Secondary Ion Mass Spectrometry (SIMS) is a well established method for sensitive surface atomic and molecular analysis. Protein analysis with conventional SIMS has been attempted numerous times; however it delivers exclusively fragment peaks assigned to α-amino acids or immonium ions. In this paper we report experiments where direct sequence information could be measured thanks to a combination of HPLC separation with matrix enhanced SIMS (ME-SIMS) on tryptic digests of intact proteins. We employ peptide mass fingerprinting (PMF) and protein identification through the detection of HPLC-separated digests of Savinase (Sav.) and bovine serum albumin (BSA), followed by MASCOT search. This is the first time that the possibility of full protein identification using LC-ME-SIMS is demonstrated in a classic proteomics workflow and that a 69 kDa protein is identified with SIMS. These results demonstrate both the relevance and the potential of LC-ME-SIMS in future high resolution proteomics studies.
J. Proteomics

MacAleese, L, Duursma, M.C, Klerk, L.A, Fisher, G, & Heeren, R.M.A. (2011). Protein identification with Liquid Chromatography and Matrix Enhanced Secondaty Ion Mass Spectrometry (LC-ME-SIMS). J. Proteomics, 74(7), 993–1001. doi:10.1016/j.jprot.2011.02.009