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Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. Expand
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DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics.
The components of complex peptide mixtures can be separated by liquid chromatography, fragmented by tandem mass spectrometry, and identified by the SEQUEST algorithm. Inferring a mixture's sourceExpand
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A Cross-platform Toolkit for Mass Spectrometry and Proteomics
Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological andExpand
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A proteomic view of the Plasmodium falciparum life cycle
The completion of the Plasmodium falciparum clone 3D7 genome provides a basis on which to conduct comparative proteomics studies of this human pathogen. Here, we applied a high-throughput proteomicsExpand
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Proteogenomic characterization of human colon and rectal cancer
Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon andExpand
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MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.
Shotgun proteomics experiments are dependent upon database search engines to identify peptides from tandem mass spectra. Many of these algorithms score potential identifications by evaluating theExpand
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IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
Tandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. A number of database searching algorithms have been developed to assignExpand
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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization ofExpand
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Proteomic parsimony through bipartite graph analysis improves accuracy and transparency.
Assembling peptides identified from LC-MS/MS spectra into a list of proteins is a critical step in analyzing shotgun proteomics data. As one peptide sequence can be mapped to multiple proteins in aExpand
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Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma
Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discoveryExpand
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