Mr. Islam,

Can you provide spectrum?

There is no such peak which I could say as a spectra. its only a noise.

I have used to following protocol in the past and had success in the MALDI-TOF MS analysis of oligonucleotides:

The following is a protocol from this reference: (Purdie et al. Bioconjugate Chem. 2016, 27, 1244-1252)

Matrix solution: 50 mg/mL 3-HPA in 1:1 MeCN:H2O

DAHC (diammonium hydrogen citrate) solution: 100 mg/mL in H2O

Matrix+DAHC solution: 45 mg/mL 3-HPA + 10 mg/mL DAHC.

Mix "clean" oligonucleotide (~20µM) equal volume with matrix+DAHC solution and spot on target and allow to dry.

It is quite critical that the oligonucleotide be desalted prior to MS analysis as these molecules bind cations readily. I use a Ziptips, dialysis, or centrifugal filtering as buffer exchange techniques to help desalt prior to analysis.

Hope this helps.

thank you Mr. Logan for your advice.

I have few questions..

1. You have mentioned three desalting technique. can you suggest me which one is most effective ? can you provide that protocol ?

2. what was the instrument parameter settings ? e.g. - plate voltage, grid voltage ?

3. Right now I am playing with Primers (20 mer, DNA) is it essential to desalt those as the manufacturer mentioned a standard desalting (?) has been done ?

Sir,

1) I don't work with oligonucleotides all that often, but for proteins, I generally favor desalting using centrifugal filters likes the ones here (http://www.emdmillipore.com/US/en/life-science-research/protein-sample-preparation/protein-concentration/amicon-ultra-centrifugal-filters/YKSb.qB.GXgAAAFBTrllvyxi,nav). If the MW of your target is small (

thanks @ logan for your I reply.

Hi, could you explain the composition of your matrix used for RNA on MALDI?

Also, do you have a webpage or a softaware that takes into account the modification such as biotin in 5' for the calculation of the molecular mass?

Best,

Sébastien

hi Sébastien Brûlé ,

I used two type of matrices

1. 20 mg/ml THAP in 90% ACN +50 mg/ml Di ammonium Hydrogencitrate + 2 mg/ml D-Fructose

2. 35 mg/ml 3-HPA in 10% ACN + 7mg/ml Di ammonium Hydrogencitrate + 4 mg/ml D fructose.

for the second part of your query, I didn't use any software for that.