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Are there publically available ion libraries that I can use to process my SWATH Acquisition data?
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A -  Over the last few years, researchers from Dr. Ruedi Aebersold’s laboratory at ETH Zurich and Dr Robert Moritz’s lab at Institute for Systems Biology (ISB) in Seattle have been working on developing whole proteome libraries for use in SWATH Acquisition studies. They are targeting the widely used proteomes that will be of very good use to the research community.  The three of such ion libraries (M. tuberculosis, human, yeast) have been made available on the ISB website ( More such libraries will become available as the SWATH application becomes more widely adopted.
An example of the use of this library can be found in the technical note “Enabling Systems Biology Driven Proteome Wide Quantitation of Mycobacterium Tuberculosis - SWATH Acquisition on the TripleTOF® 5600+ System”.  
There are two recent papers describing the generation of large ion libraries for Human and Yeast.

You can download the Pan Human and Pan Yeast libraries that are formatted for use with SWATH 2.0 data processing or OneOmics from BaseSpace.

This topic was modified 5 months ago by Trish Reed
Posted : January 29, 2015 6:56 pm

Is it possible for SCIEX to put together the locations of available ion libraries with the files modified to work with the SWATH microapp/OneOmics (I notice the swathatlas human library has only the uniprot accession codes in the peakview compatible file, not the protein names)?  It would be convenient to have a list of SCIEX software optimised library formats for quick use.

Having a dedicated SCIEX page with links spectral libraries for use with SWATH would be a pretty useful thing (maybe there is and I haven't found it yet?).

Posted : June 4, 2015 5:58 am
Community Manager
Member Admin

Hi David, great feedback and I'll work with the team to get you this information. Stay tuned!

Topic starter Posted : June 4, 2015 11:24 am
Member Admin

I think that is a really great idea!  I'm sure we could find ways to host the libraries, the bigger question would be how to develop the right libraries with the right depth such that they are very usable by the broad community.   Perhaps this is a great opportunity for crowd sourcing the generation of libraries.  We as a community could identify the top needed species and then we could split that up among SWATH labs to put some effort into developing some reasonably deep libraries.  Thoughts from the community members would be greatly appreciated on this!

Posted : June 5, 2015 11:01 am