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We first propose a new method to process peptide identification reports from databases search engines. Then via it we develop a method for unifying protein inference and peptide identification by adding a feedback from protein inference to peptide identification. The feedback information is a list of high‐confidence proteins, which is used to update an adjacency matrix between peptides. The adjacency...
A new method is presented to estimate the accuracy of peptide identification with logistic regression (LR)based on Sequest scores. Each peptide is characterized with the regularized Sequest scores ?Cn* and Xcorr*. The score regularization is formulated as an optimization problem by applying two assumptions: the smoothing consistency between sibling peptides and the fitting consistency between original...
Charge states of tandem mass spectra from low-resolution collision induced dissociation can not be determined by mass spectrometry. As a result, such spectra with multiple charges are usually searched multiple times by assuming each possible charge state. Not only does this strategy increase the overall database search time, but also yields more false positives. In this paper, we propose a new approach...
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