DTASelect与对比：用于从鸟枪法蛋白质组学中汇总和比较蛋白质鉴定结果的工具。
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics.
作者信息
Tabb David L, McDonald W Hayes, Yates John R
机构信息
Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195, USA.
出版信息
J Proteome Res. 2002 Jan-Feb;1(1):21-6. doi: 10.1021/pr015504q.
Abstract
The components of complex peptide mixtures can be separated by liquid chromatography, fragmented by tandem mass spectrometry, and identified by the SEQUEST algorithm. Inferring a mixture's source proteins requires that the identified peptides be reassociated. This process becomes more challenging as the number of peptides increases. DTASelect, a new software package, assembles SEQUEST identifications and highlights the most significant matches. The accompanying Contrast tool compares DTASelect results from multiple experiments. The two programs improve the speed and precision of proteomic data analysis.
摘要
复杂肽混合物的成分可通过液相色谱进行分离，通过串联质谱进行片段化，并通过SEQUEST算法进行鉴定。推断混合物的源蛋白需要将鉴定出的肽重新关联起来。随着肽数量的增加，这个过程变得更具挑战性。DTASelect是一个新的软件包，它整合了SEQUEST的鉴定结果，并突出显示最显著的匹配项。附带的Contrast工具可比较多个实验的DTASelect结果。这两个程序提高了蛋白质组数据分析的速度和精度。
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本文引用的文献
1
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.一种将肽的串联质谱数据与蛋白质数据库中氨基酸序列相关联的方法。
J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89. doi: 10.1016/1044-0305(94)80016-2.
2
Selective degradation of ubiquitinated Sic1 by purified 26S proteasome yields active S phase cyclin-Cdk.经纯化的26S蛋白酶体对泛素化的Sic1进行选择性降解，产生有活性的S期细胞周期蛋白 - 细胞周期蛋白依赖性激酶。
Mol Cell. 2001 Aug;8(2):439-48. doi: 10.1016/s1097-2765(01)00308-2.
3
Large-scale analysis of the yeast proteome by multidimensional protein identification technology.通过多维蛋白质鉴定技术对酵母蛋白质组进行大规模分析。
Nat Biotechnol. 2001 Mar;19(3):242-7. doi: 10.1038/85686.
4
Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes.蛋白酶体蛋白质组学：通过亲和纯化蛋白酶体的质谱分析鉴定核苷酸敏感的蛋白酶体相互作用蛋白。
Mol Biol Cell. 2000 Oct;11(10):3425-39. doi: 10.1091/mbc.11.10.3425.
5
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.使用同位素编码亲和标签对复杂蛋白质混合物进行定量分析。
Nat Biotechnol. 1999 Oct;17(10):994-9. doi: 10.1038/13690.
6
Direct analysis of protein complexes using mass spectrometry.使用质谱法直接分析蛋白质复合物。
Nat Biotechnol. 1999 Jul;17(7):676-82. doi: 10.1038/10890.
7
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J Cell Biol. 1999 Apr 19;145(2):291-304. doi: 10.1083/jcb.145.2.291.
8
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J Cell Biol. 1999 Jan 11;144(1):83-98. doi: 10.1083/jcb.144.1.83.
9
Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry.使用一种用于液相色谱 - 微喷雾和纳喷雾质谱分析的新型无 frit 电喷雾接口，从银染凝胶中鉴定低飞摩尔水平的蛋白质。
Anal Biochem. 1998 Oct 1;263(1):93-101. doi: 10.1006/abio.1998.2809.
10
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