Ray, This is because SpectraST does not recognize this way of specifying modification in "new" NIST files.
If you are comfortable compiling your own TPP, try downloading SpectraSTMspLibImporter.cpp from the latest "trunk" version of TPP, replace and re-compile. This should fix the problem. Henry On Thursday, May 28, 2020 at 3:48:01 AM UTC+8, 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/0f1e25f7-b8f5-41fe-b2d8-4d2bd2684634%40googlegroups.com.
