Dataset Information

Quantitative Analysis of PRM Markers in Hybrid Bamboo

ABSTRACT: The project aimed to quantify the differential proteins in three groups of Bambusa pervariabilis × Dendrocalamopsis grandis under different treatment conditions, in order to verify the expression changes of differential proteins in three groups under different treatment conditions.

ORGANISM(S): Bambusa Pervariabilis Bambusa Grandis

SUBMITTER: Shujiang Li

PROVIDER: PXD014364 | iProX | Mon Jun 24 00:00:00 BST 2019

REPOSITORIES: iProX

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Publications

Differential Proteomics Based on TMT and PRM Reveal the Resistance Response of Bambusa pervariabilis × Dendrocalamopisis grandis Induced by AP-Toxin.

He Qianqian Q Fang Xinmei X Zhu Tianhui T Han Shan S Zhu Hanmingyue H Li Shujiang S

Metabolites 20190810 8

Bambusa pervariabilis McClure × Dendrocalamopsis grandis (Q.H.Dai & X.l.Tao ex Keng f.) Ohrnb. blight is a widespread and dangerous forest fungus disease, and has been listed as a supplementary object of forest phytosanitary measures. In order to study the control of B. pervariabilis × D. grandis blight, this experiment was carried out. In this work, a toxin purified from the pathogen Arthrinium phaeospermum (Corda) Elli, which causes blight in B. pervariabi ...[more]

PMID: 31405188

Publication: 1/2

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Project description:BackgroundClinical samples are irreplaceable, and their transformation into searchable and reusable digital biobanks is critical for conducting statistically empowered retrospective and integrative research studies. Currently, mainly data-independent acquisition strategies are employed to digitize clinical sample cohorts comprehensively. However, the sensitivity of DIA is limited, which is why selected marker candidates are often additionally measured targeted by parallel reaction monitoring.MethodsHere, we applied the recently co-developed hybrid-PRM/DIA technology as a new intelligent data acquisition strategy that allows for the comprehensive digitization of rare clinical samples at the proteotype level. Hybrid-PRM/DIA enables enhanced measurement sensitivity for a specific set of analytes of current clinical interest by the intelligent triggering of multiplexed parallel reaction monitoring (MSxPRM) in combination with the discovery-driven digitization of the clinical biospecimen using DIA. Heavy-labeled reference peptides were utilized as triggers for MSxPRM and monitoring of endogenous peptides.ResultsWe first evaluated hybrid-PRM/DIA in a clinical context on a pool of 185 selected proteotypic peptides for tumor-associated antigens derived from 64 annotated human protein groups. We demonstrated improved reproducibility and sensitivity for the detection of endogenous peptides, even at lower concentrations near the detection limit. Up to 179 MSxPRM scans were shown not to affect the overall DIA performance. Next, we applied hybrid-PRM/DIA for the integrated digitization of biobanked melanoma samples using a set of 30 AQUA peptides against 28 biomarker candidates with relevance in molecular tumor board evaluations of melanoma patients. Within the DIA-detected approximately 6500 protein groups, the selected marker candidates such as UFO, CDK4, NF1, and PMEL could be monitored consistently and quantitatively using MSxPRM scans, providing additional confidence for supporting future clinical decision-making.ConclusionsCombining PRM and DIA measurements provides a new strategy for the sensitive and reproducible detection of protein markers from patients currently being discussed in molecular tumor boards in combination with the opportunity to discover new biomarker candidates.

Dataset Information

Quantitative Analysis of PRM Markers in Hybrid Bamboo

Publications

Differential Proteomics Based on TMT and PRM Reveal the Resistance Response of <i>Bambusa pervariabilis</i> × <i>Dendrocalamopisis grandis</i> Induced by AP-Toxin.

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