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Friday, December 16, 2005

Find Amino Acid mutation

Yesterday, we had a quiz on Mass Spectrometry. There is one question Find Amino Acid mutation:
There is a single amino acid mutation on SOD protein from ALS patient. After degradation by Lys-C proteinase and MALDI-TOF analysis, there is a molecular ion at 1689Da. But in wild type SOD protein, it should be 1765Da. That is to say the single amino acid mutation cause reduce of peptide molacular weight of 66Da. What exactly is that mutation.

In a another word: there are 20 amino acid,the difference of molecular weight is 66Da, what 2 amino acid is that. This is a simple combination. In the DOS world, I proberbly use QBasic. But now we can try MSH:


#Name of Amino acid
$AAName = @("Ala";"Arg";"Asn";"Asp";"Cys";"Glu";"Gln";"Gly";"His";"Ile";"Leu";
"Lys";"Met";"Phe";"Pro";"Ser";"Thr";"Trp";"Tyr";"Val")

#Molecular weight of amino acid
$AAMw = @(71.08;156.19;114.10;115.09;103.15;129.12;128.13;57.05;137.14;113.16;
113.16;128.17;131.20;147.18;97.12;87.08;101.11;186.21;163.18;99.13)

#Substract one verse another
for ($i=0;$i -lt 20;$i++) {
for ($j=$i; $j -lt 20;$j++) {
if ($AAMw[$i] -ge $AAMw[$j]) {
$change= $AAMw[$i] - $AAMw[$j]
}
else {
$change= $AAMw[$j] - $AAMw[$i]
}
if ($change -gt 66 -and $change -lt 67) {
if ($AAMw[$i] -ge $AAMw[$j]) {
$AAName[$i] + "(" + $AAMw[$i].Tostring() + ")" + "->" + $AAName[$j] + "("
+ $AAMw[$j].ToString() + ")" + ":" + $change.ToString()
}
else {
$AAName[$j] + "(" + $AAMw[$j].Tostring() + ")" + "->" + $AAName[$i] + "("
+ $AAMw[$i].ToString() + ")" + ":" + $change.ToString()
}

}
}
}



Results:
His(137.14)->Ala(71.08):66.06
Tyr(163.18)->Pro(97.12):66.06

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