Xenbase Image ID: 131862

Figure 1. MS Data Can Be Used to Evaluate Relative Reference Database Quality Spectra from a tryptic digest of yeast lysate were searched against the standard yeast protein database (Full DB). Shown are the number of total peptide spectral matches (blue), unique peptides (orange), or proteins (black) that were confidently identified. To simulate poor reference databases, we removed half (Half DB) or three-quarters of proteins (Quarter DB) from the reference database. The number of identified PSMs and unique peptides scale approximately with the number of proteins in the database. To test how the addition of nonsense sequences would affect the number of identified peptides, we added randomized human proteins to the full yeast database (Full DB + Nonsense). The numbers of peptides and proteins are negatively affected. To simulate a reference database in which proteins are fragmented, we divided at a random position every protein in the reference into two proteins. Whereas the number of identified peptides slightly decreases, the number of identified proteins substantially increases. Image published in: Wühr M et al. (2014) Copyright © 2014. Image reproduced with permission of the Publisher, Elsevier B. V. Larger Image Printer Friendly View

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