Chromatography Forum

Dear all,

My peptide is around 4 kda and I got 4+ and 5+ charged m/z peaks in ESI-MS spectra. I can calculate the molecular weight by hand (and the result is pretty good). But I know the scientific way to get the molecular weight from ESI is by using a deconvolution software.

I am using Xcalib 1.4 on a Thermo LCQ. But I don't know how to deconvolute the data. Did anyone know how to do it by Xcalib?

wen

Dear all,

My peptide is around 4 kda and I got 4+ and 5+ charged m/z peaks in ESI-MS spectra. I can calculate the molecular weight by hand (and the result is pretty good). But I know the scientific way to get the molecular weight from ESI is by using a deconvolution software.

I am using Xcalib 1.4 on a Thermo LCQ. But I don't know how to deconvolute the data. Did anyone know how to do it by Xcalib?

wen

What do you mean deconvolute?

If you are working with a peptide standard, go to protein prospector's MS-Product, then plug-in the sequence information and MS-Product will give you the theoretical peaks for your peptide.

You want to know how to automatically analyze the mass spectrum?

You have one peptide?
Is it a peptide standard? or is this an unknown sample?

Do you have access to MASCOT, SEQUEST databases?

How was your sample prepared? Tryptic digestion?
What is the source of your sample?

Thanks for reply.

What I need is really simple: My peptide is pure (supposely) and I want to get its M.W. In fact I can achieve this by MALDI, since MALDI usually gives SINGLYcharged ions. However for some reason I need to use ESI-MS to get its M.W. As ESI usually gives MULTIPLY charged ions, I need to deconvolute the raw data generated by ESI to get the M.W. ( I believe this process is called "deconvolution", am I right or not? Can anoyone help?)

The problem here is that you are using a low resolution mass spec so it is very difficult to make any useful charge assiment/deisotoping and deconvolution. The LCQ that you are using is not going to give you any resolution for your +4/+5 charge state peptide.

The best way to do it is to use the MS/MS capabilities of your instrument and then interpret your MS/MS spectra. There are several software that can do that such as Sequest, Mascot, Spectrum Mill or if you want you can use freeware such as XTandem etc...

There is a way to do somekind of deconvolution by using peptide fingerprinting approach where you give a list of proteins/peptides (so you narrow down the possibilites of the ions that can be seen) and then deconvolute. If you give only your standard peptide as possibility then it would be very easy for the software to figure out the charge state of you observe and give you the right answer. Mascot is able to do peptide fingerprinting and I am sure that there are other software available out there...