Thermo Fisher Scientific mzVault 2.1 Quick start guide

Brand: Thermo Fisher Scientific

Model: mzVault 2.1

Category: Software

Type: Quick start guide

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

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

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

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.

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.

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

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

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

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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Thermo Fisher Scientific mzVault 2.1 Quick start guide

Thermo Fisher Scientific mzVault 2.1 Quick start guide

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