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  • Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments.
    We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by...
    Bioinformatics : (2009)
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  • Phosphoproteomics
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  • Proteome-scale characterization of human s-acylated proteins in lipid raft-enriched and non-raft membranes.
    We describe a novel proteomic approach, designated Palmitoyl Protein Identification and Site Characterization (PalmPISC), for proteo...
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  • When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification.
    We investigate the performance of 25 MS/MS preprocessing methods on various data sets and make software for improved preprocessing o...
    Proteomics : (2009)
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  • Molecular and functional characterisation of the heat shock protein 10 of Strongyloides ratti.
    We performed mass spectrometry to identify excretory/secretory products of S. ratti. Amongst others we detected homologs of the heat...
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  • Differentiation-dependent interactions between RUNX-1 and FLI-1 during megakaryocyte development.
    We purified RUNX-1-containing multiprotein complexes from phorbol ester-induced L8057 murine megakaryoblastic cells and identified t...
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  • Proteomics and Opportunities for Clinical Translation in Urological Disease.
    The proteomics approaches to answer clinical questions have only recently been introduced. Many different technologies have been use...
    J Urol : (2009)
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  • A simple and effective method for detecting phosphopeptides for phosphoproteomic analysis.
    An immuno-dot blot method for detecting phosphopeptides is described. This method allows detection of phosphopeptides prior to analy...
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  • Discovery and Validation of Urine Markers of Acute Pediatric Appendicitis Using High-Accuracy Mass Spectrometry.
    Test performance of 57 identified candidate markers was studied in 67 patients, with median age of 11 years, 37% of whom had appendi...
    Ann Emerg Med : (2009)
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  • FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides.
    We introduce a novel MS-based quantitative strategy, FLEXIQuant, (Full-Length Expressed Stable Isotope-labeled Proteins for Quantifi...
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  • The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in Xenopus.
    We have gained insight into embryonic nutrition in the African clawed frog Xenopus laevis by studying YPs. Amphibians follow the anc...
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  • Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics.
    We present a continuous quality score that can be computed very quickly and that can be considered an approximation of the MASCOT sc...
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  • Optimizing sample handling for urinary proteomics.
    We demonstrate that the method of protein extraction, length of handling at room temperature, and repetitive freeze-thaw cycles do n...
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  • Proteomics 2008, a day of information and inspiration at Children's Hospital Boston.
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  • SALAMI (Spectrum ALignments using high Accuracy Mass and hIgh sensitivity data): how to make the best out of hybrid MS/MS data.
    We present a software algorithm that combines ion trap and orbitrap product ion spectra acquired in parallel. The hybrid product ion...
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  • Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis.
    We studied in detail the phosphorylation patterns at a single mitotic state of arrest generated by various antimitotic drugs. We exa...
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  • Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation.
    We describe the urine proteome during postnatal development in the rat and demonstrate specific proteomic changes corresponding to d...
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  • Proteomic approaches to the analysis of multiprotein signaling complexes.
    Signal transduction is one of the most active fields in modern biomedical research. Increasing evidence has shown that signaling pro...
    Proteomics 8:832 (2008)
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  • NITPICK: peak identification for mass spectrometry data.
    This contribution proposes a sparse template regression approach to peak picking called NITPICK. NITPICK is a Non-greedy, Iterative...
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  • Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis.
    DRM-enriched fractions isolated using the conventional or modified extraction methods displayed comparable profiles of known DRM-ass...
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