I've downloaded the human orbitrap HCD library (09-23-2016) from NIST <http://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:cdownload> and I'm trying to use this for spectral library searching with SpectraST. The library is in the NIST msp format so I'm first trying to convert this to the SpectraST sptxt/splib format:
> spectrast -cNout human_hcd_selected.msp SpectraST runs but doesn't seem to parse the msp file correctly, as I think it tries to interpret the charge as a modification. This is some of the stdout output on the command line: Attempting to calculate M/Z with charge = 0! Assume charge = 1. Attempting to calculate M/Z with charge = 0! Assume charge = 1. Attempting to calculate M/Z with charge = 0! Assume charge = 1. ... And this is the stderr output in the spectrast.log file: START: (Mon Mar 12 14:44:42 2018) spectrast -cNout human_hcd_selected.msp GENERAL: File offset size is 8 bytes. Big library supported. GENERAL: Pointer size is 8 bytes. MSP IMPORT: Importing .msp file "human_hcd_selected.msp". ERROR MSP IMPORT: Peptide ID has unknown modification: "A.AAAAAAQCRSPR.C". Skipped spectrum . ERROR MSP IMPORT: Peptide ID has unknown modification: "R.AAAACLDK.A". Skipped spectrum . ERROR MSP IMPORT: Peptide ID has unknown modification: "R.AAAACLDK.A". Skipped spectrum . ... The spectra that are reported to be skipped indeed don't appear in the created sptxt file. Furthermore all other spectra that are in the sptxt file have charge 0: Name: AAAAAAAAAAAAAAAGAGAGAK/0 LibID: 0 MW: 1595.8380 PrecursorMZ: 1595.8380 Status: Normal FullName: R.AAAAAAAAAAAAAAAGAGAGAK.Q/0 (CID) ... Whereas the original msp file looks like this: Name: AAAAAAAAAAAAAAAGAGAGAK/2 MW: 1597.8526 Comment: Single Pep=Tryptic Mods=0 Fullname=R.AAAAAAAAAAAAAAAGAGAGAK.Q Charge=2 Parent=798.9263 Se=1(^G1:sc=4.19823e-024) Mz_diff=7.3ppm Purity=92.1 HCD=38.8276176452637eV Scan=19217 Origfile="W16_P_5_run3.raw.FT.hcd.ch.MGF" Nreps=1/25 Sample="WHIM16_PHOSPHO_RUN3" Protein="sp|P55011|S12A2_HUMAN" Unassign_all=0.4309 Unassigned=0.1057 max_unassigned_ab=0.40 num_unassigned_peaks=3/20 FTResolution=17500 ms2IsolationWidth=2.00 ms1PrecursorAb=29381934.97 Precursor1MaxAb=42586850.38 PrecursorMonoisoMZ=798.9204 Filter="FTMS + p NSI d Full ms2 798.92@hcd27.00 [110.00-1650.00]" Num peaks: 585 ... So parsing of the msp file doesn't seem to be correct and unfortunately the only other format in which this spectral library is available is a NIST binary format. How can I use this spectral library for searching? -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
