Using NIST Search with Agilent MassHunter Qualitative Analysis Software

James Little, Eastman Chemical Company

Sept 20, 2012

Introduction

Screen captures in this document were taken from MassHunter B.05.00 and NIST MS Search 2.0 (build

May 15, 2012). However, the instructions in this document will likely be useful for earlier versions of

the software. After loading the qualitative analysis software, a standard install of the NIST software

was performed. The NIST software worked in conjunction with the Agilent software with no special

setup besides the setting of parameters in the configuration files for both programs.

A license must be purchased for the NIST software and associated EI and MS/MS databases. Users

can create their own reference databases with the software. Eastman has written macros to

combine and distribute EI and MS/MS databases nightly including spectra, structures, and

associated sample information. These capabilities can be found at the following internet

locations:

http://littlemsandsailing.wordpress.com/ http://littlemsandsailing.wordpress.com/2011/05/01/nist-search-of-ei-and-msms-databases-at-

eastman-chemical/

Table of Contents

1. Initial Setup of NIST Search Parameters

2. Converting ChemStation Data Files to MassHunter Format

3. Configuring MassHunter for Processing Nominal Mass EI GC-MS Data from MSD’s

4. Processing EI Nominal Mass Data in MassHunter

5. Processing Accurate Mass MS/MS Data

6. Adding EI and MS/MS Spectra to NIST User Library

Discussion

1. Initial Setup of NIST Search Configuration: Before sending the spectra of interest to the NIST library

from MassHunter, the NIST software must be opened and the NISTsearch parameters initialized.

The radio buttons selected in the menu are common ones we employ for EI mass spectral data. There

is more detailed information in the help topics within the NIST program.

NIST can search many different libraries and the results summed. Below, the program was setup to

search the Wiley 9, NIST, Palisaded, and three of our proprietary corporate EI libraries for a total of

1074714. One could add the NIST replicate entries library, but we find the search works fine without

initially including these additional 30932 spectra. NIST included the best EI spectrum in their opinion

in the NIST mainlib and included all other duplicates in the NIST Replib library.

NIST can be searched by many parameters besides mass spectra. We find the ability to search by

structure to be invaluable for locating model compounds for viewing fragmentation patterns in EI and

MS/MS. The structure databases to be searched are also selected in the Libraries tab in the Library

Search options menu. Below, all six databases were selected since they contain structures by first

clicking on the pull-down menu labeled “Structure Search.”

The automation settings are shown below:

We normally change the default settings in the Limits tab of the Library Search Options menu. The

minimum and maximum are selected to be equal to those used in obtaining the data. If these are not

selected, then search results will undesirably weigh the results with spectra containing only a few ions.

This is especially aggravating for many Wiley partial spectra entered from the chemical literature. NOTE:

One must also select “Apply Limits” in this tab utilize this function!

The window layouts can be changed by clicking on the “Change Layout” option:

Also, many properties of the individual windows can be changed by “right-clicking” on the window of

interest and selecting properties:

There are also several very useful options on the menu bar shown below:

The first selected with the arrow above clears the history of previous searches. The one to the right of

Clear History is “Replicates on/off” which either shows or does not show additional spectra from the

Main Replib after the search is completed. The next button is the “Best matching only” button which

eliminates all but the compound with the best match factor from the library results displayed. This

latter one is particularly useful when searching small common compounds which will always be found in

multiple databases.

The older versions of the NIST search only included minimal options for the importing of mass spectra

from external programs.

The “Multiply m/z in imported spectra by” value will need to be changed in many cases since spectra

are entered into the library with nominal mass values. The value of 0.99888 is satisfactory if the mass

sufficiency from hydrogens is causing the value to be searched to be rounded up above. A value larger

than 1 will be needed to correct for mass deficiency of compounds containing many bromines,

chlorines, fluorines, etc.

The newest version of the NIST search has a much more useful “Spectral Import Options” menu shown below:

One should attempt to get the new version with this option if accurate mass MS/MS data is being

processed. I have entered the parameters that we find most useful in most of our work. Be sure to

select “Include Synonyms” box if doing MS/MS on the Agilent QTOF since many useful parameters are

automatically imported into the NIST program that are useful for saving with library entries and

reviewing data.

All the user settings can be easily saved and restored by using the “File/Save/Configuration” button as

shown below. We normally have different ones for EI and MS/MS searches which are easily restored by

this approach.

2. Converting ChemStation Data Files to MassHunter Format: If GC-MS data is to be processed with

MassHunter, the MSD files must be converted to MassHunter format. Agilent supplies a utility, “GC

MSD Translator”:

The program interface is shown below:

3. Configuring MassHunter for Processing Nominal Mass EI GC-MS Data from MSD’s: The

MassHunter software is configured for processing GC‐MS nominal mass data by selecting the

configuration option from the MassHunter Qualitative Analysis software:

Typical parameters that we find useful are for processing nominal mass EI data from MSD

instruments are shown below:

4. Processing EI Nominal Mass Data in MassHunter: Data can be processed many different

ways. One way is to integrate the chromatogram to define peaks which are then used to extract

background corrected spectra for searching in the MassHunter “Method Editor/Spectrum/Peak

Spectrum Extraction” tab.

Another way is to automatically deconvolute the data. This is accomplished in the Method

Editor/Find Compounds by Chromatogram Deconvolution” menu in MassHunter which is shown

below:

One will have to experiment with the various parameters in this menu to get useful results.

I will describe the manual method in detail below which will also give some insight into the other

two automated options noted above. If the TIC is not automatically displayed, open the “Method

Editor/Define Chromatogram” menu and to open the TIC using the following options:

Then select a single scan or a range of scan to create a spectrum. Then “right click” on the

spectrum entry in the “Data Navigator” window or the spectrum of interest in the “MS spectrum

Results” window. The following menu will appear and select the “Search NIST MS Program”

option:

The spectrum will then be automatically searched using the settings in Section 1, the “Initial Setup of

NIST Search Parameters.”

The “Search Library for Spectra” option in the previous screen capture is for searching EI reference

libraries from within the MassHunter software. It uses a search algorithm which is very similar to that

employed in the NIST MS 2.0 search software. However, libraries must be available in the MassHunter

binary *.L format and the proper library selected from the “Method Explorer/Identify

Compounds/Search Unit Mass Library” menu.

Be sure to take advantage of the ability to automatically subtract “Background Spectra” within

MassHunter in manual searches. First create a spectrum from a single scan or range of scans at an

appropriate part of the spectrum where no component is eluting. Then save this background as a

background spectrum by” right clicking” on the spectrum then selecting “Move to Background

Spectrum” in the menu that appears:

Then turn on the background subtraction option in the Method Editor/Spectrum option:

Multiple spectra can be sent for automatic searching to the NIST program by selecting them from

the “User Spectra” section of the “Data Navigator” window. Use the “control key” on keyboard in

conjunction with a “left mouse clicks” to pick noncontiguous items in the list:

Or the “shift key” on the keyboard with “left mouse clicks” to separate contiguous entries:

Or even a combination of the two options:

After selecting the spectra of interest, “right click” on the Data Navigator window within the block of

spectra highlight to select “Search Using NIST MS Program” option. The search will begin and the

results stored in the NIST history buffer. To access this buffer, use the “pull down” menu in the NIST

search software.

The results in this “History buffer” are cleared by selecting the “Delete History” icon as shown below:

5. Processing Accurate Mass MS/MS Data: A similar approach is used to process spectra from

compounds obtained for MS/MS spectra. Of course several steps must be taken before searching:

1. Change the configuration in MassHunter to settings appropriate for MS/MS data

2. Select the appropriate libraries within the NIST program such as the nist_msms and

possibly other user created libraries

3. Automatically create a compound list with associated spectra using Auto MS/MS,

targeted MS/MS, or Molecular Feature functions within the MassHunter Method

Explorer/Find Compounds menu, or process spectra manually

4. Also useful to use MassHunter Method Explorer/Identify Compounds/Generate Formulas

option since the spectrum sent to the NIST search will have the molecular formula included in

the header for the spectrum within the NIST program

5. Make sure include synonyms is selected in NIST configuration of “Spectral Import Options” to

import additional important MS/MS spectrum from MassHunter to the NIST search program

A typical window from the “Configuration/User Interface Configuration showing typical options for MS/MS data is shown below:

6. Adding EI and MS/MS Spectra to NIST User Library: We add all new spectra to our EI and MS/MS

NIST user databases with structures and associated information (sample source, means of

characterization, links to electronic notebooks, etc.). Additional fields can be entered as user tags if

desired as demonstrated in the following link:

http://www.chemsw.com/Software-and-Solutions/Laboratory-Software/NIST-Mass-Spectral-

Database/New-Features-of-MS-Search-in-NIST08.aspx

It is fairly simple to add EI nominal mass spectra. Be sure spectra are imported correctly into NIST using

the options in the “NIST/Spectral Import Options” window. You can use a variety of programs to draw

the structure for import into the “Spectrum Information” window. In this example, I used ChemDraw

Ultra. After drawing the structure, it was selected and copied into the ChemDraw Ultra clipboard. Then

select the “Librarian” tab at the bottom of the NIST search window:

This will open the librarian window. Select the spectrum of interest with a “left click” and then select

the “ed” icon from the menu bar.

This will open the NIST “Librarian/Spectrum Information” window:

To input the structure, click the “Clipboard Struct” under the “unhappy smiley face”. This will bring the

structure into focus. Then select the “From Structure” button and the molecular formula and Mol.

Weight will be automatically calculated and entered into the “Spectrum Information” window.

Then fill in other information such as Name (can be determined automatically in drawing program and

pasted into NIST), Comments, etc. Any extraneous ions can then are removed from the list using either

a control key/left click for contiguous ions or shift/left click for noncontiguous ones. After the ions of

interest are selected, use the delete key on the computer keyboard to remove them. Note, the

molecular ion is automatically marked with an arrow on the spectrum in this window for review.

I normally then select “Add to List” button before actually entering the spectrum into the library. This

allows me to select the edited entry with a left click to highlight. After highlighted, right click on the

entry to send to MS Interpreter:

MS interpreter can then be used to automatically correlate substructure with observed ions:

Be sure MS Interpreter is properly initialized by “right” clicking in the MS Interpreter” and select

Fragment Options. Fragment options appropriate for EI spectra are shown below:

If you are using CID spectra (M+H, M+NH4) adducts or negative ions, be sure to select the “Protonate

Molecule” box in the above window.

On can also go back to the Lib Search window (selected at lower left of NIST window) and the structure

can be searched in all the databases to make sure not already present in the library or to find some

model compounds for confirmation.

If all the fragments are correct and the model compound information is consistent, the “Librarian” tab at

the bottom left of the NIST program is selected, the entry of interest highlighted, and the “ed” button on

the menu is again selected. This time the “Add to Library” option is selected and the library for entry

selected. If you are creating a new library, just type in your name of choice.

Entering accurate mass data from the Agilent QTOF into the NIST library is very similar. The major

differences are that the accurate mass data from the Agilent system automatically enters information

into separate fields for “Instrument Type,” “Spectrum type,” “Collision Energy,” and “Ionization.” This is

very convenient. I have to add this information manually to my “Comment” field for our Quattro Micro

analyses.

In addition, the QTOF brings data into NIST with accurate mass values. One can set the number of

significant figures to import using the NIST “Spectral Import Options” window as described earlier in this

document. Even though the values are displayed as accurate ones, the search still only searches the

nominal mass values.

I know the library entry steps sound relatively complicated, but after you do it a few times, the actual

time to enter a compound is very reasonable. And imagine, you will never have to identify a component

manually again after entering it into your in-house database. Furthermore, the spectra are an excellent

model compound resource for confirming the identity of unknowns.