I have an input file containing precursor mass and peak list (m/z and Intensity) of tandem mass spectrum. The file contains multiple spectrum data. I need to identify peptide using sequest and mascot approach. Is there any open source tool to identify peptide from peak list file. Software like TPP require raw or mzxml file to validate in sequest and mascot algorithm.
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.
- Badges
- Science topic
- Similar topics
- Chemistry
- General Biochemistry
- Proteomics