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Fail to import MZID as Ion library from PEAKS Studio 8.0 database search output


Hello everyone!

I am trying to import the mzIdetML file (version 1.1.0 format) from Peaks Studio 8.0 into Peakview Swath microapp.
However, I can only import the protein list but no peptide or retention time information available after the import.
I wonder if the cv value or the XML tag used in the mzid output file could not be recognized by the Peakview swath microapp.

At the Peaks Studio 8.0, they say that such file should be compatible with Skyline. I would like to ask whether it is compatible with peakview too?

I will be happy to provide some mzid file if necessary.

Thank you very much!




This topic was modified 5 months ago by Trish Reed
Posted : February 9, 2017 5:28 am

Sorry for the stupid question above. I just found the solution at the MS/MSALL with SWATH™ Acquisition MicroApp Release note Version 2.0.1, which states:

"No peptide information is shown after loading a mzIdentML file
If an mzIdentML file is loaded that is missing a <fragmentation> element, then the ion library is loaded but no peptide information is shown. Reload the mzIdentML with the required element."

I will review my mzid files then

Posted : February 9, 2017 6:23 am

I'll be very interested to see how this goes - we bought Peaks Studio 8.0 software last year and had preliminary discussions with their team, prior to purchase, about implementing a .csv export compatible with the SWATH microapp in PeakView to allow import of spectral libraries.  It was implemented (somewhat) in the 8.0 release and we've managed to get the data into PeakView and have a (partially) usable ion library for SWATH extraction - it involved renaming some columns in the .csv an saving it to a .txt extension. The export that Bioinformatic Solutions implemented for us is the "peptide-spectrum match ions".  I explained to them that PeakView Swathmicroapp needs the minimum column headers for a library file as:  

Q1, Q3, RT_detected, protein_name, isotope, uniprot_id, relative_intensity, stripped sequence, modification_sequence, Prec_z, frg_type, frg_z, frg_nr.  The order is irrelevant and it is case insensitive.

Peaks 8.0 leaves the headers in with their original names so some modification is needed:  Peptide, length, mass, m/z , RT, z, fraction, scan, sourcefile, protein, ion, pos, ion m/z, theo m/z, m/z error, ion intensity, ion charge, modification.

We therefore renamed m/z to Q1; ion m/z to Q3 etc until we'd renamed the minimum needed by PeakView (we put 99% confidence for all in this example).


Posted : February 9, 2017 7:32 am

Hello David!
Thanks a lot for your sharing.
I am now working on the conversion from PSM ion to Peakview spectral libray format

Posted : February 14, 2017 6:02 am