Protein identification using a nanoUHPLC-AP-MALDI MS/MS workflow with CID of multiply charged proteolytic peptides

•First-time demonstration of an LC-MALDI MS/MS bottom-up proteomics workflow utilizing multiply charged precursor ions.•The developed (nanoUHP)LC-MALDI method is compatible with the use of TFA in the LC mobile phase.•Off-line analysis and extremely low sample consumption allow for multiple re-analyses of the same sample.•Storage of MALDI samples on fully spotted target plates is possible for months without significant sample degradation.

Liquid AP-MALDI can produce predominantly multiply charged ESI-like ions and stable durable analyte ion yields with samples allowing good shot-to-shot reproducibility and exhibiting self-healing properties during laser irradiation. In this study, LC-MALDI MS/MS workflows that utilize multiply charged ions are reported for the first time and compared with standard LC-ESI MS/MS for bottom-up proteomic analysis. The proposed method is compatible with trifluoroacetic acid as an LC ion pairing reagent and allows multiple MS/MS acquisitions of the LC-separated samples without substantial sample consumption. In addition, the method facilitates the storage of fully spotted MALDI target plates for months without significant sample degradation.

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