A major challenge in proteomics is the lack of reproducibility in protein identification experiments. In LCMS/MS analyses where the same sample is analyzed in replicates, many of the low abundant peptides that are successfully identified by searching a sequence collection with the MS/MS data are only identified in one or a few of the replicate runs.
By using the detection, matching, and visualization approach ofDeCyder™ MS were retention time, precursor mass, and the topology of the intensity profile is utilized in combination with the matching of tandem mass spectra, it is possible to achieve repeat analysis with very high reproducibility.
Authors: Jenny Samskog, Henrik Wadensten, and John Flensburg, GE Healthcare/ Amersham Biosciences AB, Uppsala, Sweden
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