Identification of Peptide Features in Precursor Spectra Using Hardklör and Krönik

Michael R. Hoopmann1, Michael J. MacCoss2, Robert L. Moritz1

1 Institute for Systems Biology, Seattle, Washington, 2 University of Washington, Seattle, Washington
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.18
DOI:  10.1002/0471250953.bi1318s37
Online Posting Date:  March, 2012
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Abstract

Hardklör and Krönik are software tools for feature detection and data reduction of high‐resolution mass spectra. Hardklör is used to reduce peptide isotope distributions to a single monoisotopic mass and charge state, and can deconvolve overlapping peptide isotope distributions. Krönik filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC‐MS). Both software tools contain a simple user interface and can be run from nearly any desktop computer. These tools are freely available from http://proteome.gs.washington.edu/software/hardklor. Curr. Protoc. Bioinform. 37:13.18.1‐13.18.13. © 2012 by John Wiley & Sons, Inc.

Keywords: proteomics; mass spectrometry; liquid chromatography; high resolution; feature detection; deisotoping; peptide isotope distribution

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Identifying Peptide Features in Precursor Spectra Using Hardklör
  • Alternate Protocol 1: Identifying Features in High‐Resolution MS/MS Spectra Using Hardklör
  • Basic Protocol 2: Visualizing Hardklör Results Using HKViewer and Performing Additional Analysis Using Krönik
  • Support Protocol 1: Installing Hardklör and Krönik
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Literature Cited

Literature Cited
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