Start with the elimination of the protein content. Protein precipitation plates or organic solvent precipitation may be used for this purpose. Homogenize the sample by adding a small amount of ultra-pure water and next, add a certain amount of ACN to precipitate the proteome. Spin down the protein pellet and inject the supernatant after syringe filtration. To get the best peak shape you need to dilute the supernatant to decrease the ACN percentage. Alternatively, the Folch method can be applied as tertiary solvent extraction. It is advisable to spike at least one isotope molecule as an internal standard and always prepare a pool QC sample.
https://www.elsevier.com/books/modern-sample-preparation-for-chromatography/moldoveanu/978-0-12-821405-3
https://www.technologynetworks.com/analysis/articles/liquid-chromatography-including-hplc-uhplc-and-lcxlc-344048
https://www.thermofisher.com/de/de/home/industrial/mass-spectrometry/mass-spectrometry-learning-center/liquid-chromatography-mass-spectrometry-lc-ms-information/lc-ms-sample-preparation.html#:~:text=Total%20LC%2FMS%20sample%20preparation,final%20elution%20from%20the%20column.
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