As far as I know there is no open source platform that provides free access to commercial software such as Mascot. You can convert your raw data with ms-convert (which is freeware) to any desired file format (mgf, mzXML...) and then use an open source search algorithm such as Xtandem or MSGF+. I can recommend MSGF+.

It sounds like you have a peak list in a compatible format, but that is not clear from your post. Sequest is now out of patent and Comet and Tide both implement the Sequest algorithm. You can use both via SearchGUI.

http://compomics.github.io/projects/searchgui.html

Matrix Science (Mascot) will let you search a small amount of data for free, they are nice like that.

http://www.matrixscience.com/search_form_select.html

Hi Sangeetha,

It is not clear about the information you have got. If you only have a peak list with m/z and intensity, it might be difficult to deduce the peptide sequence. In case you want to, you must have a raw file so that you can use the scan number for getting the peptide sequence by using search algorithm.

Varsha

Thank you all for the informative reply.

Is there any tool to convert *.msp file of tandem mass spectra from NIST peptide spectral library to mzxml/MGF file.

Your best option would be to use a search algorithm that uses the msp format;

https://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:start

If you don't want to do that, you **may** be able to do a two step conversion using one of these tools;

https://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:libraryconversion

then going into MGF via ProteoWizard. I haven't checked if this is possible, it's an idea.