<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Nanni P</dc:creator>
  <dc:creator>Panse C</dc:creator>
  <dc:creator>Gehrig P</dc:creator>
  <dc:creator>Mueller S</dc:creator>
  <dc:creator>Grossmann J</dc:creator>
  <dc:creator>Schlapbach R</dc:creator>
  <dc:date>2013</dc:date>
  <dc:description xmlns:ns0="xml" ns0:lang="en">Mass spectrometry (MS) analysis of peptides carrying post-translational modifications is challenging due to the instability of some modifications during MS analysis. However, glycopeptides as well as acetylated, methylated and other modified peptides release specific fragment ions during CID (collision-induced dissociation) and HCD (higher energy collisional dissociation) fragmentation. These fragment ions can be used to validate the presence of the PTM on the peptide. Here, we present PTM MarkerFinder, a software tool that takes advantage of such marker ions. PTM MarkerFinder screens the MS/MS spectra in the output of a database search (i.e., Mascot) for marker ions specific for selected PTMs. Moreover, it reports and annotates the HCD and the corresponding electron transfer dissociation (ETD) spectrum (when present), and summarizes information on the type, number, and ratios of marker ions found in the data set. In the present work, a sample containing enriched N-acetylhexosamine (HexNAc) glycopeptides from yeast has been analyzed by liquid chromatography-mass spectrometry on an LTQ Orbitrap Velos using both HCD and ETD fragmentation techniques. The identification result (Mascot .dat file) was submitted as input to PTM MarkerFinder and screened for HexNAc oxonium ions. The software output has been used for high-throughput validation of the identification results.</dc:description>
  <dc:identifier>https://sonar.ch/global/documents/254342</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>info:eu-repo/semantics/altIdentifier/doi/10.1002/pmic.201300036</dc:relation>
  <dc:relation>info:eu-repo/semantics/altIdentifier/pmid/23713006</dc:relation>
  <dc:source>Proteomics. - 2013</dc:source>
  <dc:subject xmlns:ns1="xml" ns1:lang="en">Data mining</dc:subject>
  <dc:subject xmlns:ns2="xml" ns2:lang="en">High-throughput proteomics</dc:subject>
  <dc:subject xmlns:ns3="xml" ns3:lang="en">Interpretation of mass spectra</dc:subject>
  <dc:subject xmlns:ns4="xml" ns4:lang="en">Mass spectrometry</dc:subject>
  <dc:subject xmlns:ns5="xml" ns5:lang="en">Post-translational modifications</dc:subject>
  <dc:subject xmlns:ns6="xml" ns6:lang="en">Data Mining</dc:subject>
  <dc:subject xmlns:ns7="xml" ns7:lang="en">Glycopeptides</dc:subject>
  <dc:subject xmlns:ns8="xml" ns8:lang="en">High-Throughput Screening Assays</dc:subject>
  <dc:subject xmlns:ns9="xml" ns9:lang="en">Mass Spectrometry</dc:subject>
  <dc:subject xmlns:ns10="xml" ns10:lang="en">Protein Processing, Post-Translational</dc:subject>
  <dc:subject xmlns:ns11="xml" ns11:lang="en">Proteomics</dc:subject>
  <dc:subject xmlns:ns12="xml" ns12:lang="en">Reproducibility of Results</dc:subject>
  <dc:subject xmlns:ns13="xml" ns13:lang="en">Software</dc:subject>
  <dc:title xmlns:ns14="xml" ns14:lang="en">PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications.</dc:title>
  <dc:type>http://purl.org/coar/resource_type/c_6501</dc:type>
</oai_dc:dc>