LIB2NIST - Library Conversion Tool



Introduction
The LIB2NIST converter can convert

  • HP MS Libraries (with up to 4 structure libraries)
  • NIST MS user libraries
  • Text files in .MSP format with structures in MOLfile format
  • Text files in .SDF format containing both spectra and structures
  • Text files in JCAMP-DX format containing mass spectra (including HP-JCAMP)
  • Text file in .MSP or JCAMP-DX containing mass spectra and associated with it file in .SDF format containing structures

into

  • NIST MS user libraries
  • Text files in .MSP format optionally with structures saved in MOLfiles
  • Text files in HP-JCAMP format (Revision 4.10) recognized by Agilent MSD ChemStation
  • Text file in .SDF format containing mass spectra and structures

Note: In all input text files, lines must end with Carriage Return/Line Feed characters (CRLF, “\r\n”)

It is possible to convert a subset of spectra, as specified by ID numbers or CAS registry numbers.

If an input MS/MS spectrum in SDF or MSP file has more peaks than MS Search can accept, the number of peaks in the output is automatically reduced by removing the smallest peaks, typically, to 7,000-9,000. Reducing the max. number of decimal places in peak m/z values, for example, to 4 with the command line option /PeakMzDecPlaces=4 may increase the number of peaks saved in the output MS/MS spectrum. Long peak annotations may significantly reduce the number of peaks. Typically, peaks and peak annotations of a mass spectrum must fit in 140,000 bytes.

Options
The m/z values from text input files can be subject to a specified rounding transformation, usually to reduce reported m/z to integer (nominal) values.

Deselect “Include synonyms” options to omit chemical name synonyms in the output

Deselect “Keep IDs unchanged” to make sure the IDs in the newly created user library are sequential numbers (1, 2, 3,…)

Select “MS/MS spectra only” to process MS/MS spectra

“2008 MS Search compatible” option is for backward compatibility only. It degrades functionality of more recent software. Select this option to create a MS/MS library for use with NIST MS Search program obtained with NIST 08 MS Library.

For more details on the .MSP file structure see NIST MS Search User Guide, section “NIST Text Format of Individual Spectra.”

For details of the JCAMP-DX file formats see: P. Lampen, H. Hilling et al, “JCAMP-DX for Mass Spectrometry”, Applied Spectroscopy, 1994, 48 No. 12, 1545-1552.

The converter recognizes only (XY..XY) type peak tables.

For more details on MOLfiles and SDFiles see article A. Dalby, J. G. Nourse et al, J. Chem. Inf. Comput. Sci., 1992, 32, 244-255.

Only generic [G] MOLfile features are recognized by the software.

User MS Library Limitations

  • Maximum length of a chemical name or a synonym is 511 characters.
  • Maximum length of a comment is 1023 characters.
  • Maximum length of a mass spectrum is 800 peaks; in case of more than 800 peaks, the smallest peaks will be ignored by the LIB2NIST to reduce the spectrum length to 800 peaks.
  • Maximum chemical formula length is 23 characters.
  • Maximum number of spectra in the ordinary user library is 65,535.
  • Maximum ID value of a spectrum in the ordinary user library is 65,535; IDs start from 1.
  • Maximum molecular mass is 2000.
  • Maximum MS peak mass number indexed for the Default user spectrum pre-search or Any Peak search is 2000.
  • Maximum user library record length is 5200 bytes; if the spectrum does not fit then as much last synonyms as necessary to reduce the record length to 5200 are ignored.

MS/MS Library Features

  • Maximum number of spectra may exceed 65535.
  • Maximum length of a comment is 2047 characters.
  • Peaks are also saved and indexed for fast mass spectrum searching with accurate m/z values and intensities, and may have text annotations. Number of peaks saved in this format may exceed 800.
  • Maximum molecular weight, peak m/z, and precursor m/z values may exceed 2000.
  • MS/MS libraries created by Lib2NIST may not be altered by the NIST MS Search program.
  • Precursor m/z, a mandatory item in a MS/MS spectrum, cannot be exported to a HP-JCAMP file.

Import/Export of Synonyms
Files SYNON.MSP and SYNON.JDX are examples of the converter input files to illustrate how compound name synonyms can be added to the user mass spectral library.

Synonyms in the user libraries are supported by NIST MS Search Program starting from version 1.7.

To export synonyms to NIST user library or .MSP format make sure the “Include Synonyms” option is selected.

Synonyms cannot be exported to a HP-JCAMP file.

Import of Structures from MOLfiles
Molecular structures located in separate MOLfiles can be associated with the spectra located in a single .MSP file and converted into the user library.

To achieve this the MOLfiles should have predefined names and be located in the folder with same name as the name of the input .MSP file and extension .MOL.

MOLfile names
To associate a MOLfile with a compound having, for example, CAS reg. number 50555, the MOLfile should have name s50555.mol

To associate a MOLfile with a compound having, for example, ID=15 (15 is either an ordering number of the spectrum in the .MSP file or the spectrum in the .MSP file has line “ID: 15” or a spectrum in the input library has ID = 15), the MOLfile should have the name id15.mol

MOLfile location
The folder containing MOLfiles should be located in the folder where .MSP file is. For example, if .MSP file is C:\NIST11\MYSPECS.MSP then the folder with MOLfiles MUST be C:\NIST11\MYSPECS.MOL and contain files like C:\NIST11\MYSPECS.MOL\s50555.mol C:\NIST11\MYSPECS.MOL\id15.mol

When converting any .MSP file the converter always looks for a folder with a name derived from the name of the .MSP file. In the case 2 MOLfiles are associated with the particular spectrum (one by CAS reg. number, another by ID) the converter ignores the former and picks up the latter MOLfile.

The names and locations described above are exactly the same as those the converter would produce when converting to a text file in .MSP format with structures saved in MOLfiles.

Other examples
Files TEXTSAMP.MSP and STRUSAMP.SDF are sample input text files for the LIB2NIST converter. They represent two of the text file types recognized by the present version of the LIB2NIST library converter.

TEXTSAMP.MSP is self-explanatory. In addition to a mass spectrum and a name, this kind of file may contain a CAS rn, a formula, and a nominal molecular weight.

Please note the STRUSAMP.SDF format is rather strict. In consists of a series of MOLfiles. A record for each compound is made out of 5 parts, the first of them (structure) may have no atoms or bonds:

  1. Chemical structure in MOL-file format (may have no atoms or bonds)
    The first line (name) and the third line (comment) will be replaced before saving molfile into the NIST User MS library.
    If molfile contains aromatic bonds (type=4), the converter will transform them into alternate single/double bonds and completely change the whole molfile before saving it into the NIST User MS library. Aromatic bonds may be only in even-member rings.
  2. One line separating molfile from mass spectral data part:
    <MASS SPECTRUM>
  3. Mass spectrum in ASCII form, same as in TEXTSAMP.MSP. It cannot have blank lines.
  4. One blank line.
  5. One line marking the end of the record for the compound: $$$$

Please note there are no blank lines between “$$$$” line and the first line of the next record.

STRUSAM2.SDF was created by Lib2NIST from STRUSAMP.SDF. It is an example of an alternate SDF file format. This format is also recognized by the LIB2NIST.

msms_spectrum.MSP and msms_spectrum.SDF are examples of MSP and SDF files containg MS/MS spectra. A MS/MS spectrum file must have precursor m/z value. Examples of MSP files containing peptide MS/MS spectra may be found here: http://peptide.nist.gov. This site uses term “Library” for MSP files.

Download

LIB2NIST archive with x32 bit program
LIB2NIST archive with x64b it program

The LIB2NIST mass spectral data conversion program consists of the following files (which are contained in a ZIP archive): 

Lib2NIST.exe         the conversion program
CTNT66b.dll          part of conversion program
zlib1.dll            part of conversion program
libinchi_l2n.dll     InChI v.1.05 dll
HPTRANS.TBL          transliteration table used by Lib2NIST
LICENCE_InChI.pdf    required for libinchi.dll distribution; copied from 
                     http://www.inchi-trust.org/download/105/LICENCE.pdf
TransHexUnc.txt      Translation table for /TranslateHexUnc= option
doc\
   _msp_to_peplib_readme.txt      Convert MSP to PepLib 
   CMDLINE.pdf                    Explains Lib2NIST command line options
   Readme_Lib2NIST.txt            This documentation in plain text format
example\
   synon.jdx                      JCAMP-DX file example, includes synonyms
   synon.MSP                      MSP file example, includes synonyms
   Textsamp.msp                   Compound MSP file example
   Strusamp.sdf                   SDFile chemical structure example
   Strusam2.sdf                   Alternate SDFile format
   msms_spectrum.MSP              An example of MS/MS spectrum
   msms_spectrum.SDF              An example of MS/MS spectrum
   Glu-70.MOL                     An example of Glycan KCF embedded in molfile
   pep_name_minimal_example.MSP   An example of pep_name