FIGURE 1.
(A) Experimental setup. The two strains were grown under the same conditions, washed, and each injected into three lanes of the LPITM flow cell (Step 1). The bacteria were allowed to become immobilized on the flow cell surface (1a). The immobilized bacteria were treated with trypsin to generate peptides from the exposed proteins (1b), and the peptides were eluted from the flow cell channels (1c). The trypsin-digested protein sample from each lane was split into two parts (Step 2) and analyzed in triplicate LC-MS/MS injections (Step 3) or labeled separately for combined TMT semiquantitative LC-MS/MS (Step 4). (B) Data analysis strategy.