Successful protein spot identification by MALDI-TOF MS in conjunction with PMF and/or Q-TOF MS/MS with BLAST database searching.

1Statistically significant protein spot identification after MALDI-TOF MS analysis followed by PMF search of the H. contortus putative EST protein database.2Non-statistically significant protein spot identification after MALDI-TOF MS analysis followed by PMF search of the H. contortus putative EST protein database, but verified by statistically significant protein spot identification after Q-TOF MS/MS analysis.3Statistically significant protein spot identification after MALDI-TOF MS analysis followed by PMF search of the H. contortus putative EST protein database. These results were confirmed by Q-TOF MS/MS analysis.4Statistically significant protein spot identification after Q-TOF MS/MS followed by BLASTp search of the H. contortus putative EST protein database.5Non-statistically significant protein spot identification after MALDI-TOF MS analysis followed by PMF search of the H. contortus putative EST protein database. However, the observed Mw of the spots, calculated on the gel image, were correlated with the theoretical Mw of the intact protein in the best BLASTp match. These data are detailed in Tables S3 & S4.Each protein spot was excised from the 250 µg protein-loaded gel and analysed by MALDI-TOF MS. A local MASCOT PMF search of the H. contortus putative EST protein database was performed and the highest scoring EST sequence match, along with its MOWSE-based score (significance threshold score >51, p-valueH. contortus putative EST protein database was performed and the MOWSE-based score of the highest scoring EST sequence match (significance threshold score >25, p-value44, p-value

1 经基质辅助激光解吸电离飞行时间质谱（Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry, MALDI-TOF MS）分析后，通过肽质量指纹图谱（Peptide Mass Fingerprinting, PMF）检索捻转血矛线虫（Haemonchus contortus, H. contortus）推定表达序列标签（Expressed Sequence Tag, EST）蛋白质数据库，得到具有统计学显著性的蛋白斑点鉴定结果。
2 经MALDI-TOF MS分析并通过PMF检索H. contortus推定EST蛋白质数据库后，未获得具有统计学显著性的蛋白斑点鉴定结果，但该结果经四极杆-飞行时间串联质谱（Quadrupole Time-of-Flight Tandem Mass Spectrometry, Q-TOF MS/MS）分析得到的具有统计学显著性的蛋白斑点鉴定结果验证。
3 经MALDI-TOF MS分析后通过PMF检索H. contortus推定EST蛋白质数据库，得到具有统计学显著性的蛋白斑点鉴定结果，该结果经Q-TOF MS/MS分析得到验证。
4 经Q-TOF MS/MS分析后，通过基本局部比对搜索工具蛋白序列版（Basic Local Alignment Search Tool Protein, BLASTp）检索H. contortus推定EST蛋白质数据库，得到具有统计学显著性的蛋白斑点鉴定结果。
5 经MALDI-TOF MS分析后通过PMF检索H. contortus推定EST蛋白质数据库，未获得具有统计学显著性的蛋白斑点鉴定结果；但根据凝胶图像计算得到的斑点观测分子量（Mw），与最优BLASTp匹配结果中完整蛋白的理论分子量存在相关性。相关详细数据见于附表S3与S4。

从上样量为250 μg蛋白的凝胶中切取每个蛋白斑点，采用MALDI-TOF MS进行分析。对H. contortus推定EST蛋白质数据库进行本地MASCOT PMF检索，得到得分最高的EST序列匹配结果及其基于MOWSE的评分（显著性阈值评分>51，p值信息未完整给出）。本次检索后再次对H. contortus推定EST蛋白质数据库进行PMF检索，得到得分最高的EST序列匹配结果的MOWSE评分（显著性阈值评分>25，p值44，p值信息未完整给出）。