Neil Kelleher has some software for free. ProSight.

http://groups.molbiosci.northwestern.edu/kelleher/software.html

Cheers - jonas

Of course . You can try PEAKS7Studio.

thanks, but is there an open source?

Neil Kelleher has some software for free. ProSight.

http://groups.molbiosci.northwestern.edu/kelleher/software.html

Cheers - jonas

The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.

http://www.ebi.ac.uk/pride/archive/

Hi Antonio, just as a clarification, Mascot is a search engine, not a database. It's free in this link (http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=MIS), however you can only use certain databases (NCBI, etc...), so if you want to use a specific transcriptome/genome you need to pay for the server. You also have TPP (transproteomic pipeline), which is open source, but you need some bioinformatic knowledge.  

I know these database, thanks to all, but I'd like to know if is there anyone able to identify an entire protein protein, not a digest 

It all depends on the MW of your protein. Which mass spec have you used? you can probably use maldi with sinapinic acid instead of CHCA and then do a protein fingerprint analysis...

The problem you are going to face is the ridiculous mass accuracy and resolution required to even attempt this kind of identification. Obviously, as the mass increases, the number of alternative amino acid combinations that can add up to that mass increases. You very quickly get to a situation where it would be almost impossible to identify a protein purely from it's intact mass.

I'd suggest you do a literature search, but I'm not aware of any search algorithms other than ProSight, already mentioned. I'm not entirely familiar with ProSight, but it looks like it does Top Down identification. I'm guessing this isn't what you are after.

It's a safe bet the reason you are having trouble locating this kind of software is because the approach is difficult, or beyond current technology.

Good luck.

MassWiz is an open source tool to identify proteins from Mass Spec work:

Yadav et al J. Proteome Res., 2011, 10 (5), pp 2154–2160

DOI: 10.1021/pr200031z

Hi Antonio, If i understand right, you are looking to identify an intact protein using the molecular mass and you are looking for a software to 1) Deconvolute (convert multiple charge states into one) and 2) search a database to identify all the protein with this deconvoluted mass.

The major problem is in first step , different deconvolution softwares give different masses with the same raw data.This is because of the inbuilt algorithms they use(peak modelling, maximum entropy etc.). the mass could be off by 2-5 Da applying different models. As a user , you can use a High-resolution MS and use a standard protein along with your sample and make sure you get the desired mass for this standard everytime after decovolution.

2) Even if you  get an accurate mass, to match it known protein in database will be tricky. even with a window of 5 ppm will give you 20-30 hits. Alternatively, one can do MS\MS of the intact protein molecule (if mass is

thank you very much, I just have performed a deconvolution of the spectrum and from what i have seen, the mass matches with what i was looking for.

use Maxquant software..its pretty cool software and free...

http://www.maxquant.org/

have a look at

http://easyprot.unige.ch/

not used from my part but I used to use 'Phenyx', the core engine of EasyProt (MS/MS identification software Phenyx), very powerful

http://www.genebio.com/products/phenyx/

Looks like there is a little confusion here.. do we speak about TopDownProteomics? = identifying a whole intact protein? (no digestion step?)

MaxQuant, Mascot, Phenyx .. and dozens of other software are only for bottom up!

oups...sorry...yes, the question was about top-down proteomics...I was disturbed by the previous post about MaxQuant!