A Protocol for Robust Discovery Proteomics Using Nano Liquid Chromatography Using Pillar‐Array Column Technology and High‐Resolution Mass Spectrometry With Data‐Independent Acquisition

Nano liquid chromatography-mass spectrometry has come to be a key enabling technology in shotgun proteomics due to the combination of exceptional separation power, sensitivity, and comprehensiveness. However, the know-how of setting up proteomics methods to deliver robust, reliable, and meaningful results to large-scale life science experiments has remained somewhat ambiguous. This protocol outlines guidance for establishing nano-LC-MS/MS workflows focusing on comprehensive and untargeted deep proteome profiling, using state-of-the-art column technology and mass spectrometry. Employing a second-generation micropillar-array column, a trade-off is demonstrated between analysis time and chromatographic resolving power, which in turn impacts peptide and protein identification scores from a commercial HeLa reference standard. Furthermore, a straightforward workflow to develop a data-independent acquisition (DIA)-parallel accumulation-serial fragmentation (PASEF) analytical method is proposed, with a special focus on the optimization of the ESI source settings. Besides the method development, the study discusses the use of segmented gradients, and an MS-compatible surfactant in the sample diluent is also explored. Finally, the robustness of the developed method is demonstrated through consistently identifying 7558 protein groups (CV = 0.3%) as maintaining high repeatability peptide retention times (mean CV = 0.2%) and system pressure (CV = 0.4%) over 21 consecutive analyses.