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Quantitative proteomics experimental design overview. A fibroblast validation cohort (VC), HEK293T knockout cohort (KC), undiagnosed patient cohort (UDP) and supporting cohort (SC) prepared using S-Trap columns. Digested peptides were subjected to liquid chromatography tandem mass spectrometry (LC–MS/MS) data-independent acquisition (DIA). Pooled control peptides were fractionated using strong cation exchange (SCX) chromatography and data acquired as data-dependent acquisition (DDA) to generate spectral libraries for fibroblasts (Fbs), HEK293T (HEK) and PBMCs. Raw data were searched using Spectronaut software and data analyses were performed with a combination of Perseus software, Python and R.

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