Identification of Peptide Features in Precursor Spectra Using Hardklör and Krönik

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Abstract
Table of Contents
Figures
Literature Cited

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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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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Figures

Figure 13.18.1 Image of the Hardklör user interface.

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Figure 13.18.2 Sample of Hardklör output. The output is in tab‐delimited ASCII text. Each line is labeled as either spectrum (S) information or peptide feature (P) information. Details of the output file contents can be found on the Hardklör Web site at: http://proteome.gs.washington.edu/software/hardklor/tutorial.html#results.

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Figure 13.18.3 The HKViewer. This Windows‐based graphical user interface presents Hardklör results to the user on a scan‐by‐scan basis using the navigation toolbar at the top left of the window. The graph in the upper right displays the distribution of peptide features identified with Hardklör across the input scan data.

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Figure 13.18.4 Screen capture of Krönik results visualized with Microsoft Excel.

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Videos

Literature Cited

Literature Cited
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