Use of multiple reaction monitoring for multiplex analysis of colorectal cancer-associated proteins in human feces

2011 ◽  
Vol 32 (15) ◽  
pp. 1926-1938 ◽  
Author(s):  
Ching-Seng Ang ◽  
Julie Rothacker ◽  
Heather Patsiouras ◽  
Peter Gibbs ◽  
Antony W. Burgess ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Multiple Reaction Monitoring ◽  
Reaction Monitoring ◽  
Human Feces ◽  
Multiplex Analysis ◽  
Associated Proteins

scholarly journals Clinical Assay for the Early Detection of Colorectal Cancer Using Mass Spectrometric Wheat Germ Agglutinin Multiple Reaction Monitoring

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2190
Author(s):  
I-Jung Tsai ◽  
Emily Chia-Yu Su ◽  
I-Lin Tsai ◽  
Ching-Yu Lin
Keyword(s):  
Colorectal Cancer ◽  
Wheat Germ Agglutinin ◽  
Wheat Germ ◽  
Early Stage ◽  
Multiple Reaction Monitoring ◽  
Machine Learning Algorithms ◽  
Test Machine ◽  
Reaction Monitoring ◽  
Plasma Samples ◽  
Clinical Biomarkers

Colorectal cancer (CRC) is currently the third leading cause of cancer-related mortality in the world. U.S. Food and Drug Administration-approved circulating tumor markers, including carcinoembryonic antigen, carbohydrate antigen (CA) 19-9 and CA125 were used as prognostic biomarkers of CRC that attributed to low sensitivity in diagnosis of CRC. Therefore, our purpose is to develop a novel strategy for novel clinical biomarkers for early CRC diagnosis. We used mass spectrometry (MS) methods such as nanoLC-MS/MS, targeted LC-MS/MS, and stable isotope-labeled multiple reaction monitoring (MRM) MS coupled to test machine learning algorithms and logistic regression to analyze plasma samples from patients with early-stage CRC, late-stage CRC, and healthy controls (HCs). On the basis of our methods, 356 peptides were identified, 6 differential expressed peptides were verified, and finally three peptides corresponding wheat germ agglutinin (WGA)-captured proteins were semi-quantitated in 286 plasma samples (80 HCs and 206 CRCs). The novel peptide biomarkers combination of PF454–62, ITIH4429–438, and APOE198–207 achieved sensitivity 84.5%, specificity 97.5% and an AUC of 0.96 in CRC diagnosis. In conclusion, our study demonstrated that WGA-captured plasma PF454–62, ITIH4429–438, and APOE198–207 levels in combination may serve as highly effective early diagnostic biomarkers for patients with CRC.

scholarly journals Tracking the Antibody Immunome in Sporadic Colorectal Cancer by Using Antigen Self-Assembled Protein Arrays

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2718
Author(s):  
María González-González ◽  
José María Sayagués ◽  
Luis Muñoz-Bellvís ◽  
Carlos Eduardo Pedreira ◽  
Marcello L. R. de Campos ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Utility ◽  
Genetic Alterations ◽  
Western World ◽  
Sporadic Colorectal Cancer ◽  
Protein Arrays ◽  
Humoral Immune ◽  
Cellular Processes ◽  
Healthy Donors ◽  
Associated Proteins

Sporadic Colorectal Cancer (sCRC) is the third leading cause of cancer death in the Western world, and the sCRC patients presenting with synchronic metastasis have the poorest prognosis. Genetic alterations accumulated in sCRC tumor cells translate into mutated proteins and/or abnormal protein expression levels, which contribute to the development of sCRC. Then, the tumor-associated proteins (TAAs) might induce the production of auto-antibodies (aAb) via humoral immune response. Here, Nucleic Acid Programmable Protein Arrays (NAPPArray) are employed to identify aAb in plasma samples from a set of 50 sCRC patients compared to seven healthy donors. Our goal was to establish a systematic workflow based on NAPPArray to define differential aAb profiles between healthy individuals and sCRC patients as well as between non-metastatic (n = 38) and metastatic (n = 12) sCRC, in order to gain insight into the role of the humoral immune system in controlling the development and progression of sCRC. Our results showed aAb profile based on 141 TAA including TAAs associated with biological cellular processes altered in genesis and progress of sCRC (e.g., FSCN1, VTI2 and RPS28) that discriminated healthy donors vs. sCRC patients. In addition, the potential capacity of discrimination (between non-metastatic vs. metastatic sCRC) of 7 TAAs (USP5, ML4, MARCKSL1, CKMT1B, HMOX2, VTI2, TP53) have been analyzed individually in an independent cohort of sCRC patients, where two of them (VTI2 and TP53) were validated (AUC ~75%). In turn, these findings provided novel insights into the immunome of sCRC, in combination with transcriptomics profiles and protein antigenicity characterizations, wich might lead to the identification of novel sCRC biomarkers that might be of clinical utility for early diagnosis of the tumor. These results explore the immunomic analysis as potent source for biomarkers with diagnostic and prognostic value in CRC. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these novel sCRC immunomic biomarkers.

scholarly journals PSV-25 Detection of heart and aorta tissue peptide markers by the multiple-reaction monitoring method

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 362-363
Author(s):  
Daniil Khvostov ◽  
Natalya Vostrikova ◽  
Irina M Chernukha
Keyword(s):  
Amino Acid ◽  
High Performance ◽  
Multiple Reaction Monitoring ◽  
Meat Product ◽  
Meat Products ◽  
Amino Acid Sequences ◽  
Composition Analysis ◽  
Reaction Monitoring ◽  
Russian Science ◽  
Monitoring Method

Abstract Functional, particularly personalized meat-based foods are of more in demand by a consumer today. Functional additives, such as plant components and animal proteins from bovine or porcine tissues have been successfully used. With many ingredients added to foods, it is important to provide quality and composition monitoring to confirm the products’ authenticity, to identify undeclared or rarely used types of raw meat in product formulations. For example, if animal heart tissue is a component of a product formulation or if aorta tissue presents in a product due to improper trimming. Different methods are used to identify raw materials, including new approaches in proteomics and peptidomics that are considered the most effective modern methods nowadays. The purpose of the study is meat product composition analysis and special biomarker peptide identification to confirm the presence of heart and aorta tissue in a finished meat product. Over 20 amino acid sequences were checked based on earlier obtained data. Those amino acid sequences were analyzed with a high-performance liquid chromatography with mass spectrometric detection as described. The MS settings were selected using the Skyline. Signal-to-Noise ratio (S/N) over 10 units were used to choose the best peptide candidates. Seven peptides were found in porcine hearts. The best candidate was peptide VNVDEVGGEALGR (S/N - 73.10±5.3) from β-Hemoglobin. Two marker peptides from serum albumin were selected for pork aorta: TVLGNFAAFVQK (S/N 53.51±2.4) and EVTEFAK (S/N 31.69±4.1). These biomarkers showed the best detection and specificity. The multiply reaction monitoring method made it possible to identify the most/best specific peptides—biomarkers that could confirm the heart and/or aorta in meat products. The method can be used for comparative research or identification of best peptides that are specific to any type of animal tissue. The work was supported by the Russian Science Foundation, project no. 16-16- 10073.

scholarly journals Calcineurin Activity Assay Measurement by Liquid Chromatography–Tandem Mass Spectrometry in the Multiple Reaction Monitoring Mode

2014 ◽  
Vol 60 (2) ◽  
pp. 353-360 ◽  
Author(s):  
Lynn Carr ◽  
Anne-Laure Gagez ◽  
Marie Essig ◽  
François-Ludovic Sauvage ◽  
Pierre Marquet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Mononuclear Cells ◽  
Multiple Reaction Monitoring ◽  
Internal Standard ◽  
Reaction Monitoring ◽  
Activity Assay ◽  
Peripheral Blood Mononuclear ◽  
Blood Concentrations ◽  
Transplant Patients

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.

scholarly journals Comparison of Protein Immunoprecipitation-Multiple Reaction Monitoring with ELISA for Assay of Biomarker Candidates in Plasma

2013 ◽  
Vol 12 (12) ◽  
pp. 5996-6003 ◽  
Author(s):  
De Lin ◽  
William E. Alborn ◽  
Robbert J. C. Slebos ◽  
Daniel C. Liebler
Keyword(s):  
Multiple Reaction Monitoring ◽  
Reaction Monitoring
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