Reduction in Database Search Space by Utilization of Amino Acid Composition Information from Electron Transfer Dissociation and Higher-Energy Collisional Dissociation Mass Spectra
Reduction in Database Search Space by Utilization of Amino Acid Composition Information from Electron Transfer Dissociation and Higher-Energy Collisional Dissociation Mass Spectra
复制标题
DOI：
10.1021/ac3010007
复制
发表时间：
2012-08-07
影响因子：
7.4
通讯作者：
Kjeldsen, Frank
中科院分区：
文献类型：
--
作者：
Hansen, Thomas A.;Kryuchkov, Fedor;Kjeldsen, Frank
凭借高质量准确度和连续获得的电子转移解离（ETD）和高能碰撞解离（HCD）串联质谱（MS/MS），提取了可靠（>= 97%）且灵敏的碎片离子，用于识别肽序列中的特定氨基酸残基。这些特定氨基酸组成（AAC）离子的分析益处是限制数据库搜索空间并提供具有更高置信度和降低的假阴性率的肽鉴定。用>30的保守Mascot评分确定的6706个独特鉴定的肽序列用于表征AAC离子。使用ETD研究了氨基酸侧链从电荷还原的肽自由基阳离子的损失（小中性损失，SNL）。来自HCD光谱的补充AAC信息由亚铵离子提供。从ETD/HCD质谱，5162和6720可靠的SNL和亚铵离子被成功地提取，分别。在数据库搜索期间自动应用AAC信息导致肽鉴定的平均3.5倍高的置信水平。此外，在标准和扩展搜索空间中分别识别出高于显著性水平的4%和28%以上的肽。
With high-mass accuracy and consecutively obtained electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS), reliable (>= 97%) and sensitive fragment ions have been extracted for identification of specific amino acid residues in peptide sequences. The analytical benefit of these specific amino acid composition (AAC) ions is to restrict the database search space and provide identification of peptides with higher confidence and reduced false negative rates. The 6706 uniquely identified peptide sequences determined with a conservative Mascot score of >30 were used to characterize the AAC ions. The loss of amino acid side chains (small neutral losses, SNLs) from the charge reduced peptide radical cations was studied using ETD. Complementary AAC information from HCD spectra was provided by immonium ions. From the ETD/HCD mass spectra, 5162 and 6720 reliable SNLs and immonium ions were successfully extracted, respectively. Automated application of the AAC information during database searching resulted in an average 3.5-fold higher confidence level of peptide identification. In addition, 4% and 28% more peptides were identified above the significance level in a standard and extended search space, respectively.