Hi,
I want the MS2-CID spectra from orbitrap velos mass spectrometry of organism: human (Mod: C+57) for testing my peptide identification algorithm developed. Large set of orbitrap velos dataset available in pride archive. But I am unable to identify whether the spectra produced is of fragmentation type CID from their site. Can anyone guide me to get the data.
MS2 fragmentation : CID Analyser : LTQ Orbitrap velos ion trap organism: human Static Modification : Carbamidomethyl Protease: Trypsin
Dear Sangeetha,
The easiest way to check if the MSs spectra was produced by CID is to open the raw data in Xcalibur, select the MS2 spectra of any peak and in the top of the spectra you will find some letters in red like this:
ITMS - c ESI r d Full ms2 [email protected] [50.00-136.00]
The "cid" indicates the spectra was acquired in CID mode and the value of 35 is the one used (by me) as collision energy. The other data will of course vary according to the peak you select to see the MS2 and the type of analyzer (I used an Ion trap coupled to an Orbitrap, "Orbitrap Fusion")
Kind regards,
Federico Padilla
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