Fig. 1

Ultra-sensitive proteomics reveals regulation of cell adhesion in slow-cycling PDX ALL cells. A Experimental design of LRC proteome by diaPASEF. PDX cells of ALL-199 and ALL-265 were stained with the division-sensitive dye CFSE and transplanted into mice (n = 5 per sample). After 14 days, re-isolated PDX cells were enriched by magnetic cell sorting and slow-cycling, label-retaining cells (LRC) and fast-cycling (non-LRC) cells were separated by flow cytometry according to their CFSE content. Following lysis and protease digestion, purified peptides were injected into a nanoflow liquid chromatography (LC) system coupled online to a high-resolution TIMS quadrupole time-of-flight mass spectrometer (timsTOF Pro) using diaPASEF acquisition mode. The scheme shows quadrupole isolation windows in two-dimensional 1/K₀—m/z plane for diaPASEF acquisition with a 100 ms TIMS scan time and the diaPASEF MS/MS spectra correspond to the precursor ion selection. B Number of proteins quantified from a total of 3000 cells of LRC (n = 5) and non-LRC (n = 5) samples. Peptide and protein level FDR cut-off at 1%. C Appearance of LRCs and non-LRCs in principle component analysis (PCA). D Volcano plot displaying significantly regulated quantified proteins in LRC and non-LRC. E Box plot representation of ADAM10 which is significantly upregulated in LRC compared to non-LRC. Z-scored log2 protein intensity is displayed for proteins with permutation-based FDR cut-off < 0.05. F Gene Ontology (GO) enrichment analysis (Fisher’s exact test) of proteins significantly enriched in LRC and non-LRC. G GO network analysis of enriched pathways in LRC was built using the ClueGo app in Cytoscape. H String network map of ADAM10-interacting proteins from the LRC-regulated proteome. Nodes in red color indicate proteins with functional dependencies in leukemia cells (according to Depmap (https://depmap.org/portal/)). I Fisher’s exact test showing the enrichment of Cell adhesion and Metalloendopeptides terms from the ADAM10 network in LRCs