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Benchmarking DIA data analysis workflows

ABSTRACT: Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still a lot of possibilities at the data analysis level. By benchmarking different DIA analysis workflows through a ground truth sample mimicking real differential abundance samples, consisting of a differential spike-in of UPS2 in a constant yeast background, we provide a roadmap for DIA data analysis of shotgun samples based on whether sensitivity, precision or accuracy is of the essence. Three different commonly used DIA software tools (DIA-NN, EncyclopeDIA and SpectronautTM) were tested in both spectral library mode and spectral library free mode. In spectral library mode we used the independent spectral library prediction tools Prosit and MS2PIP together with DeepLC, next to the classical DDA-based spectral libraries. In total we benchmarked 12 DIA workflows. DIA-NN in library free mode or using in silico predicted libraries shows the highest sensitivity maintaining a high reproducibility and accuracy.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: An Staes

LAB HEAD: Simon Devos

PROVIDER: PXD044981 | Pride | 2024-05-06

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	B000248_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio01_DDA.raw	Raw
	B000250_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio01_DIA.raw	Raw
	B000252_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio02_DDA.raw	Raw
	B000254_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio02_DIA.raw	Raw
	B000256_Ap_6883_EXT-765_DIA_Yeast_UPS2_ratio04_DDA.raw	Raw

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