Thermo Fisher Scientific mzVault 2.1 Quick start guide

Brand
Thermo Fisher Scientific
Model
mzVault 2.1
Category
Software
Type
Quick start guide
© 2018 Thermo Fisher Scientific Inc.
All rights reserved.
You can use the Thermo mzVault™ application to browse the entries
in an mzVault library, add entries to or edit the entries in an mzVault
library, or search the entries in multiple mzVault libraries for spectra
that match a selected query spectrum.
After you create an mzVault library, you can restrict its write access.
To get started with the mzVault application, follow these topics:
•Browsing Libraries
•Building Libraries
•Searching Libraries
•Managing Password Security
Use the Browse tab to open and browse through the records in an
mzVault library.
To browse an mzVault library
1. From the application window, click the Browse tab.
2. In the Browse toolbar, click Open. Then, locate the library of
interest and click Open.
The library opens as a tabbed page and displays the Compound
List, Library Spectrum, Library Statistics, and MOL Structure
panes.
Figure 1. Browse toolbar and library page
3. To find a specific record or record set, click Filters in the Browse
toolbar. Then, set up the appropriate filters in the Select Filters
dialog box and click Apply.
For example, to browse the records for a specific formula, select
Formula from the Filter Type list, and then enter a chemical
formula in the Filter Criterion column. For each element, type its
periodic table symbol and its count. If the formulas in the library
do not contain spaces, do not use spaces in your entry.
4. To move through the library records, in the Navigate area of the
Browse toolbar, select the number of records to display, and then
use the first (<<), previous (<), next (>), and last page (>>) icons.
By default, the application opens the library to the first page and
displays up to 25 records. You can select to display 25, 50, 100,
500, 1000, or All records per page.
5. To review the information provided in each entry, do the
following:
a. In the Compound List pane, select an entry by clicking it.
The Library Spectrum and MOL Structure panes update to
display the first spectrum and the MOL structure for the
selected compound.
b. To view other spectra associated with the selected entry, click
the expand icon (+) in the left most column.
c. To display a specific spectrum in the Library Spectrum pane,
in the expanded spectrum list, select the spectrum.
mzVault 2.1 Quick Start Guide
Browsing Libraries
Note You do not need write access to open an mzVault library
and browse its records.
Revision A XCALI-97981
2
To build a library, follow these steps:
1. Open a library for editing (see Opening a Library for Editing).
2. Add records to the library in any of these ways:
•Adding Individual Compounds
•Adding Compounds from a Compound List
•Importing Files into a Library
•Merging Libraries into a Destination Library
3. Delete compounds or spectra as needed (see Deleting Entries
from a Library).
4. Save the library by clicking Save in the Build toolbar.
To open an existing library for editing or create a new library, follow
these topics:
•Opening an Existing Library
•Creating a New Library
Opening an Existing Library
To open an existing library for editing
1. Click the Browse tab.
2. In the Browse toolbar, click Open (Figure 1).
3. Locate the library of interest and click Open.
4. To edit the library, click the Build tab.
5. If the library is restricted, unlock it (see “Unlocking a Restricted
Library” on page 8).
–or–
1. Click the Build tab.
2. In th Select Library area of the Build toolbar, click New. Then,
locate the library of interest and click Save.
3. Click Yes at the prompt.
Figure 2. Build toolbar
4. If the application updates the library, click Save in the Build
toolbar.
5. If the library is restricted, unlock it (see “Unlocking a Restricted
Library” on page 8).
The library opens as a tabbed page below the toolbar. The tab label is
the library’s name.
Creating a New Library
To create a new library for editing
1. Click the Build tab.
2. In the Select Library area of the Build toolbar, click New.
3. Name the library, select its directory location, and click Save.
To add a compound to a library, follow these topics:
1. Adding a Compound to a Library
2. Adding Spectra to a Compound Entry
Adding a Compound to a Library
To add a compound to a library
1. Open a library for editing.
2. In the Compound area of the Build toolbar, click New (Figure 3).
A placeholder entry appears in the Compound List table of the
library page, the check box next to the placeholder entry is
selected, and the Compound tab appears in the tab bar.
Figure 3. New compound entry in the open library
3. To edit each of the columns for a compound entry, double-click
the table cell to make it available, and then enter text.
To add a spectrum to the compound entry, go to step 3 in the next
topic.
Adding Spectra to a Compound Entry
Use the Compound tab to add spectra to the compound entries in an
mzVault library.
Building Libraries
Tip In the mzVault application, you can recalibrate spectra before
adding them to a library. Use the application’s default
recalibration settings or modify the settings on the Default
Recalibration Parameters page. To open this page, choose Menu
> Options. Then, select Recalibration in the left pane of the
mzVault Options dialog box.
Opening a Library for Editing
Click to open an existing library or create a new library.
Adding Individual Compounds
Inactive Compound tab
Placeholder
compound entry
Click to add a new
compound entry.
Library page
3
To add a spectrum to a compound record
1. Depending on the last task, do one of the following:
• If the library of interest is not open, open it for editing. Then,
go to step 2.
• If the library of interest is open for editing and the Build tab is
active, go to step 2.
• If the library of interest is open for editing, the check box next
to the compound of interest is selected, and the Build tab is
active, go to step 3.
• If the library of interest is open for editing and the
Compound tab is active, go to step 4.
2. Select the check box to the left of the compound of interest.
The Compound tab appears in the tab bar.
3. Click the Compound tab.
4. In the Compound toolbar, click Open Raw File, locate the raw
data file containing the spectrum you want to add to the
compound, and click Open.
The Chromatogram Options, Chromatogram, Raw Spectrum,
Curated Spectrum, and MOL Structure panes appear below the
Compound List pane.
Figure 4. Compound toolbar and library page
5. In the Chromatogram Options pane, make the appropriate
selections and entries to display the filtered chromatogram of
interest in the Chromatogram pane.
Figure 5. Chromatogram Options pane with a scan filter selected
6. Do one of the following:
• To select the spectrum for a single time point, click the time
point in the Chromatogram pane.
The selected spectrum appears in the Raw Spectrum pane.
Figure 6. Spectrum from a single time point
• To create an average spectrum, do the following:
i. In the Chromatogram Options pane (Figure 5), select
the Average On check box.
ii. To select the time range to average, do one of the
following:
In the Chromatogram pane, drag the pointer
horizontally across a time range.
–or–
In the Chromatogram Options pane, type the start
and end times in the Retention Time Range boxes.
Then, click outside the time boxes or press the
ENTER key to activate averaging.
In the Chromatogram pane, a horizontal red line with start
and end markers indicates the time range to average.
Figure 7 shows the creation of an average spectrum for the
time range of 9.45 to 9.70 min in a filtered chromatogram. In
the Curated Spectrum pane, the scan header lists the number
of averaged scans, and the title bar includes the term Averaged.
Figure 7. Averaged spectrum
Note To create an average spectrum, the application averages
scans with similar scan filters across the selected time range. If
you do not select a scan filter, the application uses the scan filter
for the highest-intensity scan across the selected time range.
Selected compound in the Compound List pane of an editable library
Selected
time point
Red line with
start and end
markers
Scan
header
4
7. (Optional) To recalibrate a single spectrum, do the following:
a. Verify the chemical formula in the Formula column of the
compound entry.
b. In the Compound toolbar (Figure 4), modify the adduct
selection and charge, if necessary. Then, click Recalibrate.
Figure 8 shows a recalibrated spectrum.
Figure 8. Recalibrated spectrum
8. (Optional) To threshold a spectrum, do the following in the
Compound toolbar:
a. Select the Automatic option or the Manual option.
b. If you select the Manual option, enter an intensity level from
0 to 100% of the base peak intensity.
c. Click Threshold.
The application removes the mass peaks below the specified
intensity threshold. This figure shows a comparison between a
raw spectrum (left) and a thresholded spectrum in the Curated
Spectrum pane (right) where the application has removed the
low-intensity peaks.
9. To add the spectrum of interest to the compound entry, do the
following:
a. Click the Raw Spectrum pane or the Curated Spectrum pane
to make it active.
b. In the Compound toolbar, click Add.
The application opens the Build tab and displays the added
spectrum in the Library Spectrum pane on the tabbed library
page (Figure 9). The application also adds information about the
selected spectrum to the spectrum list for the selected compound.
Figure 9. Library with a new spectrum entry
10. To save the modified library, click Save in the Build toolbar.
To automate the process of adding compounds with spectral data to
the library, you can create and process a compound list from the
Compound List tab.
To create and process a compound list, follow these topics in order:
1. Creating, Saving, and Opening a Compound List
2. Setting Up the Spectrum Selection Parameters
3. Processing the Compound List
Creating, Saving, and Opening a Compound List
A compound list file contains a list of compounds with information
about each compound, including the compound name, formula,
associated raw data file, and so on. A compound list does not include
spectral data.
To create, save, and open compound lists, follow these topics:
•Creating a New Compound List
•Saving a New Compound List
•Opening an Existing Compound List
Creating a New Compound List
To create a new compound list
1. Click the Build tab.
2. In the Build toolbar (Figure 9), click New Compound List.
IMPORTANT For a recalibrated and thresholded spectrum, the
curation order makes a difference when applying a manual
threshold level. To retain a manual threshold level, recalibrate the
spectrum first, and then apply the manual threshold level.
Note The application does not currently support
recalibrating an average spectrum.
Tip To undo the curation, click Reset.
Adding Compounds from a Compound List
Note The Compound List tab is a contextual tab; that is, to
display it, you must click New Compound List or Open
Compound List in the Build toolbar.
5
The Compound List tab and a New_Compound List tabbed
page open (Figure 10).
Figure 10. Compound List toolbar and New_Compound List page
3. To edit the placeholder entry, do the following:
a. In the Raw File column (Figure 10), click Raw File.
b. Select a raw data file that contains scan data for the new
compound and click Open.
c. In the Formula or Precursor column, click Formula or
Precursor.
The Processing Parameters dialog box opens.
d. Enter a chemical formula or an m/z value for the precursor
ion. If needed, select a different adduct ion, charge, or both.
e. Click OK.
4. For each compound that you want to add to the compound list,
click Add in the Compound List toolbar (Figure 10) and repeat
step 3.
Saving a New Compound List
To save the compound list as an XML file
1. In the Compound List toolbar (Figure 10), click Save.
2. Name the file, select its folder, and click Save.
Opening an Existing Compound List
To open an existing compound list
1. In the Build toolbar (Figure 2), click Open Compound List.
2. Locate the XML file of interest and click Open.
The selected compound list file opens as a tabbed page below the
Compound List toolbar.
Setting Up the Spectrum Selection Parameters
The spectrum selection parameters specify which spectra to extract
from the selected raw data file for each compound entry during
processing.
To set up the spectrum selection parameters
1. If you closed the compound list.xml file, open it (see Opening an
Existing Compound List).
2. Specify the spectra to select as follows:
a. To open the Spectrum Selection Parameters dialog box, click
Spectrum Selection Parameters in the Compound List
toolbar (Figure 10).
b. Modify the parameter settings as needed.
For example, to retrieve only the best spectrum for a
compound, select the Retrieve Only One Best Spectrum Per
Compound option.
To retrieve an average spectrum, select the Retrieve One
Spectrum for Each Unique Collision Energy option, and
then select the Averaged Spectra option.
c. Click OK.
3. (Optional) To curate the retrieved spectra, do one or both of the
following in the Curate area of the Compound List toolbar:
• To remove the noise peaks, click Threshold.
• To recalibrate the spectra, click Recalibrate.
Processing the Compound List
To process a compound list, you must open an editable library.
To process a compound list
1. Open a library for editing.
2. If you closed the compound list, open it (see “Opening an
Existing Compound List” on page 5).
3. If the Compound List tab is not active, click it.
4. In the Compound List toolbar (Figure 10), click Process List.
The application processes the list and adds the entries to the open
library. When processing finishes, the status column displays
“Entry Added to Library” for each processed entry.
5. To save the modified library, click Save in the Build toolbar
(Figure 2).
Note The application does not recalibrate averaged spectra.
6
You can import NIST or MassBank files into a library that is open for
editing or a library that is unrestricted but closed.
To import files into a library, follow these topics as needed:
•Importing Files into an Opened and Editable Library
•Importing Files into a Destination Library
Importing Files into an Opened and Editable Library
To import records into a library that is open for editing
1. Open a library for editing.
2. In the Build toolbar, click Import (Figure 2).
3. In the Open dialog box, do the following:
a. Select the file type to import.
b. Locate the files and click Open.
4. To save the modified library, click Save in the Build toolbar.
Importing Files into a Destination Library
To import records into a destination library
1. Click the Build tab.
2. In the Build toolbar, click Import (Figure 2).
3. In the Import dialog box, do the following:
a. Select the file type to import (TXT, MSP, or MB), locate the
files to import from the same folder, and click Open.
b. Locate an unrestricted destination library.
c. Click OK.
The destination library opens as a tabbed page below the Build
toolbar.
4. To save the modified library, click Save in the Build toolbar..
You can merge three unrestricted libraries into a single library.
To merge two libraries into another library
1. Click the Build tab.
2. In the Build toolbar, click Merge (Figure 2).
3. In the Merge Libraries dialog box, locate the two source libraries
and the destination library, and then click Merge.
The destination library opens as a tabbed page below the Build
toolbar.
4. To save the modified library, click Save in the Build toolbar.
To delete entries from a library, follow these topics as needed:
•Deleting an Entire Compound Record
•Deleting Spectra for a Compound Entry
Deleting an Entire Compound Record
A compound record includes the compound information and the
associated spectra.
To delete a compound entry
1. Open a library for editing.
2. In the Compound List pane on the library page, select the check
box to the left of the compound entry that you want to delete
(Figure 3).
3. In the Build toolbar, click Delete (Figure 2).
4. Verify the selections in the Delete Records from Library Dialog
box, and then click OK.
5. To save the modified library, click Save in the Build toolbar.
Deleting Spectra for a Compound Entry
A compound entry can have multiple spectra associated with it.
To delete a spectrum
1. Open the library that you want to edit.
2. Click the Build tab and, if necessary, unlock the library.
3. In the Compound List pane on the library page, select at least one
check box in the Compound List table.
The Compound tab appears.
4. Click the Compound tab.
The Compound toolbar appears.
5. Select the check box to the left of the spectrum to delete.
6. In the Compound toolbar, click Delete (Figure 4).
7. Verify the selections in the Delete Records from Library Dialog
box, and then click OK.
8. To save the modified library, click Save in the Build toolbar.
Although the primary purpose of the mzVault application is to build
and maintain libraries for use in other Thermo Scientific
applications, such as Trace Finder™ or Compound Discoverer™, you
can also use it to validate your new libraries or identify individual
compounds in your experimental data.
Unlike the other applications that can do batch searches, the mzVault
application only searches for library spectra that match one query
spectrum at a time.
Importing Files into a Library
Merging Libraries into a Destination Library
Deleting Entries from a Library
Note If you delete all the spectra for a compound, the
application deletes the compound from the library.
Searching Libraries
7
To run a library search and review the results, follow these topics:
•Running a Library Search
•Reviewing the Library Search Results
To set up and run a library search, follow these topics in order:
1. Selecting the Libraries to Search
2. Setting Up the Search Parameters
3. Selecting the Query Spectrum
4. Starting the Search
Selecting the Libraries to Search
You can select up to five libraries to search.
To select the libraries to search
1. Click the Search tab.
The Search toolbar opens. Before you select the libraries to search
and open a raw data file, only the Select Libraries (Figure 11) and
Open RAW File (Figure 12) buttons are available.
2. In the Search toolbar, click Select Libraries.
3. Select up to five libraries from the same folder and click Open.
Figure 11. Search Parameters area of the Search toolbar (factory defaults)
Depending on whether you select one library or multiple
libraries, the Library Search page or the Multi-Search page opens.
The Information bar lists the library names.
After you select the libraries to search, all the parameters in the
Search Parameters area of the Search toolbar become available. In
addition, the Chromatogram Options, Chromatogram, Query
Spectrum, and Search Summary panes open. The Chromatogram
and Query Spectrum panes remain empty until you open a raw
data file.
Setting Up the Search Parameters
To set up the search parameters
In the Search parameters area of the toolbar, do the following:
• Select whether to run a Forward or Reverse search (Figure 11):
Forward: Searches the query spectrum against each library
spectrum. If the query spectrum includes a peak that is not in
a given library spectrum, the score for the match is negatively
affected. Use a forward search when the query spectrum is a
high quality spectrum—that is, when it has good
fragmentation and few low-intensity background peaks.
Reverse: Searches each library spectrum against the query
spectrum. If the query spectrum does not have peaks that are
in the library spectrum, the score for the match is negatively
affected, but the presence of additional peaks in the query
spectrum has no effect on the score. Use a reverse search if the
query spectrum includes peaks from several components or
has a lot of background noise.
• To limit the search to a subset of the library entries, click Filters.
Then, set up one or more filters and click OK.
• To limit the number of library spectra to review, do the following:
In the Hits box, type a value equal to or greater than 1.
In the Cutoff box, type a value from 0 to 100.
Selecting the Query Spectrum
To select the query spectrum
1. Select the libraries to search and set up the search parameters as
described in the previous topics.
2. In the Query Spectrum area of the Search toolbar, click Open
RAW File (Figure 12). Then, locate the raw data file of interest
and click Open.
Figure 12. Query Spectrum area of the Search toolbar (factory defaults)
The Chromatogram Options pane becomes available. The
Chromatogram pane displays the total ion current (TIC)
chromatogram, and the Query Spectrum pane displays the first
scan (RT: 0.00). In addition, the other options in the Query
Spectrum area of the Search toolbar become available.
3. In the Chromatogram Options pane, specify the chromatogram
to display in the Chromatogram pane.
4. In the Chromatogram pane, select a time point.
The Query Spectrum pane displays the selected spectrum. The
red horizontal line indicates the automatic noise threshold that
the application applies if you keep the factory default settings in
the Query Spectrum area of the Search toolbar. During a search,
the application ignores spectrum peaks below the red line.
5. In the Query Spectrum area of the Search toolbar, keep the
factory default settings (Figure 12):
• Intensity Threshold is On and set to automatic.
• Ignore Precursor is On (orange).
• Fragment Tolerance is set to automatic.
Starting the Search
To start the library search
After you select the libraries to search and a query spectrum, click
Apply in the Go area of the Search toolbar.
When the search finishes, the application populates the Search
Summary pane. In addition, the Search Results, Library
Spectrum and Difference Spectrum panes appear, and the
Chromatogram Options and Chromatogram panes are hidden as
vertical tabs at the left.
Running a Library Search
8
After you run a library search, the Search Results pane displays the
compound hits sorted by score, and the Library Spectrum pane
displays the best matching library spectrum for the selected
compound.
To review all the matching spectra for a compound
1. Click the expand icon (+) to the left of the Compound ID
column.
2. Select a spectrum from the expanded list.
The Library Spectrum and Difference Spectrum panes update.
You can restrict write access to your mzVault libraries. When you
open a restricted library for editing, the Lock icon in the Build
toolbar indicates that the library is locked.
To work with the password security feature, follow these topics:
•Restricting Write Access
•Unlocking a Restricted Library
•Changing a Password or Removing Security
To restrict write access to an mzVault library
1. Open a library with read/write access.
2. Open the Database Security page as follows:
a. To open the mzVault Options dialog box, choose Menu >
Options from the application window.
b. In the left pane, select Database Security.
The Library box displays the name and location of the library.
3. Click Restrict Access.
4. In the Apply Password dialog box, enter a password from 5 to 15
characters in length, and then click OK.
5. In the Confirm Password dialog box, reenter the same password,
and then click OK.
6. In the mzVault Options dialog box, click Save.
To unlock a restricted library
1. Open the library.
2. In the Build toolbar, click the Lock icon, .
3. In the Restricted Access dialog box, enter the password and click
OK.
To change the password or remove password security
1. Open the library.
2. In the Build toolbar, click the Lock icon to unlock the library.
3. Open the Database Security page. See step 2 of “Restricting Write
Access.”
4. In the Database Security area, click Manage Access.
The Change Password dialog box opens.
5. Do one of the following:
• To change the password, type a different password and click
OK. Then, in the Confirm Password dialog box, reenter the
new password and click OK.
• To remove the password security and grant read/write access
to all users, delete the password, and then click OK. At the
prompt, click Yes.
6. In the mzVault Options dialog box, click Save.
Trademarks
Compound Discoverer, mzVault, and TraceFinder are trademarks of
Thermo Fisher Scientific Inc. in the United States.
Reviewing the Library Search Results
Managing Password Security
Click to display
the spectrum
list.
Restricting Write Access
Unlocking a Restricted Library
Changing a Password or Removing Security
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Thermo Fisher Scientific mzVault 2.1 Quick start guide

Brand
Thermo Fisher Scientific
Model
mzVault 2.1
Category
Software
Type
Quick start guide
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