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Many software tools have been developed for the automated identification of peptides from tandem mass spectra. The accuracy and sensitivity of the identification software via database search are critical for successful proteomics experiments. A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the(More)
MOTIVATION The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem. (More)
This paper presents a new approach to distortion (phrase reordering) in phrasebased machine translation (MT). Distortion is modeled as a sequence of choices during translation. The approach yields trainable, probabilistic distortion models that are global: they assign a probability to each possible phrase reordering. These “segment choice” models (SCMs) can(More)
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