Hi Eileen, I do not know the answer to your question. I do not see anything in the documentation to suggest that this is the case. But do note that xinteract sets a default lower bound the length which you need to change, and there are some spectrast settings that may discard such spectra since they are outside the normal bounds for most experiments. See the SpectraST documentation here:
Search for the “SPECTRUM FILTERING OPTIONS” section.
May I ask one question related building library with Spectrast?
I am using Windows command to build the library. There is one question: whether Spectrast will eliminate all the peptide which is less than 6 amino acid no matter the high peptide phrophet? I am quite interested in some small peptide which is only 4-5 amino acid and would like using SpectraSt search to identify these small peptides. Is there any way that I could add these small peptide CID spectra to library?
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