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DIA-enabled discovery of alternative proteins (AltProts) in mouse heart development

ABSTRACT: In this project, we conducted an evaluation of mass spectrometry methods using mouse heart and HCT116 cell samples. The results demonstrated that the data-independent acquisition (DIA) approach outperformed data-dependent acquisition (DDA) in the identification of Altprot and canonical proteins. Subsequently, we assessed several different DIA library building methods, including traditional DDA-based library building, gas-phase fractionation(GPF) library building, and machine learning-based prediction library building. Notably, the traditional DDA library building method exhibited a higher likelihood of false positive identifications. Furthermore, we applied the aforementioned mass spectrometry methods to investigate the process of mouse heart development. Through this analysis, we identified a subset of Altprots, including ASDURF, which may potentially play crucial roles in heart development. These findings serve as a fundamental basis for future exploration and investigation of Altprot in this context.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Heart

SUBMITTER: Yuanliang Zhang

LAB HEAD: Qian Zhao

PROVIDER: PXD045956 | Pride | 2025-01-17

REPOSITORIES: pride

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			Action	DRS
	20211226_Adult_DIA_A1.raw	Raw
	20211226_Adult_DIA_A2.raw	Raw
	20211226_Adult_DIA_A3.raw	Raw
	20211226_Adult_DIA_A4.raw	Raw
	20211226_Embryo_DIA_E1.raw	Raw

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Project description:A quadrupole time-of-flight mass spectrometry coupled with a trapped ion mobility mass spectrometer operated in parallel accumulation-serial fragmentation mode has recently emerged as proteome profiling platform capable of providing four dimensional features of elution time, collision cross section, precursor and fragment ion masses of peptides. The PASEF mode has demonstrated its superior performance by providing nearly 100% ion sampling efficiency both in data-dependent acquisition and data-independent acquisition modes without sacrificing sensitivity. In addition, the substantial gain in selectivity has been proven in targeted measurements using PASEF integrated parallel reaction monitoring mode. However, because these are emerging technologies in the field of proteomics, their applicability to clinical samples has been less investigated. Cerebrospinal fluid is in direct contact with brain and has been shown to contain biomarkers related to a variety of neurological diseases although the proteomics data have been mainly generated using orbitrap-based mass spectrometers. Thus, we acquired in-depth proteome profiles of human CSF in DDA mode to generate a spectral library of 3,478 proteins. The benefit of applying the spectral library to PRM experiments was demonstrated by using CSF samples from 15 Alzheimer’s disease patients and 19 controls and utilizing the spectral library to determine elution times and ion mobility values of targeting peptide. Further, we acquired DIA data from the same CSF samples, and analyzed using the spectral library without additional efforts to generate study-specific library, which also resulted in sensitive protein identification compared to a library-free approach. Overall, we established resource of CSF proteome profiles with 4D features and demonstrated the significant gain for designing and analyzing targeted and DIA studies, which is expected to facilitate 4D proteomics of CSF to study various neurological disorders.

Dataset Information

DIA-enabled discovery of alternative proteins (AltProts) in mouse heart development

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