Creation of spectral library using DIA without DDA

Creation of spectral library using DIA without DDA mjgou  2021-06-15
Dear Skyline Team,

In our lab, we are currently using a 6560 Ion-Mobility qTOF mass spectrometer from Agilent for untargeted proteomics studies and Spectrum Mill is used to generate peptides/proteins identification lists. We are particularly interested in using Skyline to create and manage specific spectral libraries for our clinical applications. However, our workflow does not include the prior acquisitions in DDA to build the library due to the limited amount of samples. We would like to directly use the DIA acquisition files to create this library. Do you think this workflow could be compatible with Skyline?

Thanks in advance,

Best regards,

Brendan MacLean responded:  2021-06-15

Hi Marie,
Skyline can build a library from Spectrum Mill results. There is a function to export pepXML and mzXML, which can be used in the Skyline library build feature. So, if you have Spectrum Mill peptide identifications, I hope you can export this type of pepXML and mzXML. I am pretty sure others have done this successfully. I remember we had to implement support for a non-standard mzXML attribute specifying the drift time of the identified spectra.

Hope this is helpful. You might also contact Agilent for their help with getting started.