You might get problems coming from the salt content of the digestion solution (buffer). Try desalting prior to direct infusion, e.g. using ziptip pipette tips (or similar). For identification you may apply a kind of peptide mass finger printing similar to maldi-ms analysis (keep more charges in mind in the case of esi-ms).

so I could use mascot as well as, but i have to be aware from the charge state? what charge state should i have to consider? what hypothetical values?

You should consider charge states of 2 and 3 for typical tryptic peptides of up to about 12 amino acid residues (it is a very rough estimation).

ok thank you so much!!, concerning the peptide-finger printing like search, how should i set MASCOT ? 

You will want to generate a peaklist in the format of an mgf file

(see for a description of this format: www.matrixscience.com/help/data_file_help.html)

This is an ASCII file, meaning that you can generate it, if necessary, manually using notepad or any other text editor. One the same website you will also find a lot of information about what the different Mascot parameters mean and how to set them.

Depending on the ESI mass spectrometer you are using, you might also want to acquire MSMS spectra for some of the peaks that you will observe - you can do this via infusion just as well as when performing an LCMS experiment. Talk to the mass spectrometrist in the lab and he/she will be able to show you how to do this either manually or in an automated fashion. Again, you will want to take the MSMS spectra that you generate and put them into a *.mgf file to get them into a format that can be used by a search engine, such as Mascot.

ok, but in any case, could i perform the search also without writing the precursor and consequently without doing a MS/MS experiment?

Peptide mass fingerprinting works without MS/MS.

It is kind of elaborate but you may just fill in the signals manually. Prepare a signal list from the survey MS (data format see here: http://www.matrixscience.com/help/data_file_help.html) and use this for the online form of mascot (http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=PMF).

Antonio, both approaches are possible and should work provided your protein of interest is the main compound in your gel band, which is a requirement for peptide mass fingerprinting. Also, PMF does need reasonably high mass accuracy e.g. from a ToF or Orbitrap instrument, while MS/MS also works on low resolution, low accuracy instruments. For a relatively pure protein band, you can work without an LC. You should, however, desalt digested Peptides with a ZipTip or similar prior to MS, and ideally use a mass spectrometer source that is suitable for very low flow rates (nl/min range). A regular ESI source which operates at 20-200 ul/min will usually consume your sample too quickly, or you would have to dilute too much. You will also need a way to extract peaklists from your spectra, however most all MS softwares I am aware of have this capability either directly or through scripts.

Matrixscience MASCOT will work well for both types of data (PMF or MS/MS). MASCOT is VERY well documented  on the Website, so look there for information.

To really move forward with this discussion thread it would be beneficial if you shared here what kind of mass spectrometer you have available for this task. Please supply information on the available ion sources and flow rate regimes as well - a more detailed question will usually lead to more detailed answers.

Dear Sir,

We done our ESI-MS of our novel recombinant protein sample against and found varying color (green,red,yellow) of peptide when matching to our known protein sequence (isolated and purified from plant source ms spectra have identified 7 peptide). I have found all the peptide matching in our ESI-MS of recombinant protein (0ut of7 peptide we have found 3 green 1 yellow and 3 red peptide). please clarify should i consider it my recombinant protein is have same sequence as native plant protein. Secondly what could be the reason of getting varying colour peptide.

Please clarify  the significant of  peptide deduced in sequence represented with varying color like green,Red and yellow.  Could you please elaborate the percentage of  similarity level of green, yellow and green peptides????