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.

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 Cell Wall Strengthening and Remodeling Provide New Insights on Sclerotia Development of Medicinal Fungus Polyporus Umbellatus

2020 ◽  
Author(s):  
Bing Li ◽  
Le Sun ◽  
Yongmei Xing ◽  
Liu Liu ◽  
Shunxing Guo
Keyword(s):  
Cell Wall ◽  
Wall Thickening ◽  
Reaction Monitoring ◽  
Differentially Expressed Proteins ◽  
Parallel Reaction ◽  
Fungal Cell ◽  
Medicinal Fungus ◽  
Polyporus Umbellatus ◽  
Fragment Ions ◽  
Parallel Reaction Monitoring

Abstract Sclerotium is a special form of many species of fungi and cell wall thickening is a common phenomenon in sclerotium. Rational manipulation of sclerotium would be an innovative approach for pathogenic control as well as for medicinal fungal resource revival. Sclerotia of Polyporus umbellatus were used to treat multiple human diseases. However, the mechanism of thickened cell wall (TCW) is still unclear. In this study, Sequential Windowed Acquisition of all THeoretical fragment ions spectra-MS (SWATH-MS) and parallel reaction monitoring (PRM) technology were introduced to demonstrate biomarkers at protein level associated with TCW as sclerotia development from initial sclerotia (IS) to developmental and mature sclerotia (DS and MS). 72 differentially expressed proteins (DEPs) were associated with TCW, and evidence supported presence and accumulation of chitin, glycan, xylcan and hydrophobins in the cell wall of P. umbellatus sclerotia. Puctg112, a new hydrophobin in P. umbellatus expressed up sharply with DS/IS 119.85 and MS/IS 128.17, and located at cell wall and septum of hypha in sclerotia by immune colloidal gold technique. In addition, sclerotial cell wall could be remodeled via O-mannosylation, O-fucosylation and deacetylation to strengthen cell wall. This study provides new insights on fungal cell wall especially to sclerotia-formed fungus.

scholarly journals Differential urine proteome analysis of a bovine IRBP induced uveitis rat model by discovery and parallel reaction monitoring proteomics

2019 ◽  
Author(s):  
Weiwei Qin ◽  
Lujun Li ◽  
Ting Wang ◽  
Youhe Gao
Keyword(s):  
Rat Model ◽  
Urinary Protein ◽  
Urine Samples ◽  
Reaction Monitoring ◽  
Parallel Reaction ◽  
Experimental Autoimmune Uveitis ◽  
Autoimmune Uveitis ◽  
Data Independent Acquisition ◽  
Parallel Reaction Monitoring ◽  
Experimental Autoimmune

AbstractUveitis, a group of intraocular inflammatory diseases, is one of the major causes of severe visual impairment among working age population. Urine is a promising resource for biomarker research, which could sensitively reflect the changes of the body. This study was designed to explore urinary protein biomarkers for diagnosis and/or monitoring of uveitis. Experimental autoimmune uveitis (EAU) rat model induced by bovine interphotoreceptor retinoid-binding protein (IRBP) was used to mimic the uveitis. In the discovery phase, urine samples from EAU and control rats were analyzed by data independent acquisition (DIA) approach combined with high-resolution mass spectrometry. Overall, 704 high confidential proteins were identified, of which 100 were differentially expressed (37, 33, 37, and 44 on day 5, 8, 12, and 16, respectively, after bovine IRBP immunization) (1.5-fold change, P<0.05). Gene Ontology analysis of the dysregulated proteins showed that chronic inflammatory response, neutrophil aggregation and immune system processes were significantly enriched. Finally, parallel reaction monitoring (PRM) approach was used for further validation. A total of 12 urinary proteins (MMP8, NGAL, HPT, UROM, RISC, A1AG, TTHY, KNT1, C9, PTER, CBG, and FUCA1) changed significantly, even when there is no clinical manifestations and histopathological ocular damages in the EAU rats. Our findings represent the first step towards urinary protein diagnostic biomarkers for uveitis.Biological SignificanceThis is the first study investigating urinary protein candidate biomarkers for uveitis using data independent acquisition (DIA) combined with parallel reaction monitoring (PRM) in experimental autoimmune uveitis (EAU) rats. The results revealed that urine is a promising resource for early diagnostics of uveitis. Further research including clinical urine samples is needed to determine the sensitivity and specificity of these candidate biomarkers for uveitis.

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