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PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.
  • B. Ma, K. Zhang, +4 authors G. Lajoie
  • Chemistry, Medicine
  • Rapid communications in mass spectrometry : RCM
  • 30 October 2003
A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimentalExpand
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PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification*
  • J. Zhang, L. Xin, +7 authors B. Ma
  • Computer Science, Medicine
  • Molecular & Cellular Proteomics
  • 20 December 2011
A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search. Expand
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IGF and FGF cooperatively establish the regulatory stem cell niche of pluripotent human cells in vitro
Distinctive properties of stem cells are not autonomously achieved, and recent evidence points to a level of external control from the microenvironment. Here, we demonstrate that self-renewal andExpand
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Matrigel: A complex protein mixture required for optimal growth of cell culture
Numerous cell types require a surface for attachment to grow and proliferate. Certain cells, particularly primary and stem cells, necessitate the use of specialized growth matrices along withExpand
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Characterization of staphyloferrin A biosynthetic and transport mutants in Staphylococcus aureus
Iron is critical for virtually all forms of life. The production of high‐affinity iron chelators, siderophores, and the subsequent uptake of iron–siderophore complexes are a common strategy employedExpand
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The Structural Basis of Gas-Responsive Transcription by the Human Nuclear Hormone Receptor REV-ERBβ
Heme is a ligand for the human nuclear receptors (NR) REV-ERBα and REV-ERBβ, which are transcriptional repressors that play important roles in circadian rhythm, lipid and glucose metabolism, andExpand
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PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS
We describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information from tandem mass spectrometry (MS/MS) data. Expand
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Prevention of Amino Acid Conversion in SILAC Experiments with Embryonic Stem Cells *
Recent studies using stable isotope labeling with amino acids in culture (SILAC) in quantitative proteomics have made mention of the problematic conversion of isotope-coded arginine to proline inExpand
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Integrating Structure, Bioinformatics, and Enzymology to Discover Function
Structural proteomics projects are generating three-dimensional structures of novel, uncharacterized proteins at an increasing rate. However, structure alone is often insufficient to deduce theExpand
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Control of calcium oxalate crystal growth by face-specific adsorption of an osteopontin phosphopeptide.
Mineral-associated proteins have been proposed to regulate many aspects of biomineralization, including the location, type, orientation, shape, and texture of crystals. To understand how proteinsExpand
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