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. Author manuscript; available in PMC: 2011 Feb 5.

Published in final edited form as: J Proteome Res. 2010 Feb 5;9(2):761. doi: 10.1021/pr9006365

Peptide identifications from major proteins are more repeatable than those from minor proteins. Yeast data from Study 5, however, reveal that peptides from major proteins (here defined as those producing more than 32 peptides in the data accumulated for all instruments) constitute 40% of the peptides observed in all six replicates and 18% of the peptides observed in only one replicate. Peptides that are the sole evidence for a protein constitute 0% of the peptides observed in all six replicates but 13% of the peptides observed only once. These trends illustrate that major proteins contribute peptides across the entire range of repeatability. Achieving optimal sensitivity requires the acceptance of less-repeated peptides; in this data set, single-observation peptides were more than twice as numerous as any other set.

Peptide identifications from major proteins are more repeatable than those from minor proteins. Yeast data from Study 5, however, reveal that peptides from major proteins (here defined as those producing more than 32 peptides in the data accumulated for all instruments) constitute 40% of the peptides observed in all six replicates and 18% of the peptides observed in only one replicate. Peptides that are the sole evidence for a protein constitute 0% of the peptides observed in all six replicates but 13% of the peptides observed only once. These trends illustrate that major proteins contribute peptides across the entire range of repeatability. Achieving optimal sensitivity requires the acceptance of less-repeated peptides; in this data set, single-observation peptides were more than twice as numerous as any other set.

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