All, In case you run into the same problem (SpectraST not reading the latest NIST HCD libraries properly), and don't want to wait for the next official release of TPP, please read on.
Assuming you are working on the release version (TPP 5.1), these are the files that need to be replaced: https://sourceforge.net/p/sashimi/code/HEAD/tree/tags/release_5-1-0/src/Search/SpectraST/Peptide.cpp https://sourceforge.net/p/sashimi/code/HEAD/tree/tags/release_5-1-0/src/Search/SpectraST/SpectraSTMspLibImporter.cpp You can either "svn update" or just download the file and replace the one if your directory. Henry On Monday, July 16, 2018 at 12:41:56 PM UTC+8, 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, wo...@uw.edu 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 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.
