Bioinformatics for Proteomics Shu-Hui Chen(陳慧) Department of Chemistry National Cheng Kung University
Bioinformatics for Proteomics Shu-Hui Chen (陳淑慧) Department of Chemistry National Cheng Kung University
Bioinformatics I How do we find protein coding regions DNA introns and exons in genomic DNA sequences? Splicing mRNA Translation Poly- peptide Folding Protein Transport Localization ·Oligomerization PTM (Post-Translational Modification) Function Function
Transcription DNA 5’ 3’ mRNA Splicing Translation Polypeptide Folding Protein • Transport / Localization • Oligomerization • PTM (Post-Translational Modification) Function Function How do we find protein coding regions, introns and exons in genomic DNA sequences? Bioinformatics I
What is Proteomics Systematic analysis of All protein sequences All protein expression pattern All protein interactions This involves Protein isolation Protein separation Protein identification Functional characterization of all proteins
What is Proteomics ? Systematic analysis of All protein sequences All protein expression pattern All protein interactions This involves Protein isolation Protein separation Protein identification Functional characterization of all proteins
The tools of Proteomics Traditional protein chemistry assay methods struggle to establish Identity Identity requires: Specificity of measurement (Precision) Mass Spectrometry MS-based data acquisition algorithm A reference for comparison Protein sequence databases Search algorithms
The tools of Proteomics Traditional protein chemistry assay methods struggle to establish Identity Identity requires: Specificity of measurement (Precision) Mass Spectrometry MS-based data acquisition algorithm A reference for comparison Protein sequence databases Search algorithms
MS-based Proteomics and Bioinformatics MS instrument is so far not sensitive enough to resolve proteins in a biological system solely based on signals measured. MS,however,is able to acquire sufficient data for mapping a protein from the database using new computer algorithms to analyze the data. This is the field of bioinformatics
MS-based Proteomics and Bioinformatics • MS instrument is so far not sensitive enough to resolve proteins in a biological system solely based on signals measured. • MS, however, is able to acquire sufficient data for mapping a protein from the database using new computer algorithms to analyze the data. • This is the field of bioinformatics
Instrumentation Sample inlet vacuum lon source Mass analyzer Data acquisition
Ion source Mass analyzer Sample inlet Data acquisition vacuum Instrumentation
TABLE 15.9.Average Masses of Amino Acids in Their Free and Residue States" M Codes Amino Acid 3-Letter 1-Letter Residue Free Alanine Ala 71.0786 89.0938 Arginine Arg 156.1870 174.2022 Asparagine Asn 114.1036 132.1188 Aspartic acid Asp 115.0884 1331036 Cysteine Cys 103.1386 121.1538 Glutamine Gln QE 128.1304 146.1456 Glutamic acid Glu 129.1152 147.1304 Glycine Gly 57.0518 75.0670 Histidine His H 137.1408 1551560 Isoleucine Te 113.1590 131.1742 Leucine Leu 113.1590 131.1742 Lysine Lys 128.1736 146.1888 Methionine Met 131.1922 1492074 Phenylalanine Phe F 147.1762 165.1914 Proline Pro 97.1164 115.1316 Serine Ser 87.0780 105.0932 Threonine Thr H 101.1048 119.1200 Tryptophan Trp W 186.2128 204.2280 Tyrosine Tyr 63.1756 1811908 Valine Val 99.1322 117.1474 e etter customary in the MSarea.Reprinted,with permission,from M.Man and M. Wilm,Anal.Chem.66(No 24).1994,4390-4399."Error Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags".Copyright C1994 American Chemical Society
Table 9.2 Nominal mass differences between standard amino acid residues △Da Masses Respective residues 0 113-113 Leu-Ile 128-128 Lys-Gln 114-113 Asn-Ile 114-113 Asn-Leu 115-114 Asp-Asn 129-128 Glu-Gln 129-128 Glu-Lys 99-97 Val-Pro 101-99 Thr-Val 103-101 Cys-Thr 115-113 Asp-Leu 115-113 Asp-Ile 131-129 Met-Glu 3 131-128 Met-GIn 131-128 Met-Lys 4 101-97 Thr-Pro 103-99 Cys-Val (Reprinted by kind permission of Elsevier Science-NL,Sara Burgerhartsraat 25, 1055 KV,Amsterdam,The Netherlands.)
TABLE 15.2.Resolution as R=M/Am and Its Effect on Precision in MS mlz △m Resolution 士ppm Mass Range (Da) 2,000 5 400 2,500 1,995-2,005 2.000 0.5 4.000 250 1,999.5-2.000.5 2,000 0.05 40.000 25 1,999.95-2.000.05 20,000 5 4.000 250 19,995-20,005 20,000 0.5 40.000 25 19,999.5-20.000.5 20.000 0.05 400.000 2.5 19,999.95-20,000.05 200.000 5 40.000 25 199.995-200,005 200,000 0.5 400.000 2.5 199,999.5-200,000.5 200.000 0.05 4.000.000 0.25 199,999.95-200,000.05
“Bioanalytical Chemistry” Mikkelsen, S.R., published by John Wiley & Sons, Inc
MS-based Protein Identification V Mass Mapping Peptide Sequencing
MS-based Protein Identification Mass Mapping Peptide Sequencing