How Wouid You Analyse Electron Transfer Dissociation (Etd) Mass Spectra?

Question

[Attila Csordas]

Nice data analysis opportunity - details here:

'The Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) invites you to participate in a collaborative data analysis study focusing on the evaluation of proteomics laboratories in identifying electron transfer dissociation (ETD) spectra. In this study, an LC-MS/MS dataset from a yeast lysate digested with Lys-C and enriched for highly charged peptides using strong cation exchange fractionation will be provided. This study will enable participants to evaluate their data analysis capabilities and approaches relative to others in analyzing a common data set'.

What tools would you use and what settings?

[Neilfws]

The post is from the SPC list. SPC developed the Trans-Proteomic Pipeline (TPP) tools and they indicate that the TPP can handle ETD spectra. So there's your starting point. As to precisely what you would do, well that depends on the nature of the (as-yet unseen) dataset.

Answer 1

[Jdnavarro]

The most popular search engines are optimized for CID. I would give a try to new search engines that claim better performance with ETD. Off the top of my head:

• MS-GFDB (open source)
• ZCore (commercial)
• ETD scoring function
• ProteinProspector (web app?)

[Attila Csordas]

my colleague David says that ProteinProspector was originally designed for PMF not for MS/MS so he wouldn't really trust that in that respect

[Jdnavarro]

Well, in the paper I linked to they are claiming they designed a new scoring scheme for ETD from scratch. I never tried ProteinProspector but they claim very good restuls.