Chamrad Daniel C, Körting Gerhard, Schäfer Heike, Stephan Christian, Thiele Herbert, Apweiler Rolf, Meyer Helmut E, Marcus Katrin, Blüggel Martin
Protagen AG, Dortmund, Germany.
Proteomics. 2006 Sep;6(18):5048-58. doi: 10.1002/pmic.200600189.
A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.
一种名为PTM-Explorer的新型软件工具已应用于人类蛋白质组组织（HUPO）脑蛋白质组计划（BPP）中获取的液相色谱-串联质谱（LC-MS/MS）数据集。PTM-Explorer能够自动识别在典型序列数据库搜索中未得到解释的肽段MS/MS谱图。主要重点是检测翻译后修饰（PTM），但PTM-Explorer还能检测非特异性肽段裂解、质量测量误差、实验性修饰、氨基酸替换、转肽产物和未知质量位移。为避免组合问题，搜索限于一组选定的蛋白质序列，这些序列来自先前使用通用序列数据库搜索进行的蛋白质鉴定。在应用于HUPO BPP数据之前，PTM-Explorer在从小鼠晶状体获得的α-A-晶状体蛋白凝胶斑点的经过出色手动表征和评估的LC-MS/MS数据集上进行了评估。除了包括磷酸化在内的各种PTM外，还成功检测到大量实验性修饰和非特异性裂解产物，完善了所测蛋白质的一级结构信息。我们的结果表明，目前在标准数据库搜索中仍未鉴定的大量MS/MS谱图包含只能使用合适的软件工具才能阐明的有价值信息。
