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Rat retinae data for use as spectral library, for pathway remodelling as well as protein mapping

ABSTRACT: Spectral libraries generated by data-dependent acquisition (DDA) are a useful tool for the analysis of data created by data-independent acquisition (DIA) in mass spectrometry. The quality of DIA analysis is dependent on the quality of the spectral library. We used retinal rat tissue to create a spectral library of rats retina proteome. This data set may therefore be valuable for the future analysis of retinal proteins and research projects that focus on ocular disorders or function.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Retinal Cell, Retina

DISEASE(S): Eye Disease

SUBMITTER: Annika Guntermann

LAB HEAD: Caroline May

PROVIDER: PXD021937 | Pride | 2021-06-08

REPOSITORIES: Pride

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Project description:Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups. Here we developed a bioinformatics workflow called MetaboDIA to build customized MS/MS spectral libraries using a user's own data dependent acquisition (DDA) data and to perform MS/MS-based quantification with DIA data, thus complementing conventional MS1-based quantification. MetaboDIA also allows users to build a spectral library directly from DIA data in studies of a large sample size. Using a marine algae data set, we show that quantification of fragment ions extracted with a customized MS/MS library can provide as reliable quantitative data as the direct quantification of precursor ions based on MS1 data. To test its applicability in complex samples, we applied MetaboDIA to a clinical serum metabolomics data set, where we built a DDA-based spectral library containing consensus spectra for 1829 compounds. We performed fragment ion quantification using DIA data using this library, yielding sensitive differential expression analysis. </br></br> Serum metabolome of 40 age-related macular degeneration patients and 20 control samples was analyzed using untargeted mass spectrometry. We used data dependent acquisition data to build a MS/MS spectral assay library for more than 1,000 compounds and performed targeted extraction of MS2 ion chromatograms from data independent acquisition analysis.

			Action	DRS
	QExHF04907.mzXML	Mzxml
	QExHF04907.raw	Raw
	QExHF04909.mzXML	Mzxml
	QExHF04909.raw	Raw
	QExHF04911.mzXML	Mzxml

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Rat retinae data for use as spectral library, for pathway remodelling as well as protein mapping

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