Hi Ray, Maybe try with -M option, which allows you to define customized modification types. You can find more details about -M option from SpectraST wiki.
Best, Wenguang On Wednesday, May 27, 2020 at 9:48:01 PM UTC+2, Ray wrote: > > Hi, > > I was trying to convert the NIST consensus human hcd library > <https://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:lib:humanhcd20160503> > > (.msp format) to splib format with spectrast built from TPP 5.2. > > After running the command: > spectrast -cNhuman_hcd human_hcd_tryp_best.msp > > The resulting human_hcd.sptxt file contains significantly less spectra > (273,137) than the original human_hcd_tryp_best.msp file (398,373). It > seems that all peptides with modifications are discarded. > > For example, in human_hcd_tryp_best.msp file, there is an > entry: AAAAAAVGPGAGGAGSAVPGGAGPCATVSVFPGAR/3_2(0,A,Acetyl)(24,C,CAM) > > But there is not such peptide in the output human_hcd.sptxt file. Did I > miss some command-line arguments when converting the library? > > Thank you. > > Ray > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/6b78e3e0-2919-4b48-95d8-4406b7bea4aa%40googlegroups.com.
