Annotation of non-synonymous single polymorphisms in human liver proteome by mass spectrometry.
A novel strategy to annotate nsSNP-peptides in human liver proteome based on LC-ESI-MS/MS and peptide database search was proposed. Totally 115 nsSNP-peptides in human liver proteins were annotated using our method. Among them, 42 peptides were found to be amino acid mutation, 73 peptides were wild type, 5 peptides were interpreted with both mutation and wild type. The function of nsSNP-peptide was predicted using SIFT algorithm, and 2 nsSNPs were predicted to be damaged for protein function. The results here show that the strategy is very effective for annotation of nsSNP at peptide level.
Chen
Ming
M
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, PR China.
Yang
Bing
B
Ying
Wantao
W
He
Fuchu
F
Qian
Xiaohong
X
D000465:Algorithms; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D002853:Chromatography, Liquid / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D008099:Liver / Q000378:metabolism / Q000502:physiology*; D008969:Molecular Sequence Data; D009154:Mutation; D010446:Peptide Fragments; D020641:Polymorphism, Single Nucleotide; D020543:Proteome / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010446:Peptide Fragments; D020543:Proteome