p. in the control group. The ICER was -€93300, indicating that the OA care model resulted in QALYs gained and cost-savings. At a threshold of €27500, it is 99% likely that the OA care model is a cost-effective alternative.Conclusion:The results of the cost-utility analysis show that implementing a structured model for OA care in primary healthcare based on international guidelines is highly likely a cost-effective alternative compared to usual care for people with hip and knee OA. More studies are needed to confirm this finding, but this study results indicate that implementing structured OA care models in primary healthcare may be beneficial for the individual as well as for the society.Disclosure of Interests:None declared


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Muhammad Ashar Naveed ◽  
Muhammad Afnan Ansari ◽  
Inki Kim ◽  
Trevon Badloe ◽  
Joohoon Kim ◽  
...  

AbstractHelicity-multiplexed metasurfaces based on symmetric spin–orbit interactions (SOIs) have practical limits because they cannot provide central-symmetric holographic imaging. Asymmetric SOIs can effectively address such limitations, with several exciting applications in various fields ranging from asymmetric data inscription in communications to dual side displays in smart mobile devices. Low-loss dielectric materials provide an excellent platform for realizing such exotic phenomena efficiently. In this paper, we demonstrate an asymmetric SOI-dependent transmission-type metasurface in the visible domain using hydrogenated amorphous silicon (a-Si:H) nanoresonators. The proposed design approach is equipped with an additional degree of freedom in designing bi-directional helicity-multiplexed metasurfaces by breaking the conventional limit imposed by the symmetric SOI in half employment of metasurfaces for one circular handedness. Two on-axis, distinct wavefronts are produced with high transmission efficiencies, demonstrating the concept of asymmetric wavefront generation in two antiparallel directions. Additionally, the CMOS compatibility of a-Si:H makes it a cost-effective alternative to gallium nitride (GaN) and titanium dioxide (TiO2) for visible light. The cost-effective fabrication and simplicity of the proposed design technique provide an excellent candidate for high-efficiency, multifunctional, and chip-integrated demonstration of various phenomena.


HPB ◽  
2020 ◽  
Vol 22 ◽  
pp. S186-S187
Author(s):  
J. Hawksworth ◽  
N.P. Llore ◽  
M.L. Holzner ◽  
P. Radkani ◽  
E. Mesler ◽  
...  

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