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Error‐tolerant EST database searches by tandem mass spectrometry and multiTag software

The MultiTag method (Sunyaev et al., Anal. Chem. 2003 15, 1307–1315) employs multiple error‐tolerant searches with peptide sequence tags (Mann and Wilm, Anal. Chem. 1994, 66, 4390–4399) for the identification of proteins from organisms with unsequenced genomes. Here we demonstrate that the error‐tolerant capabilities of MultiTag increased the number of peptide alignments and improved the confidence of identifications in an EST database. The MultiTag outperformed conventional database searching software that only utilizes stringent matching of tandem mass spectra to nucleotide sequences of ESTs.