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Ferreira, Christina R., Karen E. Yannell, Brit Mollenhauer, et al. "Chemical profiling of cerebrospinal fluid by multiple reaction monitoring mass spectrometry." Analyst 141, no. 18 (2016): 5252–55. http://dx.doi.org/10.1039/c6an01618a.
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Hoofnagle, Andrew N., Jessica O. Becker, Michael N. Oda, Giorgio Cavigiolio, Philip Mayer, and Tomas Vaisar. "Multiple-Reaction Monitoring–Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures." Clinical Chemistry 58, no. 4 (2012): 777–81. http://dx.doi.org/10.1373/clinchem.2011.173856.
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Abstract BACKGROUND Mass spectrometric assays could potentially replace protein immunoassays in many applications. Previous studies have demonstrated the utility of liquid chromatography–multiple-reaction monitoring–mass spectrometry (LC-MRM/MS) for the quantification of proteins in biological samples, and many examples of the accuracy of these approaches to quantify supplemented analytes have been reported. However, a direct comparison of multiplexed assays that use LC-MRM/MS with established immunoassays to measure endogenous proteins has not been reported. METHODS We purified HDL from the plasma of 30 human donors and used label-free shotgun proteomics approaches to analyze each sample. We then developed 2 different isotope-dilution LC-MRM/MS 6-plex assays (for apoliporoteins A-I, C-II, C-III, E, B, and J): 1 assay used stable isotope-labeled peptides and the other used stable isotope-labeled apolipoprotein A-I (an abundant HDL protein) as an internal standard to control for matrix effects and mass spectrometer performance. The shotgun and LC-MRM/MS assays were then compared with commercially available immunoassays for each of the 6 analytes. RESULTS Relative quantification by shotgun proteomics approaches correlated poorly with the 6 protein immunoassays. In contrast, the isotope dilution LC-MRM/MS approaches showed correlations with immunoassays of r = 0.61–0.96. The LC-MRM/MS approaches had acceptable reproducibility (<13% CV) and linearity (r ≥0.99). Strikingly, a single protein internal standard applied to all proteins performed as well as multiple protein-specific peptide internal standards. CONCLUSIONS Because peak area ratios measured in multiplexed LC-MRM/MS assays correlate well with immunochemical measurements and have acceptable operating characteristics, we propose that LC-MRM/MS could be used to replace immunoassays in a variety of settings.
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Gaither, Claudia, Robert Popp, Yassene Mohammed, and Christoph H. Borchers. "Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry." Analyst 145, no. 10 (2020): 3634–44. http://dx.doi.org/10.1039/c9an01893j.
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Kim, Hyunsoo, Areum Sohn, Injoon Yeo, Su Jong Yu, Jung-Hwan Yoon, and Youngsoo Kim. "Clinical Assay for AFP-L3 by Using Multiple Reaction Monitoring–Mass Spectrometry for Diagnosing Hepatocellular Carcinoma." Clinical Chemistry 64, no. 8 (2018): 1230–38. http://dx.doi.org/10.1373/clinchem.2018.289702.
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Abstract BACKGROUND Lens culinaris agglutinin-reactive fraction of α-fetoprotein (AFP-L3) is a serum biomarker for hepatocellular carcinoma (HCC). AFP-L3 is typically measured by liquid-phase binding assay (LiBA). However, LiBA does not always reflect AFP-L3 concentrations because of its low analytical sensitivity. Thus, we aimed to develop an analytically sensitive multiple reaction monitoring–mass spectrometry (MRM-MS) assay to quantify AFP-L3 in serum. METHODS The assay entailed the addition of a stable isotope-labeled internal standard protein analog, the enrichment of AFP using a monoclonal antibody, the fractionation of AFP-L3 using L. culinaris agglutinin lectin, deglycosylation, trypsin digestion, online desalting, and MRM-MS analysis. The performance of the MRM-MS assay was compared with that of LiBA in 400 human serum samples (100 chronic hepatitis, 100 liver cirrhosis, and 200 HCC). Integrated multinational guidelines were followed to validate the assay for clinical implementation. RESULTS The lower limit of quantification of the MRM-MS assay (0.051 ng/mL) for AFP-L3 was less than that of LiBA (0.300 ng/mL). Thus, AFP-L3, which was not observed by LiBA in HCC samples (n = 39), was detected by the MRM-MS assay, improving the clinical value of AFP-L3 as a biomarker by switching to a more analytical sensitive platform. The method was validated, meeting all the criteria in integrated multinational guidelines. CONCLUSIONS Because of the lower incidence of false-negative findings, the MRM-MS assay is more suitable than LiBA for early detection of HCC.
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Jin, Jonghwa, Hophil Min, Sang Jin Kim, et al. "Development of Diagnostic Biomarkers for Detecting Diabetic Retinopathy at Early Stages Using Quantitative Proteomics." Journal of Diabetes Research 2016 (2016): 1–22. http://dx.doi.org/10.1155/2016/6571976.
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Diabetic retinopathy (DR) is a common microvascular complication caused by diabetes mellitus (DM) and is a leading cause of vision impairment and loss among adults. Here, we performed a comprehensive proteomic analysis to discover biomarkers for DR. First, to identify biomarker candidates that are specifically expressed in human vitreous, we performed data-mining on both previously published DR-related studies and our experimental data; 96 proteins were then selected. To confirm and validate the selected biomarker candidates, candidates were selected, confirmed, and validated using plasma from diabetic patients without DR (No DR) and diabetics with mild or moderate nonproliferative diabetic retinopathy (Mi or Mo NPDR) using semiquantitative multiple reaction monitoring (SQ-MRM) and stable-isotope dilution multiple reaction monitoring (SID-MRM). Additionally, we performed a multiplex assay using 15 biomarker candidates identified in the SID-MRM analysis, which resulted in merged AUC values of 0.99 (No DR versus Mo NPDR) and 0.93 (No DR versus Mi and Mo NPDR). Although further validation with a larger sample size is needed, the 4-protein marker panel (APO4, C7, CLU, and ITIH2) could represent a useful multibiomarker model for detecting the early stages of DR.
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Musharraf, Syed Ghulam, Muhammad Arif Ahmed, and Noureen Zehra. "Quantification of FAMEs in biodiesel blends of various sources by gas chromatography tandem mass spectrometry." Analytical Methods 7, no. 8 (2015): 3372–78. http://dx.doi.org/10.1039/c5ay00484e.
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Abbatiello, Susan E., D. R. Mani, Hasmik Keshishian, and Steven A. Carr. "Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry." Clinical Chemistry 56, no. 2 (2010): 291–305. http://dx.doi.org/10.1373/clinchem.2009.138420.
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Abstract Background: Multiple reaction monitoring mass spectrometry (MRM-MS) of peptides with stable isotope–labeled internal standards (SISs) is increasingly being used to develop quantitative assays for proteins in complex biological matrices. These assays can be highly precise and quantitative, but the frequent occurrence of interferences requires that MRM-MS data be manually reviewed, a time-intensive process subject to human error. We developed an algorithm that identifies inaccurate transition data based on the presence of interfering signal or inconsistent recovery among replicate samples. Methods: The algorithm objectively evaluates MRM-MS data with 2 orthogonal approaches. First, it compares the relative product ion intensities of the analyte peptide to those of the SIS peptide and uses a t-test to determine if they are significantly different. A CV is then calculated from the ratio of the analyte peak area to the SIS peak area from the sample replicates. Results: The algorithm identified problematic transitions and achieved accuracies of 94%–100%, with a sensitivity and specificity of 83%–100% for correct identification of errant transitions. The algorithm was robust when challenged with multiple types of interferences and problematic transitions. Conclusions: This algorithm for automated detection of inaccurate and imprecise transitions (AuDIT) in MRM-MS data reduces the time required for manual and subjective inspection of data, improves the overall accuracy of data analysis, and is easily implemented into the standard data-analysis work flow. AuDIT currently works with results exported from MRM-MS data-processing software packages and may be implemented as an analysis tool within such software.
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Mindaye, Samuel T., Jelena Spiric, Natalie A. David, Ronald L. Rabin, and Jay E. Slater. "Multiple Reactions Monitoring (MRM) Mass Spectrometry for Absolute Quantification of Allergens in German Cockroach (GCr) Allergen Extracts." Journal of Allergy and Clinical Immunology 139, no. 2 (2017): AB174. http://dx.doi.org/10.1016/j.jaci.2016.12.571.
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Jiang, Qikun, Yan Liu, Yunjie Wang, et al. "Simultaneous determination of entecavir and lamivudine in rat plasma by UPLC-MS/MS and its application to a pharmacokinetic study." RSC Advances 6, no. 75 (2016): 70990–98. http://dx.doi.org/10.1039/c6ra08181a.
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The study's aim is to develop and validate a rapid, selective and sensitive ultra-performance liquid chromatography-tandem mass spectrometry with multiple reaction monitoring (MRM) mode method for the simultaneous determination of entecavir and lamivudine in rat plasma.
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Seo, Chang-Seob, and Mee-Young Lee. "Quality Assessment of Insamyangpye Decoction by Liquid Chromatography Tandem Mass Spectrometry Multiple Reaction Monitoring." Processes 9, no. 5 (2021): 831. http://dx.doi.org/10.3390/pr9050831.
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Insamyangpye decoction (ISYPD) is an oriental herbal prescription used in Korea to treat lung-related diseases such as chronic obstructive pulmonary disease. ISYPD is a complex prescription consisting of 13 herbal medicines, and ISYPD sample was obtained by adding 50 L of distilled water to a mixture (5 kg) of 13 herbal medicines, extracting at 100 °C for 2 h using an electric extractor, and freeze-drying. In this study, an accurate and sensitive liquid chromatography tandem mass spectrometry (LC–MS/MS) method based on multiple reaction monitoring (MRM) was developed and verified for quality assessment of ISYPD using 10 marker components: mulberroside A (1), amygdalin (2), liquiritin apioside (3), naringin (4), poncirin (5), platycodin D (6), ginsenoside Rb1 (7), glycyrrhizin (8), saikosaponin A (9), and schizandrin (10). These marker compounds were separated using an Acquity UPLC BEH C18 column (2.1 mm × 50 mm, 1.7 μm) maintained at 30 °C with a mobile phase elution gradient of acetonitrile in distilled water, both containing 0.1% (v/v) trifluoroacetic acid. Marker components were quantified using the LC–MS/MS MRM method developed and validated, and found at 0.09–7.47 mg/g.
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Agger, Sean A., Luke C. Marney, and Andrew N. Hoofnagle. "Simultaneous Quantification of Apolipoprotein A-I and Apolipoprotein B by Liquid-Chromatography–Multiple- Reaction–Monitoring Mass Spectrometry." Clinical Chemistry 56, no. 12 (2010): 1804–13. http://dx.doi.org/10.1373/clinchem.2010.152264.
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BACKGROUND If liquid-chromatography–multiple-reaction–monitoring mass spectrometry (LC-MRM/MS) could be used in the large-scale preclinical verification of putative biomarkers, it would obviate the need for the development of expensive immunoassays. In addition, the translation of novel biomarkers to clinical use would be accelerated if the assays used in preclinical studies were the same as those used in the clinical laboratory. To validate this approach, we developed a multiplexed assay for the quantification of 2 clinically well-known biomarkers in human plasma, apolipoprotein A-I and apolipoprotein B (apoA-I and apoB). METHODS We used PeptideAtlas to identify candidate peptides. Human samples were denatured with urea or trifluoroethanol, reduced and alkylated, and digested with trypsin. We compared reversed-phase chromatographic separation of peptides with normal flow and microflow, and we normalized endogenous peptide peak areas to internal standard peptides. We evaluated different methods of calibration and compared the final method with a nephelometric immunoassay. RESULTS We developed a final method using trifluoroethanol denaturation, 21-h digestion, normal flow chromatography-electrospray ionization, and calibration with a single normal human plasma sample. For samples injected in duplicate, the method had intraassay CVs <6% and interassay CVs <12% for both proteins, and compared well with immunoassay (n = 47; Deming regression, LC-MRM/MS = 1.17 × immunoassay − 36.6; Sx|y = 10.3 for apoA-I and LC-MRM/MS = 1.21 × immunoassay + 7.0; Sx|y = 7.9 for apoB). CONCLUSIONS Multiplexed quantification of proteins in human plasma/serum by LC-MRM/MS is possible and compares well with clinically useful immunoassays. The potential application of single-point calibration to large clinical studies could simplify efforts to reduce day-to-day digestion variability.
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Gómez, E., F. J. Corrales, M. I. Mora, et al. "146 QUANTIFICATION OF PEPTIDE GROWTH FACTORS IN CATTLE UTERINE FLUID BY MULTIPLE REACTION MONITORING-LIQUID CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY." Reproduction, Fertility and Development 27, no. 1 (2015): 165. http://dx.doi.org/10.1071/rdv27n1ab146.
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Multiple reaction monitoring (MRM) allows targeted quantitative proteomics with a wide dynamic range and limit of detection down to femtomoles. We used MRM to study uterine growth factors (GF) presumed to promote embryonic development. A validated experimental model was used to recover uterine fluid (UF) and analyse GF expression in the presence or absence of embryos. Briefly, Day-6 in vitro-produced embryos (n = 50) or vehicle (sham transfer) were transferred into the uteri of each oestrus-synchronized Holstein heifer (n = 14) during nonconsecutive cycles. Blood P4 concentrations were measured on Days 0 (oestrus), 6, and 8. On Day 8, UF was recovered from embryo and sham recipients. After retrieval, UF were centrifuged and supernatants stored at –145°C. Sham and embryo UF selected for MRM were from n = 10 animals (n = 20 samples). Uterine fluid, recovered after embryo transfer, contained on average n = 43.1 ± 5.2 total and n = 34.1 ± 3.7% viable embryos per recipient. For MRM, UF samples were concentrated, and protein was precipitated and resuspended in ammonium bicarbonate. Protein (20 μg) was reduced with DTT, trypsin-digested, and desalted. Proteotypic peptides for targeted GF were selected with MRM Pilot software (ABsciex, Farmingham, MA, USA), with 3 to 5 transitions programmed for each peptide. A control, unrelated synthetic peptide was spiked as an internal standard. The area of the larger transition for the control peptide was used to normalise the area values of each other peptide. The MRM experiments were performed on a 5500 QTRAP hybrid triple quadrupole/linear ion trap mass spectrometer (ABsciex) equipped with an Eksigent 1D+plus nanoLC chromatographic system. Data analysis was performed with Analyst 1.5.2 and MultiQuant 2.0.2 softwares (ABsciex). The area of most abundant transition for each analysed peptide was used for relative quantitation. Proteins studied were betacellulin, heparin-binding EGF-like growth factor, neuregulin, artemin, connective tissue growth factor, nerve growth factor, kit ligand, stanniocalcin-1 (STC1), early pregnancy factor (EPF), and hepatoma-derived growth factor (HDGF). Proteotypic peptides were identified in all samples for HDGF, kit ligand, STC1, and EPF (n = 1, n = 1, n = 1, and n = 3 peptides, respectively), which precluded the analysis of the remaining GF. No differences in relative abundance were detected between UF containing or not containing embryos for HDGF, kit ligand, STC1, and EPF (2.85 ± 0.6 v. 4.43 ± 0.6; 0.15 ± 0.02 v. 0.16 ± 0.02; 0.03 ± 0.00 v. 0.04 ± 0.00; and 1.20 ± 0.16 v. 1.09 ± 1.16, respectively). However, STC1 and Day 8 blood P4 were highly correlated (r = 0.71; P = 0.0004), suggesting P4 regulation of STC1. Multiple reaction monitoring-LC-MS/MS is a useful technique to identify some scarce GF in UF at different dynamic ranges. MICINN, project AGL2012-37772 and FEDER. E. C. was supported by MEC-FPU-AP2009-5265. The authors are members of the COST Action FA1201 Epiconcept: Epigenetics and Periconception environment.
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Ruhaak, L. Renee, Fred P. H. T. M. Romijn, Nico P. M. Smit, et al. "Detecting molecular forms of antithrombin by LC-MRM-MS: defining the measurands." Clinical Chemistry and Laboratory Medicine (CCLM) 56, no. 10 (2018): 1704–14. http://dx.doi.org/10.1515/cclm-2017-1111.
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Abstract Background: Antithrombin (AT) is a critical regulator of coagulation, and its overall activity is typically measured using functional tests. A large number of molecular forms of AT have been identified and each individual carries multiple molecular proteoforms representing variable activities. Conventional functional tests are completely blind for these proteoforms. A method that ensures properly defined measurands for AT is therefore needed. We here assess whether mass spectrometry technology, in particular multiple reaction monitoring (MRM), is suitable for the quantification of AT and the qualitative detection of its molecular proteoforms. Methods: Plasma proteins were denatured, reduced and alkylated prior to enzymatic digestion. MRM transitions were developed towards tryptic peptides and glycopeptides using AT purified from human plasma. For each peptide, three transitions were measured, and stable isotope-labeled peptides were used for quantitation. Completeness of digestion was assessed using digestion time curves. Results: MRM transitions were developed for 19 tryptic peptides and 4 glycopeptides. Two peptides, FDTISEK and FATTFYQHLADSK, were used for quantitation, and using a calibration curve of isolated AT in 40 g/L human serum albumin, CVs below 3.5% were obtained for FDTISEK, whereas CVs below 8% were obtained for FATTFYQHLADSK. Of the 26 important AT mutations, 20 can be identified using this method, while altered glycosylation profiles can also be detected. Conclusions: We here show the feasibility of the liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM-MS) technique for the quantitation of AT and the qualitative analysis of most of its molecular proteoforms. Knowing the measurands will enable standardization of AT tests by providing in-depth information on the molecular proteoforms of AT.
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Xia, Yong-Gang, Yan Song, Jun Liang, Xin-Dong Guo, Bing-You Yang, and Hai-Xue Kuang. "Quality Analysis of American Ginseng Cultivated in Heilongjiang Using UPLC-ESI−-MRM-MS with Chemometric Methods." Molecules 23, no. 9 (2018): 2396. http://dx.doi.org/10.3390/molecules23092396.
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American ginseng (Panax quinquefolium) has long been cultivated in China for the function food and medicine. Here, ultra-high performance liquid chromatography was coupled with electrospray ionization and triple quadrupole mass spectrometry (UPLC-ESI−-TQ-MS) for simultaneous detection of 22 ginsenosides in American ginseng cultivated in Mudanjiang district of Heilongjiang. The extraction conditions also were optimized by a Box Behnken design experiment. The optimized result was 31.8 mL/g as ratio of liquid to raw materials, 20.3 min of extraction time, and 235.0 W of extraction powers. The quantitative MS parameters for these 22 compounds were rapidly optimized by single factor experiments employing UPLC-ESI−-multiple reaction monitoring or multiple ion monitoring (MRM/MIM) scans. Furthermore, the established UPLC-ESI−-MRM-MS method showed good linear relationships (R2 > 0.99), repeatability (RSD < 3.86%), precision (RSD < 2.74%), and recovery (94–104%). This method determined 22 bioactive ginsenosides in different parts of the plant (main roots, hairy roots, rhizomes, leaves, and stems) and growth years (one year to four years) of P. quinquefolium. The highest total content of the 22 analytes was in the hairy roots (1.3 × 105 µg/g) followed by rhizomes (7.1 × 104 µg/g), main roots (6.5 × 104 µg/g), leaves (4.2 × 104 µg/g), and stems (2.4 × 104 µg/g). Finally, chemometric methods, hierarchical clustering analysis (HCA) and partial least squares discrimination analysis (PLS-DA), were successfully used to classify and differentiate American ginseng attributed to different growth years. The proposed UPLC-ESI−-MRM-MS coupled with HCA and PLS-DA methods was elucidated to be a simple and reliable method for quality evaluation of American ginseng.
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Yannell, Karen E., Christina R. Ferreira, Shane E. Tichy, and R. Graham Cooks. "Multiple reaction monitoring (MRM)-profiling with biomarker identification by LC-QTOF to characterize coronary artery disease." Analyst 143, no. 20 (2018): 5014–22. http://dx.doi.org/10.1039/c8an01017j.
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Masike, Keabetswe, and Ntakadzeni Madala. "Synchronized Survey Scan Approach Allows for Efficient Discrimination of Isomeric and Isobaric Compounds during LC-MS/MS Analyses." Journal of Analytical Methods in Chemistry 2018 (2018): 1–8. http://dx.doi.org/10.1155/2018/2046709.
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Liquid chromatography-mass spectrometry- (LC-MS-) based multiple reaction monitoring (MRM) methods have been used to detect and quantify metabolites for years. These approaches rely on the monitoring of various fragmentation pathways of multiple precursors and the subsequent corresponding product ions. However, MRM methods are incapable of confidently discriminating between isomeric and isobaric molecules and, as such, the development of methods capable of overcoming this challenge has become imperative. Due to increasing scanning rates of recent MS instruments, it is now possible to operate MS instruments both in the static and dynamic modes. One such method is known as synchronized survey scan (SSS), which is capable of acquiring a product ion scan (PIS) during MRM analysis. The current study shows, for the first time, the use of SSS-based PIS approach as a feasible identification feature of MRM. To achieve the above, five positional isomers of dicaffeoylquinic acids (diCQAs) were studied with the aid of SSS-based PIS method. Here, the MRM transitions were automatically optimized using a 3,5-diCQA isomer by monitoring fragmentation transitions common to all five isomers. Using the mixture of these isomers, fragmentation spectra of the five isomers achieved with SSS-based PIS were used to identify each isomer based on previously published hierarchical fragmentation keys. The optimized method was also used to detect and distinguish between diCQA components found in Bidens pilosa and their isobaric counterparts found in Moringa oleifera plants. Thus, the method was shown to distinguish (by differences in fragmentation patterns) between diCQA and their isobars, caffeoylquinic acid (CQA) glycosides. In conclusion, SSS allowed the detection and discrimination of isomeric and isobaric compounds in a single chromatographic run by producing a PIS spectrum, triggered in the automatic MS/MS synchronized survey scan mode.
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Higgs, Richard E., Jon P. Butler, Bomie Han, and Michael D. Knierman. "Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations." International Journal of Proteomics 2013 (April 23, 2013): 1–10. http://dx.doi.org/10.1155/2013/674282.
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Recent improvements in the mass accuracy and resolution of mass spectrometers have led to renewed interest in label-free quantification using data from the primary mass spectrum (MS1) acquired from data-dependent proteomics experiments. The capacity for higher specificity quantification of peptides from samples enriched for proteins of biological interest offers distinct advantages for hypothesis generating experiments relative to immunoassay detection methods or prespecified peptide ions measured by multiple reaction monitoring (MRM) approaches. Here we describe an evaluation of different methods to post-process peptide level quantification information to support protein level inference. We characterize the methods by examining their ability to recover a known dilution of a standard protein in background matrices of varying complexity. Additionally, the MS1 quantification results are compared to a standard, targeted, MRM approach on the same samples under equivalent instrument conditions. We show the existence of multiple peptides with MS1 quantification sensitivity similar to the best MRM peptides for each of the background matrices studied. Based on these results we provide recommendations on preferred approaches to leveraging quantitative measurements of multiple peptides to improve protein level inference.
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Do, Misol, Hyunsoo Kim, Injoon Yeo, et al. "Clinical Application of Multiple Reaction Monitoring-Mass Spectrometry to Human Epidermal Growth Factor Receptor 2 Measurements as a Potential Diagnostic Tool for Breast Cancer Therapy." Clinical Chemistry 66, no. 10 (2020): 1339–48. http://dx.doi.org/10.1093/clinchem/hvaa178.
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Abstract Background Human epidermal growth factor receptor 2 (HER2) is often overexpressed in breast cancer and correlates with a worse prognosis. Thus, the accurate detection of HER2 is crucial for providing the appropriate measures for patients. However, the current techniques used to detect HER2 status, immunohistochemistry and fluorescence in situ hybridization (FISH), have limitations. Specifically, FISH, which is mandatory for arbitrating 2+ cases, is time-consuming and costly. To address this shortcoming, we established a multiple reaction monitoring-mass spectrometry (MRM-MS) assay that improves on existing methods for differentiating HER2 status. Methods We quantified HER2 expression levels in 210 breast cancer formalin-fixed paraffin-embedded (FFPE) tissue samples by MRM-MS. We aimed to improve the accuracy and precision of HER2 quantification by simplifying the sample preparation through predicting the number of FFPE slides required to ensure an adequate amount of protein and using the expression levels of an epithelial cell-specific protein as a normalization factor when measuring HER2 expression levels. Results To assess the correlation between MRM-MS and IHC/FISH data, HER2 quantitative data from MRM-MS were divided by the expression levels of junctional adhesion molecule A, an epithelial cell-specific protein, prior to statistical analysis. The normalized HER2 amounts distinguished between HER2 2+/FISH-negative and 2+/FISH-positive groups (AUROC = 0.908), which could not be differentiated by IHC. In addition, all HER2 status were discriminated by MRM-MS. Conclusions This MRM-MS assay yields more accurate HER2 expression levels relative to immunohistochemistry and should help to guide clinicians toward the proper treatment for breast cancer patients, based on their HER2 expression.
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Toymentseva, Anna A., Anastasia O. Koryagina, Alexander V. Laikov, and Margarita R. Sharipova. "Label-Free Multiple Reaction Monitoring, a Promising Method for Quantification Analyses of Specific Proteins in Bacteria." International Journal of Molecular Sciences 21, no. 14 (2020): 4924. http://dx.doi.org/10.3390/ijms21144924.
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Bacillus subtilis produces eight industrially important exo-proteases. For the detection of proteases, the activity- and antibody-based assays are normally used. Current activity-based assays require expensive multiplex chemical substrates which allow specificity determination of each enzyme. In this study, we provide evidences pertaining to the usefulness of the label-free multiple reaction monitoring (MRM) assay for a rapid identification and quantitation of specific proteins in bacteria. We used wild-type B. pumilus cells producing at least two serine proteases, subtilisin-like protease (AprBp) and glutamyl endopeptidase (GseBp), as well as optimized recombinant B. subtilis cells containing the same protease genes under control of the LIKE expression system. The Skyline software was used for the selection of three specific proteotypic peptides and their fragment ions for quantification and confirmation of AprBp and GseBp in complex mixtures. MRM indicated that the production of AprBp and GseBp exo-enzymes were respectively 0.9- and 26.6-fold higher in the culture medium of B. pumilus strain in comparison to the recombinant B. subtilis strains carrying optimized LIKE expression systems under identical conditions. The developed procedure in this study is fast, easy to perform and dependable. Additionally, it achieves accurate proteins identification and quantification in complex mixture.
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Romero, Isabel C. "A High-Throughput Method (ASE-GC/MS/MS/MRM) for Quantification of Multiple Hydrocarbon Compounds in Marine Environmental Samples." Marine Technology Society Journal 52, no. 6 (2018): 66–70. http://dx.doi.org/10.4031/mtsj.52.6.6.
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AbstractA high-throughput method was applied in small and complex environmental samples for targeting multiple organic fractions (polar, nonpolar). The analytical method consists of a single-step lipid extraction and purification procedure (accelerated solvent extraction [ASE] system) coupled with a single-run step using gas chromatography with tandem mass spectrometry, operated in multiple reaction monitoring mode (GC/MS/MS/MRM). Successful application of this method is summarized for multiple chemical groups (aliphatics, terpanes, steranes, triaromatic steroids, polycyclic aromatic hydrocarbons, and oxidation products).
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Pisitkun, Trairak, Jason D. Hoffert, Ming-Jiun Yu, and Mark A. Knepper. "Tandem Mass Spectrometry in Physiology." Physiology 22, no. 6 (2007): 390–400. http://dx.doi.org/10.1152/physiol.00025.2007.
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Tandem mass spectrometry coupled to liquid chromatography (LC-MS/MS) allows identification of proteins in a complex mixture without need for protein purification (“shotgun” proteomics). Recent progress in LC-MS/MS-based quantification, phosphoproteomic analysis, and targeted LC-MS/MS using multiple reaction monitoring (MRM) has made LC-MS/MS a powerful tool for the study of cell physiology.
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Ponomarenko, E. A., V. G. Zgoda, A. T. Kopylov, et al. "The Russian part of the human proteome project:first results and prospects." Biomeditsinskaya Khimiya 61, no. 2 (2015): 169–75. http://dx.doi.org/10.18097/pbmc20156102169.
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The article summarizes the achievements of the pilot phase (2010-2014) of the Russian part of the international project “Human Proteome” and identifies the directions for further work on the study of the human chromosome 18 proteome in the framework of the project main phase (2015-2022). The pilot phase of the project was focused on the detection of at least one protein for each chromosome 18 protein-coding gene in three types of the biological material. The application of mass spectrometric detection of proteins by the methods of multiple reactions monitoring (MRM) and gene-centric approach made it possible to detect 95% of master forms of proteins, for 60% of which the quantitative assessment of the protein content was obtained in at least one type of the biological material. The task of the main phase of the project is to measure the proteome size of healthy individuals, taking into account the modified protein forms, providing for both the bioinformatics prediction of the quantity of proteins types and the selective experimental measurement of single proteoforms. Since the ranges of protein concentrations corresponding to the normal physiological state have not been identified, the work of the main phase of the project is focused on the study of clinically healthy individuals. The absence of these data complicates significantly the interpretation of the patients’ blood proteomic profiles and prevents creating diagnostic tests. In the long term prospect, implementation of the project envisages development of a diagnostic test system based on multiple reactions monitoring (MRM) for quantitative measurement of the protein forms associated with some diseases. Development of such test systems will allow predicting the extent of risk of different diseases, diagnosing a disease at its early stage and monitoring the effectiveness of the treatment.
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Moon, Hyeong-Gon, Un-Beom Kang, Wonshik Han, Seock-Ah Im, and Dong-Young Noh. "Identification and validation of plasma protein biomarker panels for breast cancer diagnosis by using multiple reaction monitoring-based mass spectrometry." Journal of Clinical Oncology 30, no. 15_suppl (2012): 10621. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.10621.
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10621 Background: Multiple reaction monitoring-based mass spectrometry (MRM-MS) has the ability to perform a wide range of proteome analysis in a single experiment using a small volume of specimen. We aimed to develop a plasma protein signature for breast cancer diagnosis using the MRM-MS technology. Methods: Previously, we have identified lists of breast cancer-related proteins from various models of proteomic discovery including cancer plasma vs healthy plasma, cancer cell line secretome vs non-tumorigenic cell line secretome, cancer tissue vs normal tissue, and literature search. Based on these protein panels, total of 29 proteins were selected for further experiments. We verified and validated the protein signature in two independent cohorts of breast cancer patients and healthy women. Results: In the verification cohort of 80 breast cancer patients and 80 healthy women, MRM-MS showed significant differences in plasma concentration for 11 proteins. Among them, the difference was not significant for 4 proteins when the cases were limited to stage I and II patients. Based on p values and consistent expression level along the AJCC stages, we have created a plasma protein signature comprised of 3 plasma proteins. The 3 plasma protein signature effectively discriminated cancer and healthy cases with the AUC of 0.831 (sensitivity 78.7%, specificity 78.7%). The performance of the 3 plasma protein signature was validated in the cohort of 100 cancer patients and 100 healthy women. The accuracy of the 3 protein signature was still meaningful with the AUC of 0.746 and 0.797 for all stages and stage I or II patients, respectively. Conclusions: The 3 plasma protein signature for breast cancer diagnosis, developed by the MRM-MS technology, showed promising results in the present study.
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Xie, Junbo, Yanqing Zhang, Deqiang Kong, and Marhaba Rexit. "Rapid identification and determination of 11 polyphenols in Herba lycopi by HPLC–MS/MS with multiple reactions monitoring mode (MRM)." Journal of Food Composition and Analysis 24, no. 7 (2011): 1069–72. http://dx.doi.org/10.1016/j.jfca.2010.12.016.
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Kim, Sun Hee, Nan-Ee Lee, Jong Seok Lee, et al. "Identification of Mycobacterial Antigens in Human Urine by Use of Immunoglobulin G Isolated from Sera of Patients with Active Pulmonary Tuberculosis." Journal of Clinical Microbiology 54, no. 6 (2016): 1631–37. http://dx.doi.org/10.1128/jcm.00236-16.
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Point-of-care (POC) diagnostic testing of tuberculosis (TB) is a tremendous unmet need. In this study, four urinary mycobacterial antigens were identified through two independent approaches using IgG capture and immunodepletion methods. Among these, ModC was validated by a multiple reaction monitoring (MRM) method. As expected, the biomarkers elevated the clinical validity of TB diagnosis when combined with preexisting markers.
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Brioschi, Maura, Erica Gianazza, Piergiuseppe Agostoni, Beatrice Zoanni, Alice Mallia, and Cristina Banfi. "Multiplexed MRM-Based Proteomics Identified Multiple Biomarkers of Disease Severity in Human Heart Failure." International Journal of Molecular Sciences 22, no. 2 (2021): 838. http://dx.doi.org/10.3390/ijms22020838.
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Heart failure (HF) is a complex disease due to the intricate interplay of several mechanisms, which therefore implies the need for a multimarker strategy to better personalize the care of patients with HF. In this study, we developed a targeted mass spectrometry approach based on multiple reaction monitoring (MRM) to measure multiple circulating protein biomarkers, involved in cardiovascular disease, to address their relevance in the human HF, intending to assess the feasibility of the workflow in the disease monitoring and risk stratification. In this study, we analyzed a total of 60 plasma proteins in 30 plasma samples from eight control subjects and 22 age- and gender- matched HF patients. We identified a panel of four plasma proteins, namely Neuropilin-2, Beta 2 microglobulin, alpha-1-antichymotrypsin, and complement component C9, that were more abundant in HF patients in relation to disease severity and pulmonary dysfunction. Moreover, we showed the ability of the combination of these candidate proteins to discriminate, with sufficient accuracy, HF patients from healthy subjects. In conclusion, we demonstrated the feasibility and potential of a proteomic workflow based on MRM mass spectrometry for the evaluation of multiple proteins in human plasma and the identification of a panel of biomarkers of HF severity.
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Tesevic, Vele, Ivana Aljancic, Vlatka Vajs, et al. "Development and validation of LC-MS/MS method with multiple reactions monitoring mode for quantification of vanillin and syringaldehyde in plum brandies." Journal of the Serbian Chemical Society 79, no. 12 (2014): 1537–43. http://dx.doi.org/10.2298/jsc140225079t.
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An ultra-performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-QqQ-MS/MS) method with multiple reactions monitoring mode (MRM) has been developed and validated for quantification of vanillin and syringaldehyde in plum brandy. The method showed good linearity (0.05 to 10 mgL?1) and low limits of detection and quantification (LOD and LOQ were 11.6 ?gL?1 and 38.2 ?gL?1 for vanillin, and 12.7 ?gL?1 and 42.0 ?gL?1 for syringaldehyde, respectively). The overall intra-day and inter-day variations were less than 4.21%, and the overall recovery over 93.0%. The correlation coefficients (R2) of the calibration curves were higher than 0.9999. In order to evaluate if the method is suitable for use as a routine analytical tool, in 31 Serbian plum brandy samples vanillin and syringaldehide were determined.
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Zaghary, Wafaa Abdou, Ahmed Mostafa Abdalla, Emily Tawfik Hanna, and Nermeen Abdallah Shoukry. "Application of multiple reaction monitoring for quantitation of sweeteners in food products." European Journal of Chemistry 10, no. 3 (2019): 263–66. http://dx.doi.org/10.5155/eurjchem.10.3.263-266.1825.
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A coupled UPLC-MS/MS method has been developed and validated for the simultaneous quantitation of food sweeteners stevioside (STV) and aspartame (ASP). Good chromato-graphic separation was achieved on a Hypersil gold 50×2.1 mm (1.9 μm) column, using a gradient flow of 10 mM ammonium acetate, pH = 2.9 adjusted with formic acid, and 10 mM ammonium acetate in acetonitrile:water (95:5, v:v) as the mobile phase. The eluate was introduced to ESI-Mass spectrometer and scanned using multiple reaction monitoring (MRM). The method was robust, reproducible and easy to use and was validated according to ICH guidelines for the accuracy and precision giving acceptable ranges. The utilization of multiple reaction monitoring improved the selectivity of detection. Method was linear in the ranges of 2-250 ng/mL for STV and ASP. Application of this method on laboratory mixtures of the selected sweeteners was successful. The using of mass spectrometry make the method selective and measurement did not affect the presence of impurities, additive and other ingredients of detection due to the simplicity and sensitivity of this method allows the utilization of method in quality control of STV and ASP.
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Wright, Michael J., Rebecca L. Thomas, Phoebe E. Stanford, and Andrea R. Horvath. "Multiple Reaction Monitoring with Multistage Fragmentation (MRM3) Detection Enhances Selectivity for LC-MS/MS Analysis of Plasma Free Metanephrines." Clinical Chemistry 61, no. 3 (2015): 505–13. http://dx.doi.org/10.1373/clinchem.2014.233551.
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Abstract BACKGROUND LC-MS/MS with multiple reaction monitoring (MRM) is a powerful tool for quantifying target analytes in complex matrices. However, the technique lacks selectivity when plasma free metanephrines are measured. We propose the use of multistage fragmentation (MRM3) to improve the analytical selectivity of plasma free metanephrine measurement. METHODS Metanephrines were extracted from plasma with weak cation exchange solid-phase extraction before separation by hydrophilic interaction liquid chromatography. We quantified normetanephrine and metanephrine by either MRM or MRM3 transitions m/z 166→134→79 and m/z 180→149→121, respectively. RESULTS Over a 6-month period, approximately 1% (n = 21) of patient samples showed uncharacterized coeluting substances that interfered with the routine assay, resulting in an inability to report results. Quantification with MRM3 removed these interferences and enabled measurement of the target compounds. For patient samples unaffected by interferences, Deming regression analysis demonstrated a correlation between MRM3 and MRM methods of y = 1.00x − 0.00 nmol/L for normetanephrine and y = 0.99x + 0.03 nmol/L for metanephrine. Between the MRM3 method and the median of all LC-MS/MS laboratories enrolled in a quality assurance program, the correlations were y = 0.97x + 0.03 nmol/L for normetanephrine and y = 1.03x − 0.04 nmol/L for metanephrine. Imprecision for the MRM3 method was 6.2%–7.0% for normetanephrine and 6.1%–9.9% for metanephrine (n = 10). The lower limits of quantification for the MRM3 method were 0.20 nmol/L for normetanephrine and 0.16 nmol/L for metanephrine. CONCLUSIONS The use of MRM3 technology improves the analytical selectivity of plasma free metanephrine quantification by LC-MS/MS while demonstrating sufficient analytical sensitivity and imprecision.
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Taylor, Allen D., Hana Vaisocherová, Jonathan Deeds, Stacey DeGrasse, and Shaoyi Jiang. "Tetrodotoxin Detection by a Surface Plasmon Resonance Sensor in Pufferfish Matrices and Urine." Journal of Sensors 2011 (2011): 1–10. http://dx.doi.org/10.1155/2011/601704.
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Tetrodotoxin (TTX) poisoning is most commonly associated with consumption of pufferfish. TTX is a low molecular weight (~319 Da) neurotoxin that selectively blocks voltage-sensitive Na+-gated ion channels. The standard method accepted worldwide for monitoring TTX toxicity in food matrices is the mouse bioassay. Ethical concerns from live animal testing, low sample throughput, and analytical inaccuracies have led to the need for an alternative method. We have previously established that surface plasmon resonance (SPR) sensors can quantify TTX in aqueous buffer samples by an antibody-based inhibition assay. In this paper, we report the extension of the assay for the detection of TTX in both clinical- and food-relevant matrices. The assay was optimized for application to three relevant complex matrices: pufferfish liver extract, pufferfish muscle extract, and human urine. Matrix effects are discussed and calibration curves are presented. Naturally contaminated pufferfish liver and muscle extracts were analyzed by the SPR method, and the data is compared to liquid-chromatography electrospray-ionization multiple reactions monitoring mass spectrometry (LC/ESI/MRM/MS) data. Ten samples, including three from a poisoning incident, two control monkfish samples, and five toxic pufferfish samples, were analyzed using this method, and the data is compared to LC/ESI/MRM/MS analysis of the samples.
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Carr, Lynn, Anne-Laure Gagez, Marie Essig, François-Ludovic Sauvage, Pierre Marquet, and Louis Noel Gastinel. "Calcineurin Activity Assay Measurement by Liquid Chromatography–Tandem Mass Spectrometry in the Multiple Reaction Monitoring Mode." Clinical Chemistry 60, no. 2 (2014): 353–60. http://dx.doi.org/10.1373/clinchem.2013.213264.
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Abstract BACKGROUND Blood concentrations of the calcineurin inhibitors (CNIs) cyclosporine and tacrolimus are currently measured to monitor immunosuppression in transplant patients. The measurement of calcineurin (CN) phosphatase activity has been proposed as a complementary pharmacodynamic approach. However, determining CN activity with current methods is not practical. We developed a new method amenable to routine use. METHODS Using liquid chromatography–multiple reaction monitoring mass spectrometry (LC-MRM-MS), we quantified CN activity by measuring the dephosphorylation of a synthetic phosphopeptide substrate. A stable isotope analog of the product peptide served as internal standard, and a novel inhibitor cocktail minimized dephosphorylation by other major serine/threonine phosphatases. The assay was used to determine CN activity in peripheral blood mononuclear cells (PBMCs) isolated from 20 CNI-treated kidney transplant patients and 9 healthy volunteers. RESULTS Linearity was observed from 0.16 to 2.5 μmol/L of product peptide, with accuracy in the 15% tolerance range. Intraassay and interassay recoveries were 100.6 (9.6) and 100 (7.5), respectively. Michaelis–Menten kinetics for purified CN were Km = 10.7 (1.6) μmol/L, Vmax = 2.8 (0.3) μmol/min · mg, and for Jurkat lysate, Km = 182.2 (118.0) μmol/L, Vmax = 0.013 (0.006) μmol/min · mg. PBMC CN activity was successfully measured in a single tube with an inhibitor cocktail. CONCLUSIONS Because LC-MRM-MS is commonly used in routine clinical dosage of drugs, this CN activity assay could be applied, with parallel blood drug concentration monitoring, to a large panel of patients to reevaluate the validity of PBMC CN activity monitoring.
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Rahayu, Riana Suastari, Iryanti Eka Suprihatin, and Wiwik Susanah Rita. "IDENTIFIKASI PEWARNA MERAH K3 (CI 15585) DALAM PRODUK KOSMETIK SEDIAAN PERONA MATA SECARA LC- MS/MS." CAKRA KIMIA (Indonesian E-Journal of Applied Chemistry) 5, no. 1 (2017): 34. http://dx.doi.org/10.24843/ck.2017.v05.i01.p05.
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ABSTRAK : Identifikasi merah K3 dalam sediaan perona mata secara LC-MS/MS dilakukan untuk mengkonfirmasi keberadaannya yang sering kali ditemukan dalam konsentrasi kecil. Metode spektrofotometeri UV-VIS dan HPLC tidak cukup untuk mengkonfirmasi keberadaan merah K3 yang dinyatakan positif dengan metode KLT. Optimasi metode dilakukan pada kondisi spektrometer massa dan sistem kromatografi cair yang berlaku pada LC-MS/MS sebelum dilakukan proses identifikasi. Hasil optimasi menunjukkan identifikasi merah K3 dengan LC-MS/MS menggunakan teknik ionisasi elektrospray (ESI) dan sistem Multiple Reaction Monitoring (MRM) pada mode ionisasi negatif. Ion prekursor pada m/z 375 dan ion produk pada m/z 204, 80, 140 digunakan untuk identifikasi.
 
 ABSTRACT : Identification of red dye (CI 15585) using LC-MS/MS in eye shadow was performed to confirm its presence in very low concentrations. The UV-VIS spectrophotometry and HPLC are not sufficient to confirm the presence of red dye identified by the TLC. The optimation of the method was carried out under the condition applicable to LC-MS / MS prior to identification process. Optimation results show that red dye can be identified with LC-MS/MS using electrospray ionization technique (ESI) and Multiple Reaction Monitoring (MRM) system under negative ionization mode. The precursor ion at m / z 375 and the product ions at m / z 204, 80, 140 are used for identification.
 
 
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Faraz, Ina, Arslan Ali, Faraz Ul Haq, et al. "Sensitive Determination of C-Alkylated Flavonoids by HPLC-ESI-MS/MS Using Multiple Reaction Monitoring Approach: Pseudarthria hookeri as a Case Study." Journal of Chromatographic Science 57, no. 10 (2019): 944–49. http://dx.doi.org/10.1093/chromsci/bmz072.
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Abstract One of the major problems with the formulation of herbal medicines is the quality control of plant material to ensure its efficacy and safety. Quality control of medicinal plants requires analysis of many bioactive compounds present in the plant. C-alkylated flavonoids are an important bioactive subclass of flavonoids. A simple, rapid, sensitive and selective method is presented here for the quantification of bioactive C-alkylated flavonoids. This is the first quantitative method for analysis of C-alkylated flavonoids based on the multiple reaction monitoring (MRM) approach so far. This study focuses on method development for quantification of bioactive C-alkylated flavonoids. Quantification of a total of five C-alkylated flavonoids was done employing the MRM approach on an HPLC-QqQ-MS instrument. LODs and LOQs for quantified flavonoids were in the range of 0.41–1.32 and 1.23–3.96 ng/mL, respectively. Linear calibration curves between 25 and 1500 ng/mL were obtained with the regression coefficients of ≥0.996. Accuracy (% bias) and precision (% RSD) of the analyses were found to be less than 5%. Developed HPLC-ESI-MS/MS can be employed as a quality control method of plant raw materials.
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Park, Jisook, Eun-Bi Go, Ji Sun Oh, Jong Kyun Lee, and Soo-Youn Lee. "Multiple-Cycle Polymeric Extracellular Vesicle Precipitation and Its Evaluation by Targeted Mass Spectrometry." International Journal of Molecular Sciences 22, no. 9 (2021): 4311. http://dx.doi.org/10.3390/ijms22094311.
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The multiple roles of extracellular vesicles (EVs) in pathogenesis have received much attention, as they are valuable as diagnostic and prognostic biomarkers. We employed polymeric EV precipitation to isolate EVs from clinical specimens to overcome the limitations of ultracentrifugation (UC), such as low protein yields, a large volume of specimens used, and time requirements. Multiple-cycle polymeric EV precipitation was applied to enhance the purity of the EV fractions with a small sample volume. Then, the purity was assessed using a multiple reaction monitoring (MRM) panel consisting of alpha-2-macroglobulin (A2M), thrombospondin 1 (THBS 1), galectin 3 binding protein (LGALS3BP), and serum albumin (ALB). For purity evaluation, the EV fractions isolated from blood specimens were subjected to shotgun proteomics and MRM-based targeted proteomics analyses. We demonstrate that the modified method is an easy and convenient method compared with UC. In the shotgun proteomics analysis, the proteome profile of EV fraction contains 89% EV-related proteins by matching with the EVpedia database. In conclusion, we suggest that multiple-cycle polymeric EV precipitation is not only a more effective method for EV isolation for further proteomics-based experiments, but may also be useful for further clinical applications due to the higher EV yield and low sample requirements.
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Mwando, Elliott, Amos Massele, Enoch Sepako, and Kwenga Sichilongo. "A method employing SPE, MRM LC-MS/MS and a THF–water solvent system for the simultaneous determination of five antiretroviral drugs in human blood plasma." Analytical Methods 9, no. 3 (2017): 450–58. http://dx.doi.org/10.1039/c6ay02442d.
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Zhang, Chao Jie, Geng Zhang, Lu Ting Chen, Qian Chen, and Qi Zhou. "A New Method Using Liquid Chromatography Tandem Mass Spectrometry to Detect NDMA in Water." Advanced Materials Research 742 (August 2013): 355–58. http://dx.doi.org/10.4028/www.scientific.net/amr.742.355.
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This study focused on using liquid Chromatography Tandem Mass Spectrometry to detect N-Nitrosodimethylamine (NDMA) at trace concentrations in water. The water sample was preconcentrated by solid-phase extraction method. To find an elution which can obtain higher recovery, three reagents with different organic solvents were examined. After comparing the recoveries and the standard deviation of the elution, finally the dichloromethane was determined as the elution of the experiment. Then the concentrated sample was analyzed by a method combining SPE pretreatment and LC separation with tandem mass spectrometry using multiple reaction monitoring (MRM).
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Novikova, S. E., T. E. Farafonova, O. V. Tikhonova, et al. "Mass-spectrometric MRM analysis of FDA-verified proteins in the blood plasma of healthy volunteers." Biomeditsinskaya Khimiya 66, no. 4 (2020): 294–316. http://dx.doi.org/10.18097/pbmc20206604294.
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The proteomic composition of a biological sample serves as the most important feature of a biological object, and it allows discriminating normal and pathological conditions. Targeted mass spectrometric analysis, namely, multiple reaction monitoring (MRM) using synthetic isotopically-labeled internal standard (SIS), is the main alternative to the ELISA method for the analysis of diagnostically significant proteins. Based on the MRM results, a prototype test system has been developed; it employs the targeted mass spectrometric method for multiplex, quantitative analysis of FDA-verified proteins in whole blood plasma. Using this approach, it was possible to measure the content of 42 proteins in 31 samples in a concentration range spanning five orders of magnitude. The interindividual variability for 30 of the 42 registered proteins was less than 40%. The largest scatter was observed for haptoglobin (68%), immunoglobulin heavy constant delta IGHD (90%), angiotensin (72%), sex hormone-binding globulin SHBG (100%) and lipoprotein-(a) (136%). The obtained results on the concentration of proteins correlate with published data (Hortin et al., 2008, Clinical Chemistry, 54, 1608) with R2=0.84. The developed prototype test system based on targeted mass spectrometric analysis of proteins can be considered as an alternative to methods using monoclonal antibodies.
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Nguyen Thi, Ha Binh, Thu Nguyen Thi, Ngoc Lan Dang Thi, Hai Nguyen Thi, and Son Tran Cao. "Simultaneous screening of 5 allergens in food by using liquid chromatography triple quadrupole mass spectrometry." Heavy metals and arsenic concentrations in water, agricultural soil, and rice in Ngan Son district, Bac Kan province, Vietnam 2, no. 3 (2019): 121–28. http://dx.doi.org/10.47866/2615-9252/vjfc.70.
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The liquid chromatography tandem mass spectrometry with electrospray ionization (ESI) source in multiple reactions monitoring (MRM) mode has been used to detect five allergen including milk, egg, peanut, soyabean, and walnut in milk, dairy products, and confectionery. The allergenic proteins from food matrices were extracted with an extraction buffer (50 mM of TRIS- saline, 2 M of urea, and 25 mM of DTT) and then enzymatically digested with trypsin to form peptides. The peptides were eventually detected on a LC-MS/MS Triple Quad 5500 system from AB SCIEX. As a result, each allergen was characterized by a corresponding specific peptide. The limit of detection was of 3 &micro;g/g for milk, 5 &micro;g/g for peanut, 10 &micro;g/g for soyabean and walnut and 20 &micro;g/g for egg.
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Bharate, Jaideep Bibishan, Ram Ashrey Vishwakarma, Sandip Bibishan Bharate, Manoj Kushwaha, and Ajai Prakash Gupta. "Quantification of the Polyisoprenylated Benzophenones Garcinol and Isogarcinol Using Multiple Reaction Monitoring LC/Electrospray Ionization-MS/MS Analysis of Ultrasound-Assisted Extracts of Garcinia indica Fruits." Journal of AOAC INTERNATIONAL 97, no. 5 (2014): 1317–22. http://dx.doi.org/10.5740/jaoacint.13-137.
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Abstract This paper describes a method that includes an optimized extraction process and identification and quantification of two anticancer compounds (garcinol and isogarcinol) by LC/electrospray ionization (ESI)-MS/MS in the multiple reaction monitoring (MRM) mode. The study aimed to develop a fast, accurate, and sensitive method for the quantification of garcinol and isogarcinol in different extracts of Garcinia indica fruits. The compounds were detected using LC/ESI-MS/MS in the positive-ion mode and quantified in the MRM mode using a transition mass of m/z 603.3/411 taken as the quantifier and 603.3/343.2 as the qualifier for garcinol and isogarcinol. Five point calibration curves were linear in the range of 2 to 10 ng/mL for garcinol and 0.5 to 6 ng/mL for isogarcinol, with a correlation coefficient of ≥0.990 for both. LOQ for garcinol and isogarcinol was 0.06 and 0.05 ng/mL, respectively, while LOD was 0.021 and 0.017 ng/mL respectively. Our work demonstrated optimization of extraction procedure, fast and highly sensitive quantification (pg level LOQ), and validation of the developed method for the investigated compounds in fruit extracts of G. indica.
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Ntasi, Georgia, Anthony Tsarbopoulos, Emmanuel Mikros, and Evagelos Gikas. "Targeted Metabolomics: The LC-MS/MS Based Quantification of the Metabolites Involved in the Methylation Biochemical Pathways." Metabolites 11, no. 7 (2021): 416. http://dx.doi.org/10.3390/metabo11070416.
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Biochemical methylation reactions mediate the transfer of the methyl group regulating vital biochemical reactions implicated in various diseases as well as the methylation of DNA regulating the replication processes occurring in living organisms. As a finite number of methyl carriers are involved in the methyl transfer, their quantification could aid towards the assessment of an organism’s methylation potential. An Hydrophilic Interaction Chromatography-Liquid Chromatography Multiple Reaction Monitoring (HILIC-LC-MRM) mass spectrometry (MS) methodology was developed and validated according to Food & Drug Administration (FDA), European Medicines Agency (EMA), and International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) for the simultaneous determination of nine metabolites i.e., B12, folic acid, 5-methyltetrahydrofolate, S-adenosylmethionine, S-adenosylhomocysteine, betaine, phosphocholine, N,N-dimethylglycine, and deoxythymidine monophosphate in human blood plasma. The sample pretreatment was based on a single step Solid-phase extraction (SPE) methodology using C18 cartridges. The methodology was found to accurately quantitate the analytes under investigation according to the corresponding dynamic range proposed in the literature for each analyte. The applicability of the method was assessed using blood donor samples and its applicability demonstrated by the assessment of their basal levels, which were shown to agree with the established basal levels. The methodology can be used for diagnostic purposes as well as for epigenetic screening.
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Banerjee, Kaushik, Rahul H. Savant, Soma Dasgupta, Sangram H. Patil, Dasharath P. Oulkar, and Pandurang G. Adsule. "Multiresidue Analysis of Synthetic Pyrethroid Pesticides in Grapes by Gas Chromatography with Programmed Temperature VaporizingLarge Volume Injection Coupled with Ion Trap Mass Spectrometry." Journal of AOAC INTERNATIONAL 93, no. 2 (2010): 368–79. http://dx.doi.org/10.1093/jaoac/93.2.368.
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Abstract A multiresidue analysis method was optimized and validated for simultaneous estimation of 21 synthetic pyrethroid pesticides and their isomers in grape matrix at 10 ng/g and higher levels. The method involves extraction of a 10 g sample with 10 mL ethyl acetate, cleanup by dispersive SPE with primary-secondary amine (25 mg) sorbent, and estimation by GC/MS/MS large volume injection (LVI) through a programmed temperature vaporizer (PTV) injector. The PTV-LVI parameters of the gas chromatograph and the multiple reaction monitoring (MRM) parameters of the ion trap mass spectrometer were optimized for each compound to achieve the highest S/N. For each analyte, the unique and most abundant MRM transition was used for quantification, along with the next most abundant MRM transition for confirmatory identification. The abundance ratio of the confirmatory to quantifier MRMs was used to ensure unambiguous residue monitoring in unknown samples within a 20 tolerance range at the 10 ng/g level. The analytes were separated on a TR-5MS capillary column within a 22 min run time. The method was selective and sensitive and ensured separation of the synthetic pyrethroids from high-boiling matrix components. The LOD and LOQ of the analytes ranged between 0.5 to 3.1 and 2.5 to 10 ng/g, respectively. Linearity of solvent and matrix-matched calibrations between 2.0 and 250 ng/g was established for each compound with r2 &gt; 0.99. Recovery at 10, 25, and 50 ng/g levels of fortification in grapes ranged within 77115 with associated RSD values (n 8) up to 20.
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Krieg, Laura, Alexandra Schaffert, Matthias Kern, et al. "An MRM-Based Multiplexed Quantification Assay for Human Adipokines and Apolipoproteins." Molecules 25, no. 4 (2020): 775. http://dx.doi.org/10.3390/molecules25040775.
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Adipokines and apolipoproteins are key regulators and potential biomarkers in obesity and associated diseases and their quantitative assessment is crucial for functional analyses to understand disease mechanisms. Compared to routinely used ELISAs, multiple reaction monitoring (MRM)-based mass spectrometry allows multiplexing and detection of proteins for which antibodies are not available. Thus, we established an MRM method to quantify 9 adipokines and 10 apolipoproteins in human serum. We optimized sample preparation by depleting the two most abundant serum proteins for improved detectability of low abundant proteins. Intra-day and inter-day imprecision were below 16.5%, demonstrating a high accuracy. In 50 serum samples from participants with either normal weight or obesity, we quantified 8 adipokines and 10 apolipoproteins. Significantly different abundances were observed for five adipokines (adipsin, adiponectin, chemerin, leptin, vaspin) and four apolipoproteins (apo-B100/-C2/-C4/-D) between the body mass index (BMI) groups. Additionally, we applied our MRM assay to serum samples from normal weight children and human adipocyte cell culture supernatants to proof the feasibility for large cohort studies and distinct biological matrices. In summary, this multiplexed assay facilitated the investigation of relationships between adipokines or apolipoproteins and phenotypes or clinical parameters in large cohorts, which may contribute to disease prediction approaches in the future.
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Srivastava, Neha, Supriya Kumari, Kishore Nair, Samsul Alam, and Syed K. Raza. "Determination of Organophosphorous Pesticides in Environmental Water Samples Using Surface-Engineered C18 Functionalized Silica-Coated Core-Shell Magnetic Nanoparticles–Based Extraction Coupled with GC-MS/MS Analysis." Journal of AOAC INTERNATIONAL 100, no. 3 (2017): 804–9. http://dx.doi.org/10.5740/jaoacint.16-0312.
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Abstract The present paper depicts a novel method based on magneticSPE (MSPE) for the determination of organophosphorus pesticides (OPs) such as phorate, malathion, and chlorpyrifos in environmental water samples. In this study, C18 functionalized silica-coated core-shell iron oxide magnetic nanoparticles (MNPs) were used as a surface-engineered magnetic sorbent for theselective extraction of pesticides from aqueous samples, followed by GC-MS and GC–tandem MS analysis for confirmative determination of the analytes. Various important method parameters, including quantity of MNP adsorbent, volume of sample, effective time for extraction, nature of the desorbing solvent, and pH of the aqueous sample, were investigated and optimized to obtain maximum method performance. Under the optimized instrumental analysis conditions, good linearity (r2 value ≥0.994) was achieved at the concentration range of 0.5–500 μg/L. Recoveries were in therange of 79.2–96.3 and 80.4–97.5% in selective-ion monitoring and multiple reaction monitoring (MRM) modes, respectively, at the spiking concentrations of 1, 5, and 10 μg/L. MRM mode showed better sensitivity, selectivity, and low-level detection (0.5 μg/L) of analytes. The novel MSPE method is a simple, cheap, rapid, and eco-friendly method for the determination of OPs in environmental water samples.
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Yanagida, Mitsuaki, Kensuke Hamamura, Kenji Takamori, and Yoshihiko Araki. "The simultaneous quantification of candidate serum biomarker peptides for hypertensive disorders of pregnancy." Annals of Clinical Biochemistry: International Journal of Laboratory Medicine 56, no. 4 (2019): 457–65. http://dx.doi.org/10.1177/0004563219839084.
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Background Hypertensive disorders of pregnancy are defined as syndromes characterized by high blood pressure that develop after 20 weeks of pregnancy. The pathogenesis of hypertensive disorders of pregnancy has not been fully elucidated, and the most effective treatment is the termination of pregnancy. Therefore, methods for an early predictive diagnosis should be developed to rescue both the mother and the child. Methods Previously, we explored the serum peptides whose concentration varied specifically between patients with hypertensive disorders of pregnancy and normal pregnant women using peptidomics analysis and identified seven candidate marker peptides. To quantify the marker peptides more reliably, we attempted to quantify these peptides simultaneously by multiple reaction monitoring using liquid chromatography/tandem mass spectrometry (LC-MRM/MS). Non-labelled and stable isotope-labelled forms of the seven peptides were synthesized as standards, and the multiple reaction monitoring transitions for their quantification were determined. Results As the retention of the peptides by the reversed-phase column was dependent on their hydrophobicity, two solvent compositions were required for the retention of all peptides. Under these conditions, we detected the peptides by LC-MRM/MS using a column-switching method. Further, we succeeded in quantifying the peptides in the serum of pregnant women using stable isotope dilution. Conclusion Our new peptidomics method has great value for peptides, particularly those that have no specific antibody as a detection tool. Using this system, the serum peptides in patients with hypertensive disorders of pregnancy can be validated as diagnostic markers of hypertensive disorders of pregnancy. Further, this method can potentially be applied to the general quantification of other serum peptides.
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Kennedy, Jacob J., Jeffrey R. Whiteaker, Laura C. Kennedy, et al. "Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues." Clinical Chemistry 67, no. 7 (2021): 1008–18. http://dx.doi.org/10.1093/clinchem/hvab047.
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Abstract Background Conventional HER2-targeting therapies improve outcomes for patients with HER2-positive breast cancer (BC), defined as tumors showing HER2 protein overexpression by immunohistochemistry and/or ERBB2 gene amplification determined by in situ hybridization (ISH). Emerging HER2-targeting compounds show benefit in some patients with neither HER2 protein overexpression nor ERBB2 gene amplification, creating a need for new assays to select HER2-low tumors for treatment with these compounds. We evaluated the analytical performance of a targeted mass spectrometry-based assay for quantifying HER2 protein in formalin-fixed paraffin-embedded (FFPE) and frozen BC biopsies. Methods We used immunoaffinity-enrichment coupled to multiple reaction monitoring-mass spectrometry (immuno-MRM-MS) to quantify HER2 protein (as peptide GLQSLPTHDPSPLQR) in 96 frozen and 119 FFPE BC biopsies. We characterized linearity, lower limit of quantification (LLOQ), and intra- and inter-day variation of the assay in frozen and FFPE tissue matrices. We determined concordance between HER2 immuno-MRM-MS and predicate immunohistochemistry and ISH assays and examined the benefit of multiplexing the assay to include proteins expressed in tumor subcompartments (e.g., stroma, adipose, lymphocytes, epithelium) to account for tissue heterogeneity. Results HER2 immuno-MRM-MS assay linearity was ≥103, assay coefficient of variation was 7.8% (FFPE) and 5.9% (frozen) for spiked-in analyte, and 7.7% (FFPE) and 7.9% (frozen) for endogenous measurements. Immuno-MRM-MS-based HER2 measurements strongly correlated with predicate assay HER2 determinations, and concordance was improved by normalizing to glyceraldehyde-3-phosphate dehydrogenase. HER2 was quantified above the LLOQ in all tumors. Conclusions Immuno-MRM-MS can be used to quantify HER2 in FFPE and frozen BC biopsies, even at low HER2 expression levels.
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Zuas, Oman. "Extraction of Chemical Warfare Agents from Soils: Case Study on O-ethyl S-2-(diisopropylamino)ethyl methylphosphonothiolate (VX)." Jurnal Natur Indonesia 11, no. 1 (2012): 1. http://dx.doi.org/10.31258/jnat.11.1.1-7.
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Extraction of chemical warfare agents, O-ethyl S-2-(diisopropylamino)ethyl methylphosphonothiolate (VX) in soilsample has been carried out. The extraction was performed using six different solvents including 1% TEA/MeOH,1% NH4OH/MeOH, water pH 2 at the ambient temperature , water pH 2 at temperature 4 0C, water pH 7 at ambienttemperature, and water pH 7 at temperature 4 0C. Percent recovery of VX in soil samples was quantitativelydetermined by mean LC-MS using selected reaction monitoring (SRM). Among the solvents used, water pH 2 attemperature 40C gave the best extraction capability that was indicated by the highest percent recovery of VXobtained. Storing effect of spiked samples was also investigated by extracting the samples containing VX usingwater at pH 2/40C and the degradation product was then identified using multiple reaction monitoring (MRM). Fromthe study, two degradation products were identified as Bis[2-(diisopropylamino)ethyl]disulphide and ethylmethylphosphonate.
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Jin, Jonghwa, Yun Hyi Ku, Yikwon Kim, et al. "Differential Proteome Profiling Using iTRAQ in Microalbuminuric and Normoalbuminuric Type 2 Diabetic Patients." Experimental Diabetes Research 2012 (2012): 1–31. http://dx.doi.org/10.1155/2012/168602.
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Diabetic nephropathy (DN) is a long-term complication of diabetes mellitus that leads to end-stage renal disease. Microalbuminuria is used for the early detection of diabetic renal damage, but such levels do not reflect the state of incipient DN precisely in type 2 diabetic patients because microalbuminuria develops in other diseases, necessitating more accurate biomarkers that detect incipient DN. Isobaric tags for relative and absolute quantification (iTRAQ) were used to identify urinary proteins that were differentially excreted in normoalbuminuric and microalbuminuric patients with type 2 diabetes where 710 and 196 proteins were identified and quantified, respectively. Some candidates were confirmed by 2-DE analysis, or validated by Western blot and multiple reaction monitoring (MRM). Specifically, some differentially expressed proteins were verified by MRM in urine from normoalbuminuric and microalbuminuric patients with type 2 diabetes, wherein alpha-1-antitrypsin, alpha-1-acid glycoprotein 1, and prostate stem cell antigen had excellent AUC values (0.849, 0.873, and 0.825, resp.). Moreover, we performed a multiplex assay using these biomarker candidates, resulting in a merged AUC value of 0.921. Although the differentially expressed proteins in this iTRAQ study require further validation in larger and categorized sample groups, they constitute baseline data on preliminary biomarker candidates that can be used to discover novel biomarkers for incipient DN.
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Hu, Alex, William S. Noble, and Alejandro Wolf-Yadlin. "Technical advances in proteomics: new developments in data-independent acquisition." F1000Research 5 (March 31, 2016): 419. http://dx.doi.org/10.12688/f1000research.7042.1.
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The ultimate aim of proteomics is to fully identify and quantify the entire complement of proteins and post-translational modifications in biological samples of interest. For the last 15 years, liquid chromatography-tandem mass spectrometry (LC-MS/MS) in data-dependent acquisition (DDA) mode has been the standard for proteomics when sampling breadth and discovery were the main objectives; multiple reaction monitoring (MRM) LC-MS/MS has been the standard for targeted proteomics when precise quantification, reproducibility, and validation were the main objectives. Recently, improvements in mass spectrometer design and bioinformatics algorithms have resulted in the rediscovery and development of another sampling method: data-independent acquisition (DIA). DIA comprehensively and repeatedly samples every peptide in a protein digest, producing a complex set of mass spectra that is difficult to interpret without external spectral libraries. Currently, DIA approaches the identification breadth of DDA while achieving the reproducible quantification characteristic of MRM or its newest version, parallel reaction monitoring (PRM). In comparative de novo identification and quantification studies in human cell lysates, DIA identified up to 89% of the proteins detected in a comparable DDA experiment while providing reproducible quantification of over 85% of them. DIA analysis aided by spectral libraries derived from prior DIA experiments or auxiliary DDA data produces identification and quantification as reproducible and precise as that achieved by MRM/PRM, except on low‑abundance peptides that are obscured by stronger signals. DIA is still a work in progress toward the goal of sensitive, reproducible, and precise quantification without external spectral libraries. New software tools applied to DIA analysis have to deal with deconvolution of complex spectra as well as proper filtering of false positives and false negatives. However, the future outlook is positive, and various researchers are working on novel bioinformatics techniques to address these issues and increase the reproducibility, fidelity, and identification breadth of DIA.
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Ku, Eu Jeong, Kyung-Cho Cho, Cheong Lim, et al. "Discovery of plasma biomarkers for predicting the severity of coronary artery atherosclerosis by quantitative proteomics." BMJ Open Diabetes Research & Care 8, no. 1 (2020): e001152. http://dx.doi.org/10.1136/bmjdrc-2019-001152.
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IntroductionCardiovascular disease (CVD) in patients with diabetes is the leading cause of death. Finding early biomarkers for detecting asymptomatic patients with CVD can improve survival. Recently, plasma proteomics—targeted selected reaction monitoring/multiple reaction monitoring analyses (MRM)—has emerged as highly specific and sensitive tools compared with classic ELISA methods. The objective was to identify differentially regulated proteins according to the severity of the coronary artery atherosclerosis.Research design and methodsA discovery cohort, a verification cohort and a validation cohort consisted of 18, 53, and 228 subjects, respectively. The grade of coronary artery stenosis was defined as a percentage of luminal stenosis of the major coronary arteries. Participants were divided into six groups, depending on the presence of diabetes and the grade of coronary artery stenosis. Two mass spectrometric approaches were employed: (1) conventional shotgun liquid chromatography tandem mass spectrometry for a discovery and (2) quantitative MRM for verification and validation. An analysis of the covariance was used to examine the biomarkers’ predictivity beyond conventional cardiovascular risks.ResultsA total of 1349 different proteins were identified from a discovery cohort. We selected 52 proteins based on the tandem mass tag quantitative analysis then summarized as follows: chemokine (C-X-C motif) ligand 7 (CXCL7), apolipoprotein C-II (APOC2), human lipopolysaccharide-binding protein (LBP) and dedicator of cytokinesis 2 (DOCK2) in diabetes; CXCL7, APOC2, LBP, complement 4A (C4A), vitamin D-binding protein (VTDB) and laminin β1 subunit in non-diabetes. Analysis of covariance showed that APOC2, DOCK2, CXCL7 and VTDB were upregulated and C4A was downregulated in patients with diabetes showing severe coronary artery stenosis. LBP and VTDB were downregulated in patients without diabetes, showing severe coronary artery stenosis.ConclusionWe identified significant associations between circulating APOC2, C4A, CXCL7, DOCK2, LBP and VTDB levels and the degree of coronary artery stenosis using the MRM technique.
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Bhardwaj, Megha, Tobias Terzer, Petra Schrotz-King, and Hermann Brenner. "Comparison of Proteomic Technologies for Blood-Based Detection of Colorectal Cancer." International Journal of Molecular Sciences 22, no. 3 (2021): 1189. http://dx.doi.org/10.3390/ijms22031189.
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Blood-based protein biomarkers are increasingly being explored as supplementary or efficient alternatives for population-based screening of colorectal cancer (CRC). The objective of the current study was to compare the diagnostic potential of proteins measured with different proteomic technologies. The concentrations of protein biomarkers were measured using proximity extension assays (PEAs), liquid chromatography/multiple reaction monitoring–mass spectrometry (LC/MRM-MS) and quantibody microarrays (QMAs) in plasma samples of 56 CRC patients and 99 participants free of neoplasms. In another approach, proteins were measured in serum samples of 30 CRC cases and 30 participants free of neoplasm using immunome full-length functional protein arrays (IpAs). From all the measurements, 9, 6, 35 and 14 protein biomarkers overlapped for comparative evaluation of (a) PEA and LC/MRM-MS, (b) PEA and QMA, (c) PEA and IpA, and (d) LC/MRM-MS and IpA measurements, respectively. Correlation analysis was performed, along with calculation of the area under the curve (AUC) for assessing the diagnostic potential of each biomarker. DeLong’s test was performed to assess the differences in AUC. Evaluation of the nine biomarkers measured with PEA and LC/MRM-MS displayed correlation coefficients >+0.6, similar AUCs and DeLong’s p-values indicating no differences in AUCs for biomarkers like insulin-like growth factor binding protein 2 (IGFBP2), matrix metalloproteinase 9 (MMP9) and serum paraoxonase lactonase 3 (PON3). Comparing six proteins measured with PEA and QMA showed good correlation and similar diagnostic performance for only one protein, growth differentiation factor 15 (GDF15). The comparison of 35 proteins measured with IpA and PEA and 14 proteins analyzed with IpA and LC/MRM-MS revealed poor concordance and comparatively better AUCs when measured with PEA and LC/MRM-MS. The comparison of different proteomic technologies suggests the superior performance of novel technologies like PEA and LC/MRM-MS over the assessed array-based technologies in blood-protein-based early detection of CRC.