Recent Developments in Data Independent Acquisition (DIA) Mass Spectrometry: Application of Quantitative Analysis of the Brain Proteome

Abstract

Mass spectrometry is the driving force behind current brain proteome analysis. In a typical proteomics approach, a protein isolate is digested into tryptic peptides and then analyzed by liquid chromatography–mass spectrometry. The recent advancements in data independent acquisition (DIA) mass spectrometry provide higher sensitivity and protein coverage than the classic data dependent acquisition. DIA cycles through a pre-defined set of peptide precursor isolation windows stepping through 400–1,200 m/z across the whole liquid chromatography gradient. All peptides within an isolation window are fragmented simultaneously and detected by tandem mass spectrometry. Peptides are identified by matching the ion peaks in a mass spectrum to a spectral library that contains information of the peptide fragment ions' pattern and its chromatography elution time. Currently, there are several reports on DIA in brain research, in particular the quantitative analysis of cellular and synaptic proteomes to reveal the spatial and/or temporal changes of proteins that underlie neuronal plasticity and disease mechanisms. Protocols in DIA are continuously improving in both acquisition and data analysis. The depth of analysis is currently approaching proteome-wide coverage, while maintaining high reproducibility in a stable and standardisable MS environment. DIA can be positioned as the method of choice for routine proteome analysis in basic brain research and clinical applications.

Impact of the Glycemic Level on the Salivary Proteome of Middle-Aged and Elderly People With Type 2 Diabetes Mellitus: An Observational Study

“…During the DIA process, it is independent of the composition of precursor ions for their fragmentation to implement the approach, and thus, this method improves the accuracy and precision of quantitation and has gained much popularity (Zhang et al, 2020a). This technique is widely used in various body fluids, including blood, cerebrospinal fluid, urine, and tears but is less applied in saliva (Li et al, 2020;van der Laan et al, 2020;Cheung et al, 2021;Jia et al, 2021).…”

A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration

“…This method is claimed to cover most of the low abundance and small peptides [ 50 ]. DIA identifies peptides within the selected m/z windows, and thus has merits like low missing value and good data reproducibility [ 51 , 52 ]. In addition, the protein identification can be performed by various searching engines, such as DIA-Umpire PECAN [ 53 ], or DirectDIA [ 51 ], but not limited to the conventional genome-wide species-specific database that is used in traditional MS/MS ion mass spectrum.…”

Molecular Pathways Involved in Frontotemporal Lobar Degeneration with TDP-43 Proteinopathy: What Can We Learn from Proteomics?

“…The MS workflow consists of three principal steps: (1) sample preparation including dissection, cell lysis, and protein extraction; (2) protein digestion and separation, where peptides are usually fractionated by liquid chromatography based on their hydrophobicity; and (3) protein identification and quantitation by MS, using either peptide labeling or a label-free strategy [ 12 ]. MS techniques are constantly improving, as illustrated by the current transition from traditional data-dependent acquisition (DDA; limited number of precursor peptides are semi-randomly selected) towards data-independent acquisition (DIA; identification of nearly all detectable peptides within a selected mass range), resulting in higher sensitivity and protein coverage [ 14 ]. For further technical details and examples in relation to neurodegeneration, we refer to a number of recent reviews [ 15 , 16 , 17 , 18 ].…”