Library Conversion Tool

Introduction

The LIB2NIST converter can convert data

From:

  • 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


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

Options
User MS Library Limitations
MS/MS Library Features

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

The LIB2NIST mass spectral data conversion program consists of the following files (which are contained in a ZIP archive): lib2nist.exe the conversion program ctNT66.dll part of conversion program zlib1.dll part of conversion program hptrans.tbl transliteration table used by Lib2NIST 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 example of a MS/MS spectrum msms_spectrum.SDF example of a MS/MS spectrum CMDLINE.pdf explains LIB2NIST command line options Readme_lib2NIST.txt description of the program

Download LIB2NIST (version 1.0.4.39 build 06/02/2014)

This page was last updated 07/05/2012.