Serum KLKB1 as a Potential Prognostic Biomarker for Hepatocellular Carcinoma Based on Data-Independent Acquisition and Parallel Reaction Monitoring

2021 ◽  
Author(s):  
Yi-Qun Che ◽  
Yue Zhang ◽  
Han-Bing Li ◽  
Di Shen ◽  
Wei Cui
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Biomarker ◽  
Reaction Monitoring ◽  
Parallel Reaction ◽  
Data Independent Acquisition ◽  
Parallel Reaction Monitoring

Combinatory Data-Independent Acquisition and Parallel Reaction Monitoring Method for Deep Profiling of Gangliosides

2020 ◽  
Vol 92 (15) ◽  
pp. 10830-10838
Author(s):  
Hua Li ◽  
Ruilian Xu ◽  
Lijun Yang ◽  
Hemi Luan ◽  
Shili Chen ◽  
...  
Keyword(s):  
Reaction Monitoring ◽  
Parallel Reaction ◽  
Monitoring Method ◽  
Data Independent Acquisition ◽  
Parallel Reaction Monitoring

scholarly journals Data-Independent Acquisition and Parallel Reaction Monitoring Mass Spectrometry Identification of Serum Biomarkers for Ovarian Cancer

2017 ◽  
Vol 12 ◽  
pp. 117727191771094 ◽  
Author(s):  
Navin Rauniyar ◽  
Gang Peng ◽  
TuKiet T Lam ◽  
Hongyu Zhao ◽  
Gil Mor ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Reaction Monitoring ◽  
Parallel Reaction ◽  
Reactive Protein ◽  
Data Independent Acquisition ◽  
Clinical Assay ◽  
Parallel Reaction Monitoring ◽  
Literature Searches ◽  
Mass Spectrometry Identification ◽  
Immunological Assays

A data-independent acquisition (DIA)/parallel reaction monitoring (PRM) workflow was implemented to identify improved ovarian cancer biomarkers. Data-independent acquisition on ovarian cancer versus control sera and literature searches identified 50 biomarkers and indicated that apolipoprotein A-IV (ApoA-IV) is the most significantly differentially regulated protein. Parallel reaction monitoring with Targeted Ovarian Cancer Proteome Assay validated differential ApoA-IV expression and quantified 9 other biomarkers. Random Forest (RF) analyses achieved 92.3% classification accuracy and confirmed ApoA-IV as the leading biomarker. Indeed, all samples were classified correctly with an [ApoA-IV] breakpoint. The next best biomarkers were C-reactive protein, transferrin, and transthyretin. The Targeted Ovarian Cancer Proteome Assay suggests that ApoA-IV is a more reliable biomarker than had been determined by immunological assays and it is a better biomarker than ApoA-I, which is in the OVA1 test for ovarian cancer. This research provides a PRM/RF approach together with 4 promising biomarkers to speed the development of a clinical assay for ovarian cancer.

scholarly journals PRM-MS Quantitative Analysis of Isomeric N-Glycopeptides Derived from Human Serum Haptoglobin of Patients with Cirrhosis and Hepatocellular Carcinoma

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 563
Author(s):  
Cristian D. Gutierrez Reyes ◽  
Yifan Huang ◽  
Mojgan Atashi ◽  
Jie Zhang ◽  
Jianhui Zhu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Operating Characteristic ◽  
Roc Curves ◽  
Glycosylation Site ◽  
Reaction Monitoring ◽  
Parallel Reaction ◽  
Serum Haptoglobin ◽  
Parallel Reaction Monitoring ◽  
Early Hcc ◽  
Auc Value

Currently, surveillance strategies have inadequate performance for cirrhosis and early detection of hepatocellular carcinoma (HCC). The glycosylation of serum haptoglobin has shown to have significant differences between cirrhosis and HCC, thus can be used for diagnosis. We performed a comprehensive liquid chromatography—parallel reaction monitoring—mass spectrometry (LC-PRM-MS) approach, where a targeted parallel reaction monitoring (PRM) strategy was coupled to a powerful LC system, to study the site-specific isomerism of haptoglobin (Hp) extracted from cirrhosis and HCC patients. We found that our strategy was able to identify a large number of isomeric N-glycopeptides, mainly located in the Hp glycosylation site Asn207. Four N-glycopeptides were found to have significant changes in abundance between cirrhosis and HCC samples (p < 0.05). Strategic combinations of the significant N-glycopeptides, either with alpha-fetoprotein (AFP) or themselves, better estimate the areas under the curve (AUC) of their respective receiver operating characteristic (ROC) curves with respect to AFP. The combination of AFP with the isomeric sialylated fucosylated N-glycopeptides Asn207 + 5-6-1-2 and Asn207 + 5-6-1-3, resulted with an AUC value of 0.98, while the AUC value for AFP alone was 0.85. When comparing cirrhosis vs. early HCC, the isomeric N-glycopeptide Asn207 + 5-6-0-1 better estimated AUC with respect to AFP (AUCAFP = 0.81, and AUCAsn207 + 5-6-0-1 = 0.88, respectively).

scholarly journals Thesaurus: quantifying phosphoprotein positional isomers

2018 ◽  
Author(s):  
Brian C. Searle ◽  
Robert T. Lawrence ◽  
Michael J. MacCoss ◽  
Judit Villén
Keyword(s):  
Reaction Monitoring ◽  
Positional Isomers ◽  
Parallel Reaction ◽  
Akt Signaling Pathway ◽  
Data Independent Acquisition ◽  
Fragment Ions ◽  
Parallel Reaction Monitoring ◽  
Functional States ◽  
Specific Fragment ◽  
Neighboring Sites

AbstractProteins can be phosphorylated at neighboring sites resulting in different functional states, and studying the regulation of these sites has been challenging. Here we present Thesaurus, a search engine that detects new positional isomers using site-specific fragment ions from parallel reaction monitoring and data independent acquisition mass spectrometry experiments. We apply Thesaurus to analyze phosphorylation events in the PI3K/AKT signaling pathway and show neighboring sites with distinct quantitative profiles, indicating regulation by different kinases.

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