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使用肽指纹图谱进行数据库搜索----示意

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:)刚才在精华版看到一些朋友问到在用MALDI测得肽段分子量后怎么进行数据库搜索的问题,觉得有必要给新手们详细阐明一下,所以贴出了我自己硕士毕业论文中的相关部分与大家共享,也请高手批评指正。我的样品种属是小鼠,我举例的这个SPOT没有鉴定出来,呵呵。
2.蛋白斑点PRO2

Fig.9 peptide mass fingerprint(PMF) of PRO2 digested by trypsin
利用MASCOT程序进行检索
输入肽段质量数为:935.49 1570.91 1578.89 1641.88 1758.98 1994.08 2558.37 2581.36 2594.50 2597.50 2722.33
检索参数
Database searched SWISSPROTTaxonomy Mus musculusEnzyme trypsinMax missed cleavages 1 or 2Fixed modifications are CarbamidomethylProtein mass NonePeptide mass tolerance ±0.5 DaMass values are monoisotopicReport top 20
搜索结果如下:
(1) gi|20894496 Mass: 41060 Total score: 44 Peptides matched: 4 hypothetical protein XP_156355 [Mus musculus]
gi|284950 Mass: 10568 Total score: 27 Peptides matched: 2 Ig kappa chain V region - mouse
(2 )gi|20820877 Mass: 16730 Total score: 44 Peptides matched: 3 hypothetical protein XP_149891 [Mus musculus]
(3 )gi|28523811 Mass: 34454 Total score: 38 Peptides matched: 3 similar to protease [Mus musculus]
gi|20833889 Mass: 12794 Total score: 32 Peptides matched: 2 hypothetical protein XP_150900 [Mus musculus]
gi|20911605 Mass: 11530 Total score: 32 Peptides matched: 2 hypothetical protein XP_158628 [Mus musculus]
gi|20820603 Mass: 15669 Total score: 31 Peptides matched: 2 hypothetical protein XP_158099 [Mus musculus]
gi|28482850 Mass: 18455 Total score: 28 Peptides matched: 2 hypothetical protein XP_283657 [Mus musculus]
gi|26353630 Mass: 19939 Total score: 28 Peptides matched: 2
换PeptIdent程序进行检索,参数如下
Parameters Parameters set
Database searched SWISS-PROTProtein mass range 40-60KDaPI range 4-6Species searched Mus musculusDigested used TrypsinPeptide mass accurance ±0.5DaCysteines are treated with IdoacetamidePeptide masses are monoisotopicNumber of peptides required for match 4Number of missed cleavage sites 1Number of matching proteins display 20

结果如下:
Score peptide matches AC ID Description pI Mw
(1)0.64 7 Q02566 MYH6_MOUSE Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha). - Mus musculus (Mouse). 5.57 223565.34
(2)0.64 7 P97313 PRKD_MOUSE DNA-dependent protein kinase catalytic subunit (EC 2.7.1.37) (DNA- PKcs) (P460). - Mus musculus (Mouse). 6.70 471387.70
(3)0.55 6 Q61555 FBN2_MOUSE_1 CHAIN 1: FIBRILLIN 2. - Mus musculus (Mouse). 4.71 310393.74
(4)0.45 5 P97929 BRC2_MOUSE Breast cancer type 2 susceptibility protein. - Mus musculus (Mouse). 6.23 370663.75
(5)0.45 5 P59242 CING_MOUSE Cingulin. - Mus musculus (Mouse). 5.72 136446.87
在NCBInr数据库中,检索到的蛋白没有一个MOWSE分值在62分以上(p﹤0.05),最高分值仅为44分,且为一假设蛋白,故不能得出正确结果。换SWISSPROT数据库检索,分值最高的Adseverin (Scinderin) (Gelsolin-like protein)为37分,也不能正确鉴定。PeptIdent所检索到的Q02566 MYH6_MOUSE Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha). - Mus musculus (Mouse).虽然匹配肽段数达到了7个,但由于序列覆盖率仅为6.8%,仍然得不到正确鉴定。综合上述结果,不能鉴定PRO2的蛋白质种属。
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