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Synergistic utilization of FAIMS and Ion Trap to Improve LFQ quantitation for Trace Samples

ABSTRACT: This project utilize the state of the art FAIMS device and systematically optimized the parameters for LC, FAIMS and MS/MS acquisition method. Finally, the optimized method was successfully applied to the animal model to uncover novel targets for therapy.

ORGANISM(S): Mus Musculus

SUBMITTER: Qi Chen

PROVIDER: PXD059534 | iProX | Tue Apr 15 00:00:00 BST 2025

REPOSITORIES: iProX

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Evaluation and Optimization of High-Field Asymmetric Waveform Ion Mobility Spectrometry for Multiplexed Quantitative Site-specific N-glycoproteomics

Project description:The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has shown to improve the scope of bottom-up proteomics. The benefits of FAIMS for quantitative N-glycoproteomics have not been investigated yet. In this work, we optimized FAIMS settings for N-glycopeptide identification, with or without the tandem mass tag (TMT) label. The optimized FAIMS approach significantly increased the identification of site-specific N-glycopeptides derived from the purified IgM protein or human lymphoma cells. We explored in detail the changes in FAIMS mobility caused by N-glycopeptides with different characteristics, including TMT labeling, charge state, glycan type, peptide sequence, glycan size and precursor m/z. Importantly, FAIMS also improved multiplexed N-glycopeptide quantification, both with the standard MS2 acquisition method and with our recently developed Glyco-SPS-MS3 method. The combination of FAIMS and Glyco-SPS-MS3 provided the highest quantitative accuracy and precision. Our results demonstrate the advantages of FAIMS for improved mass-spectrometry-based qualitative and quantitative N-glycoproteomics.

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Low Level of Dietary Organic Trace Elements Improve the Eggshell Strength, Trace Element Utilization, and Intestinal Function in Late-Phase Laying Hens.

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Coupling high-field asymmetric ion mobility spectrometry with capillary electrophoresis-electrospray ionization-tandem mass spectrometry improves protein identifications in bottom-up proteomic analysis of low nanogram samples

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An integrated 5'- and 3'-end RNA sequencing platform for high-throughput transcriptome quantitation and annotation

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