Hi Henry, Thanks for your efforts!
It would be useful to already have access to the new SpectraST version to handle those MSP files. Is there a daily TPP release available or something? Thanks, Wout On Sunday, July 15, 2018 at 9:41:56 PM UTC-7, Henry Lam wrote: > > Wout, > > I replied your email separately, but let me also repeat here for the > benefit of others who might be reading it. > > The newer HCD libraries from NIST use a slightly different formats, and > SpectraST was not prepared for it. It will be fixed in the next release of > TPP, but if you need something sooner, please reply to this email. > > Henry > > On Tuesday, March 13, 2018 at 6:19:45 AM UTC+8, [email protected] wrote: >> >> 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 [email protected] >> [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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
