This program was directly referenced in the paper "A novel proteomic screen for peptide-protein interactions" (PDF) by Waltraud X. Schulze and Matthias Mann. 2003. Journal of Biological Chemistry (JBC). Abstract.
It was also the basis for the Nature paper "Proteomic characterization of the human centrosome by protein correlation profiling" (PDF) by Jens S. Andersen, Christopher J. Wilkinson, Thibault Mayor, Peter Mortensen, Erich A. Nigg, Matthias Mann. 2003. Abstract. Full text. On 2004-02-16 this paper was number 4 on Nature’s top 10 most downloaded papers.
SILAC is originally described in "Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics." (full text) by Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. 2002. Abstract 1. Abstract 2.
SILAC is described in greater detail in "Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC)." (full text NOT available online) by Ong SE, Kratchmarova I, Mann M. 2003. Abstract.
Triple encoding for SILAC is described in "Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics." (full text as PDF file) by Blagoev B, Ong SE, Kratchmarova I, Mann M. 2004. Local copy. Abstract.
MS3 scoring is described in "Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation" by Jesper V. Olsen and Matthias Mann. 2004. As PDF file. Abstract.