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An efficient parallelization of phosphorylated peptide and protein identification
peptide protein identification
2010/12/20
Protein sequence database search based on tandem mass spectrometry is an essential method for
protein identification. As the computational demand increases, parallel computing has become an important...
Speeding up Tandem Mass Spectrometry Based Database Searching by Peptide and Spectrum Indexing
Mass Spectrometry Database Searching Peptide Spectrum Indexing
2010/12/21
Database searching is the technique of choice for shotgun proteomics, and to date much research effort has been spent on improving its effectiveness. However, database searching faces a serious challe...
pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra
Peptide Sequencing dentification HCD Spectra
2010/12/21
De novo peptide sequencing has improved remarkably in the past decade as a result of better
instruments and computational algorithms. However, de novo sequencing can correctly interpret only ∼3...
PeakSelect: preprocessing tandem mass spectra for better peptide identification
preprocessing tandem mass spectra peptide identification
2010/12/17
We present a new preprocessing method, PeakSelect, to improve the accuracy and efficiency of
Tandem Mass-Spec peptide (protein) identification. The fundamental difference between noise and fragment i...
Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences
post-translational modifications spectral pairs peptide mass
2010/12/20
Peptide identification via tandem mass spectrometry is the basic task of current
proteomics research. Due to the complexity of mass spectra, the majority of mass spectra cannot be interpreted at pres...
Mining Tandem Mass Spectral Data to Develop a More Accurate Mass Error Model for Peptide Identification,
Spectral Data Mass Error Model Peptide Identification
2010/12/17
The assumption on the mass error distribution of fragment ions plays a crucial role in
peptide identification by tandem mass spectra. Previous mass error models are the
simplistic uniform or normal ...
Find: A Novel Web-based Application for Automated Identification of Peptide and Protein by MS/MS Data
Automated Identification Peptide Protein by MS/MS Data
2010/12/14
To identify the unknown peptide sequences from the observed experimental MS/MS spectra, database searching is currently the most popular and reliable approach in high-throughput proteomics studies. We...
Beyond Shared Peak Count: Finding and Using Correlations in MS/MS Data for Peptide Identification
Beyond Shared Peak Count Correlations MS/MS
2010/12/14
Shared Peak Count (SPC), i.e. the number of matched peaks between the experimental MS/MS spectrum and the theoretical one predicted from a peptide sequence in the database, is a widely used scoring me...
Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry,
correlate fragment ions peptide identification tandem mass spectrometry
2010/12/14
The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches
for peptide identification by database searching. Until now, an efficient scoring algorithm ...