Integration of data‐independent acquisition (DIA) with co‐fractionation mass spectrometry (CF‐MS) to enhance interactome mapping capabilities

Abstract

Proteomics technologies are continually advancing, providing opportunities to develop stronger and more robust protein interaction networks (PINs). In part, this is due to the ever‐growing number of high‐throughput proteomics methods that are available. This review discusses how data‐independent acquisition (DIA) and co‐fractionation mass spectrometry (CF‐MS) can be integrated to enhance interactome mapping abilities. Furthermore, integrating these two techniques can improve data quality and network generation through extended protein coverage, less missing data, and reduced noise. CF‐DIA‐MS shows promise in expanding our knowledge of interactomes, notably for non‐model organisms (NMOs). CF‐MS is a valuable technique on its own, but upon the integration of DIA, the potential to develop robust PINs increases, offering a unique approach for researchers to gain an in‐depth understanding into the dynamics of numerous biological processes.

mini-Complexome Profiling (mCP), an FDR-controlled workflow for global targeted detection of protein complexes

“…These samples are then analyzed using DIA-MS with short gradients (Bludau et al, 2023;Fossati et al, 2021a). The integration of CF-MS with DIA-MS has been demonstrated to produce highly reproducible and comprehensive complexome profiling data (Hay et al, 2023). The use of short gradients for DIA-MS acquisition leads to only a minor loss of information compared to longer gradient acquisitions, while also increasing throughput.…”

Profiling Protein–Protein Interactions in the Human Brain by Refined Cofractionation Mass Spectrometry

“…Moreover, CF-MS can analyze the distribution of the same protein in different fractions, elucidating the stoichiometries and dynamics of any given protein within distinct coisolated complexes. Integrating CF-MS with the data-independent acquisition (DIA) method has been shown to improve the sensitivity of the CF-MS technique. − Unlike the data-dependent acquisition (DDA) mode, which selects peptides based on their intensity for fragmentation, The DIA selects all peptides within a defined m / z range . Thus, incorporating DIA in CF-MS expands protein coverage, reducing missing data …”

“…38 Thus, incorporating DIA in CF-MS expands protein coverage, reducing missing data. 36 While global interactome studies with CF-MS have been applied to a wide diversity of organisms and model systems, 28,29,33,39 this approach has yet to be applied to human clinical samples, such as brain tissues. However, understanding the human brain protein interactome is crucial to decipher human-specific and brain-specific characteristics as well as related brain functions and diseases, including Alzheimer's disease (AD), Parkinson's disease, and schizophrenia.…”

“…Integrating CF-MS with the data-independent acquisition (DIA) method has been shown to improve the sensitivity of the CF-MS technique. − Unlike the data-dependent acquisition (DDA) mode, which selects peptides based on their intensity for fragmentation, The DIA selects all peptides within a defined m / z range . Thus, incorporating DIA in CF-MS expands protein coverage, reducing missing data …”