MS search

The results of data treatment are documented and evaluated in ES 5 and the interpretation in ES 6 is guided by the analyst s constraints and requirements. For instance, simple visual pattern comparisions may be acceptable for sample identification, or a combined database (GC-FTIR/GC-MS), (PGC/FTIR), (GC/TA), etc., analysis may be required. Judgmental decisions must be trained into the system as to depth of analysis, its acceptability and reliability (e.g., the hit quality index (HQI) of the MS search combined with that from the FTIR search may confirm within a 95% confidence level the GC peak or sample identity). 

The capability to identify compounds outside the target analyte list is one of the greatest advantages offered by GC/MS. Searching the EPA/NIST spectral library, the computer finds the best matching library spectra for an unknown compound and tentatively identifies it using the best fitting spectrum. The retention time information is not available for this compound as it is not part of the calibration standard, hence only tentative identification. These tentatively identified compounds (TICs) can be also quantified to provide an estimated concentration value. 

The third of the three adjacent peaks (29.207 minutes) is readily identified as 2-hydroxybenzaldehyde (salicylaldehyde) by comparison of the MS or IR spectrum with library data. It should be noted that the automated search routine in the MS software picked 3-and 4-hydroxybenzaldehyde as better matches than the 2-hydroxy compound, even though the 76 ion in the spectrum of the unknown is present only in the mass spectrum of the 2-hydroxy compound. However, the IR search routine correctly identified the 2-isomer. This illustrates that casual operators who rely on automated search routines for compound identification are much less likely to make errors when they have access to both IR and MS searching. 

The new analytical data is validated on the basis of the electronic version of the data as the true master copy. In the past, the hard copy used to be the only master copy for all techniques. This new approach applies only to the data that can be managed by electronic means. So far this approach has been successfully applied to the validation of MS technique only. The main reason for that is the availability of the software for managing the MS data (NIST MS Search). In future, procedures shall be developed for the other analytical techniques, for example IR, to be based on the electronic version as the true master copy. 

To facilitate the validation process on the basis of the above approach, the MS electronic data is contributed to the OPCW Laboratory in any of the following electronic formats JCAMP, NIST ASCII, AMDIS, and NIST MS Database. Contributing laboratories provide mostly the NIST MS Database format, with structures. The OPCW Code and the Schedule number are placed in the synonym field of the database. The file is submitted to the OPCW Laboratory either as the NIST MS User Database or the corresponding set of text files representing the MSP (Spectral) and MOL (Structure) information. The NIST MS Search/Analysis programs are used for the management of the MS electronic data and also GC(RI) once merged with the MS data. 

In the case where MS analytical data has been contributed in the other formats, it is prepared into a NIST MS Database, using the NIST MS Search program. This program is used to create MS spectral files from the following electronic formats JCAMP, NIST ASCH, AMDIS, and NIST MS Database. If the analytical data contains no chemical structure, the structure is created in ISIS Draw and then imported into the database as an MOL file. The information associated with the MS analytical data is handled by the NIST program. 

OPCW code Chemical name CAS Schedule Link to PDF file Link to NIST MS search... 

The electronic MS on-site databases are prepared from the certified electronic version of the OCAD (e-OCAD). This version is compiled using the NIST programs (NIST MS Search/Analysis and AMDIS) and is in the form of a NIST MS Database. The e-OCAD does not contain Gas Chromatography retention indices (GC(RI)) that are required for on-site use. To create an electronic MS onsite database, the certified version of e-OCAD, which at the moment contains only MS data, is merged with the certified (GC(RI)), which is in an excel spreadsheet. After merging these data, an AMDIS version of the database is created, which is compatible with the AMDIS software used by the on-site GC/MS equipment (for more details on the software, refer to Chapter 2 and Chapter 4) (5). The MS on-site database can be sent for an inspection as a whole database or as an extract of the whole database. AMDIS is software that is used by the GC/MS on-site equipment... 

The OPCW Laboratory performs functional tests on the authenticated, certified, and on-site analytical databases. These are tests that verify that the analytical database is functional. So far, this procedure is fully developed for the MS analytical databases. The electronic version of OCAD (which so far consists of MS analytical data only) is tested with the NIST MS Search/Analysis program. The on-site MS analytical databases are tested using AMDIS software. A NIST or AMDIS library is created and this becomes the target library for a library search. A search is performed on a newly measured MS spectrum (raw data files) containing a number of chemicals that are present in the target library. Identification of the targeted spectrum indicates that the created library is functional. 

The MST/EPA/NIH Mass Spectral Library 1998 database ( www.nist.gov/ srd/analv.htm) is the product of a muftiyear, comprehensive evaluation and expansion of the world s most widely used mass spectral reference library, and is sold in ASCII or Windows versions. It contains 108,000 compounds with electron ionization spectra, chemical structures, and molecular weights. It is available with the NIST MS Search Program for GC/MS deconvolution, MS interpretation, and chemical substructure analysis. The NIST chemistry WebBopk ( http //webbook.nist.gov) is a. free online system that contains the mass spectra of over 12,000 compounds (this Standard Reference Data Program also has IR and UV-Vis spectra). 

Straightforward identification by retrieval of candidate compounds/molecular structures. Examples of such systems are Biemann s MS search, McLafferty s MS/ PBM system, and our MS, C-NMR, high resolution H-NMR and LC-UV library search systems. ... 

Fig. 1. Chromatogram of fresh Mimusop elengi flower. GC system Column TR-5 (5%phenyl-95%dimethylpolysiloxane), 30m, 0.25 am, 0.25 mm ID Oven temperature program 60 °C to 180 C at 3 °C.min-i, to 280°C.min-i at 10 °C.min-i (hold 5 min) Run time 55.00 min Carrier gas flow rate (Helium) 1 ml/min Transfer line temperature (Interface temp.) 275 °C Ion source 220 C. Scan mode full scan 35-650 m/z Scan rate 2000amu/s Solvent delay time 3min. Instrument TraceGC ultra. Model K05200B20000070, Italy/MS Model TraceDSQ,USA Software Xcalibur 1.4 Library NIST MS Search...

Mascot (Matrix Science) search algorithm and the International Protein Index (available online at http //www.ebi.ac.uk/IPI), or similar database. The search against the normal database combined with the corresponding reversed or randomized database is an excellent vahdation method for MS/MS searches of large data sets. 

In a personal communication to one of us (PRG), Fred McLafferty, one of the leading mass spectro-metrists in the country, estimated that at least 50% of the first hits of all GC/MS searches are incorrect. 

The NIST library is available with a new version of the NIST Mass Spectral (MS) Program (v.2.0g) and the enhanced versions of MS Interpreter and AMDIS, the mass spectral interpretation tools with thermodynamics-based interpretation of fragmentation and chemical substructure analysis. The binary format has not changed from the 2002 version, although several new files have been added that associate equivalent compounds and link individual compounds to the RI library. Raw data files are provided in both an SDFile format (structure and data together) as well in earlier formats. The SDFile format holds the chemical structure as a MOLFile and the data in a simple ASCII format. The NIST MS Search Program is also part of many commercial instrumental GC-MS software suites. 

Available formats and compatibility The hbrary is available in two formats Chemstation (Agilent) and the NIST MS Search (Bruker, JEOL, LECO, Perkin Elmer, Thermo, Varian, Waters). Other formats are available on request. 

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