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Robust, Precise and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme

ABSTRACT: Current deep proteome profiling methods rely on fractionations, elaborate chromatography and mass spectrometry setups or display suboptimal quantitative precision. We set out to develop an easy-to-use one shot DIA method that achieves high quantitative precision and high proteome coverage. We achieve this by focusing on a small mass range of 430-670 m/z using small isolation windows without overlap. With this new method we were able to quantify over 9200 protein groups in HEK lysates with an average coefficient of variance of 3.2 percent. We then applied our newly developed Narrow Mass Range method to murine samples to investigate the effect of PGC-1alpha knock-out on skeletal muscle, where we could increase proteome coverage by 98 percent as compared to a data dependent acquisition method. We believe that our method will be especially helpful in quantifying low abundant proteins in samples with a high dynamic range.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Alexander Schmidt

PROVIDER: MSV000092186 | MassIVE | Fri Jun 16 02:56:00 BST 2023

REPOSITORIES: MassIVE

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