Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process.
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process.
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DOI：
10.1186/1471-2105-6-285
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发表时间：
2005-11-30
影响因子：
3
通讯作者：
Reinert K
中科院分区：
文献类型：
--
作者：
Wolski WE;Lalowski M;Martus P;Herwig R;Giavalisco P;Gobom J;Sickmann A;Lehrach H;Reinert K
生物质谱法用于分析多肽和蛋白质。质谱产生一个测量的质量电荷比和电离肽强度的列表，这被称为峰列表。为了对潜在的氨基酸序列进行分类，通常将获得的光谱与合成光谱进行比较。开发合适的直接峰表比较方法对许多应用都是有利的。两两峰表比较是一个多阶段的过程，由嵌入在两个峰表中的峰的匹配、归一化、峰强度的缩放和不相似性度量组成。在我们的分析中，我们侧重于二元和基于强度的措施。我们修改了测量方法，以包含质谱测量精度和非匹配峰的特性。我们比较了使用两两峰表比较的不同因素获得的峰表对的标记与序列数据库搜索确定的标记相同或不同。为了阐明这些因素对峰表比较的影响，我们采用以ROC曲线下偏面积为因变量的方差型分析方法。方差分析提供了洞察影响两两峰表比较结果的各种因素的相关性。对于大型MS/MS和PMF数据集，方差分析的结果是一致的，这强有力地表明，本文提出的结果可能适用于许多不同类型的肽质量测量。
Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is called a peak-list. In order to classify the underlying amino acid sequence, the acquired spectra are usually compared with synthetic ones. Development of suitable methods of direct peak-list comparison may be advantageous for many applications. The pairwise peak-list comparison is a multistage process composed of matching of peaks embedded in two peak-lists, normalisation, scaling of peak intensities and dissimilarity measures. In our analysis, we focused on binary and intensity based measures. We have modified the measures in order to comprise the mass spectrometry specific properties of mass measurement accuracy and non-matching peaks. We compared the labelling of peak-list pairs, obtained using different factors of the pairwise peak-list comparison, as being the same or different to those determined by sequence database searches. In order to elucidate how these factors influence the peak-list comparison we adopted an analysis of variance type method with the partial area under the ROC curve as a dependent variable. The analysis of variance provides insight into the relevance of various factors influencing the outcome of the pairwise peak-list comparison. For large MS/MS and PMF data sets the outcome of ANOVA analysis was consistent, providing a strong indication that the results presented here might be valid for many various types of peptide mass measurements.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
3.4
作者：
Giavalisco, P;Nordhoff, E;Gobom, J
通讯作者：
Gobom, J
影响因子：
7.4
作者：
Clauser, KR;Baker, P;Burlingame, AL
通讯作者：
Burlingame, AL
影响因子：
4.3
作者：
Chamrad, DC;Koerting, G;Blueggel, M
通讯作者：
Blueggel, M
影响因子：
3.7
作者：
FOWLKES, EB;MALLOWS, CL
通讯作者：
MALLOWS, CL