Adding SILAC label in quantitation configuration

pFindStudio / pLink2

pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.

http://pfind.ict.ac.cn/software/pLink/index.html

22 stars 1 forks source link

Adding SILAC label in quantitation configuration #77

Open BrandonMurugan opened 4 years ago

BrandonMurugan commented 4 years ago

Hi there,

I was wondering how I would go about adding SILAC modifications to the quantitation configuration? I'm having some trouble figuring out the 15N configuration and adapting it for SILAC.

Thanks for the great piece of software!

Brandon

01joy commented 4 years ago

Dear @BrandonMurugan ,

If your SILAC labeling is ¹³C₆¹⁵N₄ arginine (Arg10) and ¹³C₆¹⁵N₂ lysine (Lys8), please add the following configuration in quantitation of pConfig.

Name: SILAC-Arg10Lys8 Label info: R:K{N,15N}R:K{C,13C}R:R{N,15N}R:R{C,13C}

For the rules of label info, every R:K{N,15N} is a rule, it means: for residue (R) Lys (K), replace its N as 15N. You can see in Amino Acids tab of pConfig that K contains two Ns, so this rule will replace two Ns as two 15Ns.