Seven Golden Rules

Project Partner:
Tobias Kind, Oliver Fiehn


Tobias Kind, Oliver Fiehn
Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry.
BMC Bioinformatics 2007, 8:105
Download the open-access article here [PDF]

Provided project software:

Parts of the software are published under the Creative Commons (by) license. This license lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. The 7GR EXCEL + HR2 software was recently validated with EXCEL 2003 and WIN XP as well as EXCEL 2007 and VISTA Ultimate 64bit.
Download the supplement data and CC-by project software here [LINK]


Picture service:

All text and pictures from the 7GR on this website can be freely downloaded and reused via the CC-by
Download the picture archive with 44 example graphics as [ZIP].

Short Introduction:

The Seven Golden Rules are used on our laboratory to overcome the problem of wrong molecular formula
assignments from LC-MS, GC-MS, FT-ICR-MS data. They were developed for research and advances in structure elucidation of small molecules. Follow the navigation on the left for some additional comments and experimental data.

(All text and pictures from the 7GR on this website can be freely downloaded and reused via the CC-by


Links to external software used in the project:


  1. TEXTPAD ($$)
  2. MWTWIN Molecular Weight Calculator (free) and Formula Generator for Windows
  3. MS EXCEL ($$$) + Visual Basic
  4. Mercury6 (free) for calculation of isotopic pattern (Algorithm by Alan L. Rockwood, Programming by Steve Van Orden) a free implementation is libmercury++
  5. 4a) high accuracy and high speed isotopic pattern generator here or at web (free) by Pentti Somerharju and Perttu Haimi
  6. Borland C compiler (free) (C++Builder )
  7. Statistica Dataminer v7 academic license ($$$$)
  8. Structure generators Molgen (DEMO) and Molgen-Online
  9. Deterministic Structure Generator from the Chemistry Development Kit CDK (free)
  10. Molecular formula generator CHEFOG from Chemsoft provided within the chemedu package (free).
  11. Molecular formula generator HiRes MS (free) by Joerg Hau (the new version HR2 is much faster - see supplement)
  12. NIST MS Search program (free) - the NIST05 database itself is commercial
  13. ChemAxon molconvert (free), cxcalc (academic license), JCHEM full (academic license)
  14. SDF toolkit by Bruno Bienfait (free)
  15. ChemAxon Instant-JChem (free academic version)
  16. Windows Server 2003 Resource Kit Tools (free) - use qgrep (other free versions have bugs)
  17. Microsoft Visual C++ 2005 Express compiler (free)
  18. EPA EPISuite (free)
  19. SMOG molecular isomer generator (Structural Molecular Generation) (free)
  20. Beilstein Crossfire for searching the Beilstein database of organic compounds and properties
  21. Scifinder Scholar for searching the CAS database

Databases and Services (updated):

  1. The CACTUS - Chemical Structure Lookup Service (CSLS) - from NCI and Chemnavigator
  2. The PubChem database (free) - download the whole PubChem DB here: PubChem FTP
  3. The Dictionary of Natural Products ($$$$) Web version and SDF version from Informa PLC
  4. The KEGG database (free)
  5. The peptide DB and metabolome DB (free)
  6. The NIST and WILEY mass spectral database ($$$$)
  7. The DrugBank database (free)
  8. The BioSpider service (free)
  9. The MDL Beilstein database ($$$$$)
  10. The CAS database ($$$$$ academic or $$$$$$ commercial)
  11. The ChemSpider DB (free) - largest information enhanced DB with mass spectrometry API