Design of an hexapeptide database for proteomics studies
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The document discusses the creation of a hexapeptide database using a selection of 15 amino acids while excluding specific ones. It details the number of possible hexapeptides and their mass distributions, along with the frequency of amino acid compositions within the database. Finally, it references a study on synthesizing random hexapeptide libraries compatible with mass spectrometry analysis.
Design of an hexapeptide database for proteomics studies
- 1. Insilico Design of a hexapeptide database Autor: Jeovanis Gil Valdés Yasset Perez Riverol
- 2. Introducción • Generate a database of hexapeptides using the combination of all 15 aminoacids: No included: Metionine (M), Triptophan (W), Cysteine (C), Isoleucine (I), Aspártic (D). • Idenx the database in Mascot for searching of peptide archives.
- 3. Number of Peptides by Mass Number Peptides vs Mass Value 10000 8000 6000 4000 2000 0 475 737 785 818 845 871 896 922 955 1034 Mass Value Number of Peptides Count Peptides The number of posible heaxapeptides correspond with the number of permutations with repetition of N elements in p posicions: PR = Np = 156 = 11’390’625. The number of aminoacids compositions correspond with the number of combinations with repetition of N elements in p posicions: N k ⎛ + − = N p p n ( 1)!/ !( 1)! 1 ⎞ − − + = ⎟⎟⎠ ⎜⎜⎝ p CR CR = 20!/6! 14! = 38’760 Mav = 824.187237 Da. Mmax = 1111.417485 (YYYYYYD) Mmin = 475.166265 (GGGGGGD) Cmax = 8820 (Mass:821.403155) P = 0.000113379.
- 5. Peptide Distribution by Mass 3,20,50,100 PPM
- 6. Aminoacid compositions Number of unique composition masses: CMU = 15'106. Composi'on aminoacid Count % Ppep'des % Mases 19 0,28 0,03 18 0,36 0,03 17 0,46 0,05 16 0,38 0,05 15 0,87 0,12 14 1,19 0,18 13 1,92 0,30 12 2,39 0,42 11 3,24 0,64 10 3,59 0,77 9 4,45 1,03 8 6,59 1,75 7 7,31 2,26 6 7,82 2,88 5 9,30 4,24 4 11,62 6,84 3 13,26 11,53 2 13,37 19,46 1 11,61 47,43
- 7. Aminoacid compositions Aminoacid frecuency Aminoacid composi'on with this aminoacid Q-‐ 1 6791 N-‐ 1 6789 L-‐ 1 6745 V-‐ 1 6701 T-‐ 1 6700 S-‐ 1 6698 G-‐ 1 6621
- 8. References Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis. Y Masforrol, J Gil, LJ González, Y Pérez-Riverol, J Fernández-de-Cossío, et al. ACS combinatorial science 14 (3), 145-149