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A D The following figures are divided in eight parts and are named panel A to H respectively (see figure on the right). For each mixture spectrum M we identify the top pair of single-peptide spectrum from the library. This top pair is referred to as A and B. A always refer to the high-abundance peptide in the mixture. Panel A: MS1 isotopic profile for A Panel B: MS1 isotopic profile for M Panel C: MS1 isotopic profile for B Panel H: Empty Panel D: MS2 for A Panel E: MS2 for M Panel F: MS2 for B Panel G: Artificially constructed mixture spectrum by combining A and B together and scaling them with our estimated alpha B E C F G H