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O-glycosylation is one of the most important, frequent and complex post-translational modifications. This modification can activate and affect protein functions. Here, we present three support vector machines models based on physical properties, 0/1 system, and the system combining the above two features. The prediction accuracies of the three models have(More)
Protein SUMO modification is an important post-translational modification and the optimization of prediction methods remains a challenge. Here, by using Support Vector Machines algorithm (SVM), a novel computational method was developed for SUMO modification site prediction based on Sequential Forward Selection (SFS) of hundreds of amino acid properties,(More)
We estimated the reproducibility of tandem mass spectra for the widely used collision-induced dissociation (CID) of peptide ions. Using the Pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). However, across different experiments and(More)
Protein N-glycosylation plays an important role in protein function. Yet, at present, few computational methods are available for the prediction of this protein modification. This prompted our development of a support vector machine (SVM)-based method for this task, as well as a partial least squares (PLS) regression based prediction method for comparison.(More)
Adipocyte is not only a central player involved in storage and release of energy, but also in regulation of energy metabolism in other organs via secretion of peptides and proteins. During the pathogenesis of insulin resistance and type 2 diabetes, adipocytes are subjected to the increased levels of insulin, which may have a major impact on the secretion of(More)
In order to find evidence for translation of alternatively spliced transcripts, especially those that result in a change in reading frame, we collected exon-skipping cases previously found by RNA-Seq and applied a computational approach to screen millions of mass spectra. These spectra came from seven human and six mouse tissues, five of which are the same(More)
One of the important objectives in mass spectrometry-based proteomics is the identification of post-translationally modified sites in cellular and extracellular proteomes. Proteomics techniques have been particularly effective in studying protein phosphorylation, where tens of thousands of new sites have been recently discovered in all domains of life. Such(More)
T cell receptor (TCR) reflects the status and function of T cells. We previously developed a gene melting spectral pattern (GMSP) assay, which rapidly detects clonal expansion of the T cell receptor β variable gene (TCRBV) in patients with HBV by using quantitative real-time reverse transcription PCR (qRT-PCR) with DNA melting curve analysis. However, the(More)