使用Hardklör和Krönik在前体谱中鉴定肽段特征。
Identification of peptide features in precursor spectra using Hardklör and Krönik.
作者信息
Hoopmann Michael R, MacCoss Michael J, Moritz Robert L
机构信息
Institute for Systems Biology, Seattle, Washington, USA.
出版信息
Curr Protoc Bioinformatics. 2012 Mar;Chapter 13:Unit13.18. doi: 10.1002/0471250953.bi1318s37.
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.
摘要
Hardklör和Krönik是用于高分辨率质谱特征检测和数据缩减的软件工具。Hardklör用于将肽同位素分布缩减为单一的单同位素质量和电荷状态，并且能够对重叠的肽同位素分布进行去卷积处理。Krönik对通过Hardklör从液相色谱质谱联用（LC-MS）过程中获得的数据所识别的肽特征进行过滤、验证和汇总。这两个软件工具都具有简单的用户界面，并且几乎可以在任何台式计算机上运行。这些工具可从http://proteome.gs.washington.edu/software/hardklor免费获取。
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本文引用的文献
1
Automated assignment of charge states from resolved isotopic peaks for multiply charged ions.
J Am Soc Mass Spectrom. 1995 Jan;6(1):52-6. doi: 10.1016/1044-0305(94)00091-D.
2
Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions.
J Am Soc Mass Spectrom. 1995 Apr;6(4):229-33. doi: 10.1016/1044-0305(95)00017-8.
3
Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics.
Mol Cell Proteomics. 2011 Dec;10(12):M111.009910. doi: 10.1074/mcp.M111.009910. Epub 2011 Sep 13.
4
The fasted/fed mouse metabolic acetylome: N6-acetylation differences suggest acetylation coordinates organ-specific fuel switching.
J Proteome Res. 2011 Sep 2;10(9):4134-49. doi: 10.1021/pr200313x. Epub 2011 Aug 16.
5
Ultrahigh-speed calculation of isotope distributions.
Anal Chem. 1996 Jul 1;68(13):2027-30. doi: 10.1021/ac951158i.
6
Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation.
J Proteome Res. 2010 Dec 3;9(12):6786-94. doi: 10.1021/pr100637q. Epub 2010 Oct 26.
7
Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking.
J Proteome Res. 2010 Jul 2;9(7):3583-9. doi: 10.1021/pr1001115.
8
Comparison of database search strategies for high precursor mass accuracy MS/MS data.
J Proteome Res. 2010 Feb 5;9(2):1138-43. doi: 10.1021/pr900816a.
9
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.
Mol Cell Proteomics. 2009 Dec;8(12):2759-69. doi: 10.1074/mcp.M900375-MCP200. Epub 2009 Oct 14.
10
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.
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