Proteomic stable isotope probing. 1. Methodology development: (1) Shotgun proteomics analysis with high-resolution tandem mass spectrometry using LTQ-Orbitrap; (2) Peptide identification and enrichment ratio estimation by a new algorithm: Sipros - freely available at code.google.com/p/sipros. 2. Validation using standard samples with known 15N enrichment ratios: thousands of proteins identified and enrichment ratio estimated accurately. Re-growth of microbial biofilm: (1) Track the incorporation of 15N into the regrowing biofilm. Use the established biofilm as control. (2) Selective migration of microorganisms during different phases of re-growth. Pathway analysis revealed metabolic activities of the migrating microorganisms.
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