Dataset Information

High-throughput proteomics and phosphoproteomics of rat tissues using micro-flow Zeno SWATH

ABSTRACT: We investigated the combined sensitivity of micro-flow liquid chromatography with a ZenoTOF mass spectrometer for high throughput proteomic and phosphoproteomic analysis of rat tissues. Comparing the proteomes acquired using data-independent acquisition (DIA) on the ZenoTOF 7600 with the previous generation TripleTOF 6600, more proteins were quantified using a fifth of the sample load and a third of the instrument time. Zeno SWATH data was evaluated using replicate injections of rat organ digests to compare FragPipe and DIA-NN computational pipelines. FragPipe identified more proteins in 7 of the 8 rat organs, with an extra 12% and 17% observed in heart and muscle tissue respectively. The number of identified peptides per protein were higher with FragPipe and the precision of missing values across replicate injections was more consistent. Single-shot phosphopeptide enrichment from 100 µg rat tissue, without fractionation, was acquired using data-dependent acquisition (DDA) on both instruments. A total of 5,108 phosphosites were quantified with a negligible increase in phosphosites found using the ZenoTOF 7600 relative to the 6600. Using DIA on the ZenoTOF, 8,013 phosphosites were quantified using Spectronaut.

INSTRUMENT(S): SCIEX instrument model

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Spleen, Heart, Testis, Brain, Lung, Liver, Kidney

SUBMITTER: Erin Humphries

LAB HEAD: Phillip J.

PROVIDER: PXD045472 | Pride | 2024-06-02

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20190717_RRP_SWISS_Canon_Rat_PhosphoSpikeMix.fasta	Fasta
	20220901_EMH_HEK_MS2acc01_100VW_7600_ZS.wiff	Wiff
	20220901_EMH_HEK_MS2acc01_100VW_7600_ZS.wiff.scan	Wiff
	20220901_EMH_HEK_MS2acc01_25VW_7600_ZS.wiff	Wiff
	20220901_EMH_HEK_MS2acc01_25VW_7600_ZS.wiff.scan	Wiff

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High-throughput proteomics and phosphoproteomics of rat tissues using micro-flow Zeno SWATH

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