Mnova 12 – Starting guide

Includes Mnova NMR, NMRPredict, and MS

Released on 27SEP2017
 Outline to this starting guide

• Overview of Mestrelab and Mnova

• Open and process 1D and 2D NMR data
• Multiplet Analysis for 1D 1H NMR
• Assign 1D peaks to a structure
• Assign 1D and 2D spectra
• Report analysis results
• Basic handling of multiple spectra
• Predict, assign and verify
• LC/GC/MS data processing

Note: This tutorial covers only the NMR, NMRPredict and Msplugins of Mnova 2
 A Fast Growing Company

• 1996: A research project in University of Santiago de Compostela, Spain,

developed a free Software, MestReC, for NMR processing.

• 2004: Mestrelab Research incorporated in Santiago de Compostela.

• 2004: New MestReNova (Mnova) platform and NMR plugin released.

• 2006: NMRPredict Desktop for NMR prediction.

• 2009: MS plugin for LC/GC/MS data analysis.

• 2009: Global Spectral Deconvolution (GSD) algorithm released for NMR.

• 2011: DB plugin for Database Management of NMR and MS.

• 2012: Verify plugin for auto structure verification.

• 2012: qNMR plugin for quantitative NMR analysis.

• 2013: Reaction Monitoring plugin for NMR-based reaction kinetics studies.

• 2014: Screen plugin for high-throughput ligand-protein binding analysis.

• 2015: SMA (plugin for simple mixture analysis) Mbook (ELN), Mnova app for tablets.

• 2016: The office in Santiago doubles in size with a glorious table football!

• 2017: Mnova 12, Structure Elucidation, Binding, IUPAC Name.

• An R&D company with over 35 people and >80,000 registered users.

3
 Mnova products and applications
NMR

Arrayed
Quant.
2D
1D

Users
Chemists Specialists

LC/MS
GC/MS

Note: This tutorial covers only the NMR, NMRPredict and MS plugins of Mnova
4
 Download and activate your Mnova license
INSTALLATION

➢ Download and install Mnova The Host ID for this computer

www.mestrelab.com. Choose
Location of the license file
Help > License Manager to
open the License Manager
dialog.

➢ Activate Mnova using your

purchased license files, or apply
for 45 day free trial licenses
Mnova Plugin names
(Click Get/Install Licenses)

➢ Make sure that there are green

checkmarks for NMR and other
License expiring date
plugins that are supposed to be Service licenses
activated
License issued date

➢ For managing campus/site/

concurrent licenses, see here
 Mnova preferences
PREFERENCES

Mnova allows changes to Mnova’s interface options for Plugins, Database, NMR, MS, Molecule,
Scripting and Drawing Tools. They can be edited in ‘File/Preferences’

Besides choosing your preferences on

the different topics, Mnova 12 allows
you to select your preferred interface
(Theme) between the classic or the new
ribbon control.

6
 1H processing and analysis:
PROCEDURE General procedure

➢ Open the raw data

➢ Pre-process the FID: drift correct, apodize, zero fill, linear
predict, etc.
➢ Fourier transform
➢ Phase correct and baseline correct
➢ Chemical shift reference
➢ Peak pick, integrate, multiplet analysis
➢ Structure verification and peak assignment
➢ Report and publish
1H NMR (600 MHz, DMSO-d6) δ 12.25
(s, 1H), 7.19 (d, J = 7.8 Hz, 2H), 7.10
(d, J = 7.9 Hz, 2H), 3.62 (q, J = 7.1 Hz,
1H), 2.41 (d, J = 7.2 Hz, 2H), 1.80 (dt, J
= 13.5, 6.8 Hz, 1H), 1.34 (d, J = 7.1 Hz,
3H), 0.85 (d, J = 6.7 Hz, 6H).

Note: Most of these steps are done automatically by Mnova. However, you retain full control at all times

7
 Mnova comes with example datasets
DATA FILE EXAMPLES

➢ An installation of Mnova comes with a set of 1D and 2D NMR, LC/MS data, and the structure
of quinine for practice. On Windows, they are typically located in
C:\Program Files (x86)\Mestrelab Research S.L\MestReNova\examples\datasets

➢ Drag the folders or individual files into Mnova to open these practical example

8
 Open and transform NMR data
PROCESSING
➢ Go to File/Open to open the fid (or ser) file of the raw data
➢ Or, drag & drop a folder from the Data Browser onto the Mnova canvas
➢ Mnova will automatically process the spectrum
➢ All data is brought in, and depending on your preferences, is processed to the desired extent.
(manual or automatic)

Use the Data Browser to open

spectra.
(View/Panels/Data Browser)

9
 Display the acquisition parameters
PROCESSING

➢ Go to View/Tables… Parameters to view the acquisition

parameters
➢ Press Report to report the parameters as a text box on the page

Use the green handles to move,

rotate and resize the text box.
Every object in Mnova can be
relocated and resized.

10
 Report a Processing Template
PROCESSING/REPORTING

➢ A report of the Processing Parameters can be generated using your preferred report
template for 1D and 2D spectra. A customized template can be easily added

Apodization
Exponential: 0.50 Hz
Zero Filling and LP
Spectrum Size: 65536
Fourier Transform
Protocol: None
Swap Halves: true
Mirror Image: true
Real FT: false
Phase Correction
Method: Imported
PH0: -141.00 °
PH1: -4.39 °
Baseline Correction
Method: Bernstein Polynomial Fit
Polynomial Order: 3

Peak Picking
Method: GSD
Refinement: Ref1
Auto Classify: true
Multiplet Analysis
Method: Peaks
Minimum Area: 0 %
 Phase, baseline correction & reference
PROCESSING

➢ Press for phase

correction if peaks are not
symmetric*

➢ Press for baseline

correction if baseline is not
zero*

➢ Press to calibrate the

chemical shift reference if
the solvent or TMS peak is
not at the right ppm

*Click the arrow next to the tool icon for options, such as manual phasing and manual baseline correction.
See Help > Contents > Processing Basics for more details.

12
 Automatic phase correction
PROCESSING

➢ Regions Analysis: good for most cases

➢ Global: good for spectra without negative
and big solvent peaks
➢ Selective: DEPT type of spectra with
negative peaks
➢ Metabonomics: spectra with big solvent
peaks
➢ Whitening: usually for 2D

13
 Manual phase correction
PROCESSING

➢ Set the Pivot Point

➢ PH0: zero-order correction (left mouse
button + scroll up/down)
➢ PH1: first-order correction (right mouse
button + scroll up/down)
➢ Ctrl + scrolling: fine tuning

14
 Baseline correction
PROCESSING

Choose a function to model the baseline:

➢ (Bernstein) Polynomial Fit: small base errors

➢ Splines or Ablative: for medium base errors
➢ Whittaker: For more serious base errors. Use
with caution and make sure the bases of
peaks are not compromised. Use appropriate
parameter values to tune the fit
➢ Multipoint B.C.: Manually define base points

15
 Multipoint baseline correction
PROCESSING

Improves the automatic

detection of the control points

It estimates the noise regions

and finds a lower number of
control points for them

16
 Referencing chemical shifts
ANALYSIS

Reference by entering the value

Graphic Reference
(two clicks)

17
 Absolute Reference for automatically
ANALYSIS referencing multi-spectra/nuclei

➢ Use a referenced 1H from the same instrument/probe/solvent/temperature

➢ Auto references other nuclei
➢ Auto-references other spectra (1D and 2D)
➢ Saves settings in Preferences to do it automatically

18
 Visualize your spectrum
DISPLAY OPTIONS

Zoom in/Zoom out (or press Z) *

Zoom out
Full spectrum (or press F)
Manual Zoom in to defined ppm range
Pan spectrum (or press P)**
Expansion – click&drag to draw an inset (or press E)
Previous Zoom
Next Zoom

Fit to Highest Intensity (or press H)

Fit to highest compound peak
Increase Intensity (or rotate mouse wheel)
Decrease Intensity (or rotate mouse wheel)
Crosshair Cursor (or press C) for measuring J-couplings
Cut (or press X) to hide parts of the spectrum

Press E, then click and

drag to define the
range for the inset

*Press Z several times to toggle between

horizontal/vertical/box zoom
** Press P several times to toggle between
free/horizontal/vertical panning

19
 Change spectrum display properties
DISPLAY PROPERTIES

➢ Double click on the background of a spectrum to open the Properties dialog

➢ Display properties are divided into logical sections
➢ Click on Set as Default to save settings for spectra opened in the future

Tip: Use the Save tool to save the

properties to a file, and distribute
it to other users for consistent
display & reporting

20
 Display of 2D spectra
DISPLAY PROPERTIES

➢ Use the Plot Mode tools to change to bitmap or contour display, etc.
➢ Change other display properties by double-clicking on the spectrum
to open the Properties dialog:
• Legend
• Color Palette
• Contours
• Traces

Tip: You can set a line width for 2D contours

independent of that for 1D curves.

21
 Attach 1D to 2D spectra
ANALYSIS

➢ Open 1D and 2D spectra in the same document. They are displayed in separate pages.
If you don’t see the Pages panel, choose View/Pages
➢ Select a 2D spectrum, then drag a 1D from the Pages panel to attach it to the 2D as an
external trace
➢ It can be done automatically through File/Preferences/NMR

Change the Y intensity of the traces:

Place the cursor on the trace and scroll the mouse wheel, or
click Ctrl+Shift+arrow keys.
Move the baseline of a trace: Shift + mouse wheel
Change the space of the attached 1D’s: Double click on the
spectrum and open the Properties dialog.

22
 Analyze and report multiplets of 1H NMR
ANALYSIS & REPORTING

➢ Mnova provides two approaches to multiplet analysis:

• Fully automatic: peak picking, integration and multiplet analysis all done by one click, with
peaks deconvolved using GSD* and types classified
• Manual: click and drag to pick each multiplet interactively
➢ In either case, you can refine the results interactively, and report them in the selected
journal or patent formats

1H NMR (400 MHz, CDCl3) δ 8.62 (d, J = 4.5 Hz, 1H), 7.95 (d, J = 9.2 Hz,
1H), 7.46 (d, J = 4.5 Hz, 1H), 7.30 (dd, J = 9.2, 2.7 Hz, 1H), 7.21 (d, J =
2.8 Hz, 1H), 5.73 (ddd, J = 17.1, 10.3, 7.6 Hz, 1H), 5.48 (d, J = 4.4 Hz,
1H), 4.99 – 4.85 (m, 2H), 3.87 (s, 3H), 3.44 – 3.31 (m, 2H), 3.11 (td, J =
8.5, 8.1, 4.0 Hz, 1H), 3.05 (dd, J = 13.8, 10.1 Hz, 1H), 2.69 – 2.56 (m,
2H), 2.35 – 2.11 (m, 1H), 1.79 (h, J = 2.7 Hz, 1H), 1.76 – 1.62 (m, 2H),
1.61 – 1.36 (m, 2H).

*GSD (Global Spectral Deconvolution):

See Help > Contents > Analysis tools >
Peak Picking > GSD for details.

23
 Fully automatic multiplets analysis
ANALYSIS & REPORTING

➢ Click to do automatic multiplet analysis

➢ By default, Mnova does the following automatically:
• Picks peaks using GSD* (if no peaks were picked) and classifies their types (compound,
solvent, impurity peaks etc.), all controlled by Peak Picking Options
• Groups picked peaks into multiplets and fits them to J-coupling patterns, then
calculates their integrals, all controlled by Multiplet Analysis Options
• Estimates the total number of nuclides (NN), and normalizes the integrals for each
multiplet

The number of nuclides

(NN) of the multiplet
Total # of nuclides from all
the multiplets and the #
of protons in the molecule
(if present)
Normalized integral of
the multiplet.

*GSD (Global Spectral Deconvolution): See Help > Contents > Analysis tools > Peak Picking > GSD for details
 Pick multiplets manually
ANALYSIS

➢ Manual Multiplet Analysis offers more control (J is the shortcut key)

➢ Zoom into each multiplet, click and drag to define the following:
▪ Peak picking threshold
▪ Integration region
➢ Mnova picks the peaks in the region, fits them to a J-coupling pattern and defines the
multiplet in the same way as in automatic multiplet analysis

Click and drag to define the

integration region and peak
picking threshold and a
doublet will be picked.

25
 Multiplet Manager
ANALYSIS
➢ Double click on a multiplet label to open the Multiplet Manager
➢ Use it to inspect and change the properties of the multiplets, including the normalization of the
integrals, J-coupling patterns and constants, etc.
Add/Delete multiplet peaks
Navigate to the
Previous/Next multiplet

Delete the current multiplet

Properties of the current
multiplet

The # of protons this Use this tool to simulate

multiplet corresponds to. the multiplet
Changing this number
affects only the current
multiplet Use this tool to measure J
constant manually

Normalized integral of the

multiplet. Changing it affects
all multiplets # of protons in the
molecule (if present)

Integration region of the Absolute integral of the

multiplet multiplet

26
 Handy tools for multiplet analysis
ANALYSIS

Full View: Display the whole spectrum and zoom-in area. Drag the
The Auto Cut tool will hide all noise-only regions of
purple box to move to other multiplets. Choose View/Full View to
the spectrum. Choose View/Cuts/Auto Cut
open the Full View panel, which can be docked as shown

Multiplet label: Click

on it to set it as the
current active one

Multiplet bar: Use it to

split a multiplet into 2,
or to change its range

Manual multiplet analysis: Press J, then click Multiplet Manager shows the properties of
and drag across peaks to define the range and the currently picked multiplet. (Double click on
peak picking threshold a multiplet label to open it)

27
 Split partially overlapping multiplets (1)
ANALYSIS

Show Peak Curves to display the

GSD peaks (displayed in blue)

Drag this white box to split the Tip: You can also change the display of the deconvolution peak curves
multiplet into two distinct multiplets in Properties Dialog > Peaks > Curve tab

28
 Split partially overlapping multiplets (2)
ANALYSIS
 Tools to verify multiplet analysis results
ANALYSIS

Go to Properties/
Multiplets and turn on
the ‘J’s Tree’ option

Use the simulation tool in the

Multiplet Manager to simulate
the multiplet and compare
 Override the multiplet results
ANALYSIS with the Multiplet Manager

➢ Override the analysis results of a multiplet in Multiplet Manager

➢ In this example, the multiplet was estimated to be a “qdd”. The simulated multiplet does
not agree with the observed spectrum, and hence it is wrong
➢ Select “m” from the ‘Class’ pull-down menu to override it

Choose “m” from the

drop-down menu to
override the results

Use the simulation tool

to simulate the
multiplet and compare
 Re-assign peaks to multiplets
ANALYSIS

➢ If a peak is assigned to a wrong group, use the Add Multiplet Peak

tool in the Multiplet Manager to re-assign it to a different group
➢ In the following example two peaks were re-assigned, forming a
different pair of doublets:
 Report multiplets
REPORTING

➢ Click on Report Multiplets to report the results in a

particular journal format
➢ To change the journal format: Go to
View/Tables/Multiplets to display the Multiplets Table
➢ Then click on Setup Report

Tip: From the Multiplet Table, click Copy Multiplets and then paste the texts to your document. Click on Copy Table and
then paste the spreadsheet to your document. The table can be customized using Setup Table.

33
 GSD Peak picking
ANALYSIS

➢ When peak-picking or multiplet analysis is done, by default Mnova does a global

spectral deconvolution (GSD), then uses the deconvolved peaks as peak-picking results
➢ Go to View/Tables… Peaks to display the table
➢ Choose to display the deconvoluted peaks (blue) and the residuals (cyan) as shown below in
Properties/Peaks/Curve

See more details about GSD:

http://mestrelab.com/resources/gsd

34
 To integrate peaks independently
ANALYSIS of multiplet analysis

➢ Press to do auto integration or press “I” to do it

manually
➢ Double click on an integral curve to popup the
Integral Manager:

* Note: The results from

Integration are independent of
those from the Multiplet
Analysis
Use Integration Options to
change the method and other
parameters

➢ Type a value to normalize the integrals

➢ Browse, delete, change, split integrals interactively if
needed
Click and drag the left
green box to change the
range of the integral.

35
 Why are integrals from multiplet analysis
ANALYSIS different from regular integration? (1)

(GSD) Peaks-based integration when running multiplet analysis

➢ When the peaks have irregular shapes, Peaks-based multiplet analysis may give
significantly different integration results than regular Sum-based integration
➢ In the example below, Peaks-based multiplet analysis extracts the regular peaks but
ignores the irregular ones (usually) due to exchangeable protons

36
 Why are integrals from multiplet analysis
ANALYSIS different from regular integration? (2)

Sum-based integration

➢ When Sum-based integration is done, all peaks are included by adding point intensity by
point intensity within the integration region
➢ Depending on the goal of the analysis, one must choose the appropriate integration
method
 Force Mnova to use Integration
ANALYSIS results in multiplet analysis

Combine Sum-based integration and multiplet analysis

➢ If Integration is done prior to automatic multiplet analysis, the Integration results

(integration regions and integral values) will be used by the automatic Multiplet
Analysis routine
 Predict NMR spectra from
PREDICTION molecular structures

➢ Open a new document (File/New) or a new page

(Edit/Create New Page)
➢ Copy a structure from ChemDraw or ChemSketch,
then paste to Mnova
➢ Or, open a .mol, .cdx, or .sdf file
➢ Select a spectrum, and click the appropriate icon
from the Predict ribbon

Tips:
1. Choose Prediction Options to change settings
2. You can turn on/off the atom numbers by right-
clicking on the structure and choose Properties
3. You can open the Prediction Table to list the
predicted shifts and J-couplings, and manually change
them

A separate license of Mnova NMRPredict Desktop is

needed
 Predict NMR data & compare
with the molecular structure
PREDICTION

➢ Open a 1H (or 13C) spectrum in a new page

➢ Copy the structure from ChemDraw or
ChemSketch
➢ Go to Analysis/Predict & Compare. The
predicted spectrum is stacked with the
experimental one for visual comparison

You can drag the

label of a predicted
peak to change its
chemical shift. You
can also change the
predicted J-
couplings in the 1H
Prediction Table.

40
 Efficient working environment for peak
INTERFACE assignment for multiple spectra

Full View allows you to navigate

among the peaks easily The structure(s) is
shared for all
“linked” spectra
and assigned
peaks are color
coded
Click on a peak top or a multiplet
label, and then on an atom to assign it.
Pages View The structure can
allows you be shown on the
to navigate spectrum plot or
among the in the compound
spectra window
easily

The assignment
results are listed
here. You can
delete or change
assignments here,
and choose which
spectra to be
“linked”

Tip: Don’t mix spectra from different samples in the same document. Don’t open the same structure multiple times. Instead, use
the Compounds Table to report the structure to the spectrum when needed. You can copy/paste and display multiple spectra
side-by-side on the same page.
41
 Assign a multiplet to an atom
ASSIGNMENTS

➢ Press the A key (or choose Assignments/Manual Assignment) to enter Manual Assignment mode

2. Then click on the atom

1. In Manual the atom to assign it to
assignment mode, first the multiplet
Assignments
click on the multiplet suggestions are
label. The cursor will highlighted by a
change to suitable color code.

3. Assignment label is Assignments are

displayed. automatically
transferred to the rest
of 1D and 2D spectra in
your document.

Tip: After the assignment, the atom label is changed to green. The multiplet label shows the atom label. The multiplet label can be
turned off by unchecking Analysis/Multiplet Analysis/Multiplets Boxes
42
 Predict NMR & help you assign peaks
ASSIGNMENTS

➢ Open a 1H (or 13C) spectrum in a new page, do multiplet analysis or peak picking as usual
➢ Copy a structure from ChemDraw or ChemSketch
➢ Go to Analysis/Predict & Compare. The predicted spectrum will be stacked with the
experimental one for visual comparison
➢ Switch to Superimposed Mode so you can assign the multiplets/peaks guided by the
predicted peaks

Use Shift + Up Arrow key to

change the active spectrum
and see the multiplet labels as
well as predicted peak labels.
In Assignment mode, click on a
multiplet label and then on an
atom to make the assignment.

Blue: predicted peaks

Red: observed peaks

43
 Automatic assignment of 1H spectra*
ASSIGNMENTS

➢ Open a 1H spectrum in a new page, and copy your structure from ChemDraw or ChemSketch
➢ Select Analysis/Assignments/Automatic Assignment. Mnova will do multiplet analysis (if not
done yet), predict the 1H spectrum, and automatically assign the 1H peaks
➢ Automatic assignment is also available for 2D HSQC and 13C spectra

*A separate Mnova NMRPredict Desktop

license is needed in addition to Mnova NMR
Tip: Multiplets can be cleaned up prior to
automatic assignment. Also, try Mnova
Verify to automatically verify proposed
structures
(http://resources.mestrelab.com/starting-
guide-to-mnova-verify)
 Display and browse assignment results
ASSIGNMENTS

➢ Go to View/Tables…Assignments to open the table

➢ The Table and the structure are correlated: You can click on a row to highlight the atom (and
its assigned peak), or vice versa.

Tip: right-click on an atom and go to Edit Atom Data from the pop up menu to change its label. Changed labels will be used in the
Assignments table and other relevant reports.

45
 2D spectral assignment
ASSIGNMENTS
➢ Assign the 1D 1H peaks, and then assign HSQC cross peaks, or vice versa
➢ Assignments in one spectrum are carried over to all other spectra in the same document. All
spectra in the same document are “correlated” by default
➢ To assign atoms in a HSQC, press the “A” key to enter Assignment mode. Click on an atom in the
molecular structure. Next click on the cross peak to assign it *

1H assignments from 1D spectrum

or HSQC.

13C assignments from HSQC.

*By Default, Mnova automatically snaps to a peak top (with interpolation). Press the Shift key one time to toggle it off in order to
manually locate the peak center. To see more choices, press and hold Alt key while assigning a peak
46
 Assigning a HMBC peak
ASSIGNMENTS
➢ In Assignment mode, click the center of the HMBC peak shown below, and then click on H7 while
holding the Alt key *
➢ In the Assign pop-up window, choose the options as shown below. Click OK to assign the peak to
both H7 and C5

1. Click the center of the peak in

assignment mode

2. While holding Alt

3. Choose ‘Keep Original’ for F2 to key, click H7
use the 1D 1H shift (instead of that
from 2D). Choose C5 for F1, and
choose ‘Keep Original’ to use the
1D 13C shift

* Since chemical shifts from 1D NMR is usually of higher resolution than 2D, we recommend you to use 1D shifts whenever possible.
To access such choices, press and hold the Alt key while assigning a peak
 Display 2D assignments on a
ASSIGNMENTS
molecular structure

➢ Report the structure from the Compounds Table *

➢ Select Edit/Properties to change the display properties of the structure
➢ Choose to display various connectivities for assigned atom pairs

*Don’t open the same structure multiple times. Instead, use the Compounds able to report the structure to the pages where needed

48
 Selective display of 2D
AUTOMATION/SCRIPTING
spectral connectivities

➢ Use the check boxes in the Assignment table to toggle the display of arrows

Uncheck here if you want to hide

all the NOESY connectivities
related to H-26 on the structure
 Report spectral assignments
REPORTING in journal format

➢ Select Scripts/Report/Peak Assignments… to report the assignment results in journal format

➢ The report can be pasted into an external document

50
 Annotate and report manually
REPORTING
➢ Annotations, such as arrows, boxes, and text, etc. can be added using the toolbar along the
bottom of the Mnova window
➢ The display of objects can be customized by right-clicking, and then selecting Properties
➢ Tables of Peaks, Integrals, Parameters, etc. can be opened by selecting View/Tables…
Contents can be reported or copied to other documents

Tips:
*Copy a molecule from ChemDraw or ChemSketch,
or open .mol or .sdf files
*Use View/Layout Templates menu to generate and
apply layout templates, or request an auto-
formatting script from Mestrelab
*Copy/paste any object(s) to your document with
high resolution
*Click to export to PDF in the Quick Access
toolbar

51
 Create a layout template
REPORTING

➢ Once all page objects are laid our correctly, choose View/Layout Templates/Create Layout
Template Document…, and save the layout file to disk
➢ The content of all page items is removed to leave a template with placeholders
➢ To use a layout template, open a new FID and/or molecular structure onto the template, and
it will be auto-formatted to the desired size and location
➢ If you have a spectrum already opened, choose View/Layout Templates/Lay Out In Template
Document… to apply a template

52
 Apply layout templates to specific
REPORTING
pages of a document

➢ A layout template can now be applied to a specific page of a document

with several pages. The zoom ranges can also be set in the template

➢ A layout template can be applied to a specific page

of a document that contains several pages
➢ Zoom ranges can also be set in the template

53
 Auto format using Mnova script
AUTOMATION/SCRIPTING

➢ Mnova has a powerful scripting engine that allows you to automate many operations,
including processing, analysis and reporting *
➢ Below is an sample result from running an Mnova script

* We provide development service for more complex batch processing and reporting requirements

54
 Auto Process, Analyze and Report
AUTOMATION/SCRIPTING

Example: Auto Process, Analyze, and Report a 1D spectrum using the Mnova
script, PAR.qs

➢ Open a 1D 1H spectrum, run the script. It does the following: **

• Re-processes the spectrum with a line-broadening value of 0.3 Hz; enhanced correction for
Bruker Group Delay, if applicable; zero-filling to double the data size, or to at least 64K points;
and, baseline correction using 3rd order Bernstein polynomial
• Automated peak-picking and multiplet analysis using the current settings
➢ Manually verify and correct the multiplet analysis results
➢ Run the script again, and it will generate a report similar to the one on the previous slide
➢ Processing, analysis and reporting options can be easily customized by editing the script
➢ This script also works for 13C and other nuclei, though in a slightly different way (e.g., it
picks and reports peaks instead of multiplets)
➢ This script only does formatting if it is a 2D

• ** The script can be edited, and the settings customized

• Write to support@mestrelab.com and ask for PAR.qs. It’s free for academia
• To run the script, first save it to a directory on the computer
• Next, choose Scripts > Run Script, navigate to the directory, and open it

55
 Open and stack multiple 1D spectra
AUTOMATION/SCRIPTING

➢ Open several 1D spectra in

the same document
➢ Select some or all of them
in the Pages view
➢ Press to stack them in a
new page
➢ Change the display to
another Stack Mode, such
as Superimposed mode

Tip: - You can also drag a 1D from a different page using the Pages view, which add it to
the current page as a new element in the stack
- When multiple pages are selected, you can choose the Superimposed tool to
superimpose them directly
- If you want to stack all the 1D spectra from a certain folder on the computer, select
Scripts/Import/Directory Spectra Stack…
 Change display properties
STACKED SPECTRA of stacked spectra

➢ Right click on it and select Properties: (or double click on the spectral window)

Enter 0 here if you don’t

like the tilt angle.

Enlarge the top/bottom

margins for better 3D
effects.

Check here if you want to

clip the peaks.

Change colors of spectra.

Click here to set

the changes as
default.

57
 Handle stacked spectra (1)
STACKED SPECTRA

➢ Click to toggle on the Stacked Items table. To increase the vertical To decrease vertical
intensity of selected or intensity of selected or
➢ Use this table to do the following: all spectra all spectra
▪ Delete spectra from the stack
▪ Change order of the spectra in the stack
▪ Change the Y-intensity of selected spectra
▪ Choose which ones to display
▪ Choose which ones to adjust

Click and drag here to change

the order of a spectrum in the
stack

Tip: Read Help > Contents on

more advanced data analysis,
such as reaction monitoring,
metabolomics, relaxation Uncheck the ones you want to Check the ones that you want
studies, DOSY processing etc. hide without deleting to be ‘active’

58
 Handle the stacked spectra (2)
STACKED SPECTRA

Click
Adjust
Stacked
Items

The cursor has to be inside the blue dialogue box

- Click&drag to shift an ‘active’ spectrum horizontally
- Click&drag to adjust the vertical offset between stacked spectra
- Reset intensities
- Reset shifts
 Superimpose multiple 2D
STACKED SPECTRA

➢ Multiple 2D can be stacked or superimposed in the same way as 1D spectra

➢ Press the Shift + Up Arrow key to change the active spectrum
➢ Right-click on the spectrum, and select Properties to change the color of the contours for the
active spectrum

The title shows the currently

‘active’ spectrum.

60
 LC/GC-MS data formats compatibility
LG/GC/MS

Vendor Windows Mac Linux

Agilent Chemstation MassHunter Ion Trap

Waters MassLynx Compass Openlynx MassLynx MassLynx

Thermo Xcalibur Exactive Q-Exactive

Bruker1 XMass Compass XMass XMass

JEOL MSQ 1000 FastFlight

AC SCIEX Analyst Data Explorer

Shimadzu2 LabSolutions v3 Labsolution v5

mzData, mzXML mzData, mzXML mzData, mzXML mzData, mzXML

NetCDF ANDI-MS NetCDF ANDI-MS

Advion Expression Data Express

1. Bruker software is required to be installed on the same computer (or users can download and install CompassXtract, as instructed in
http://mestrelab.com/resources/bruker-compass-mnova-ms/).
2. LabSolutions software is required to be installed on the same computer

Note: In all of the formats above, raw data can be opened in Mnova on the same computer with vendor software installed, convert it to an Mnova
binary file, then send it to other users with Mnova. This can also be done in batch mode or in real-time using an Mnova script. This is an effective
workaround for Mac and Linux users
61
 Open LC or GC-MS data
LG/GC/MS

➢ Go to File/Page Setup/Orientation and change the page orientation to portrait if you wish
➢ Go to Data Browser to open any file in the folder containing raw data, or drag&drop the
folder from Windows Explorer (or Finder) into Mnova
➢ Mnova will automatically convert your data and pick peaks

TIC

Mass spectrum
(at highest TIC)

62
 Common interface for all
LG/GC/MS analytical techniques

Easily combine your MS & NMR data on the page in an Mnova document

Note: When multiple spectral objects are opened they are loaded onto separate pages. You can copy (or cut)
and paste them to the same page later
Tip: Use the ‘Bring to Back/Front’, ‘Align’, and ‘Tile’ tools to arrange objects nicely

63
 Browse the mass spectra
LG/GC/MS

➢ Press to switch to crosshair cursor, and click

on the TIC to display the mass spectrum at that
retention time, or click-and-drag to display co-
added spectra.
➢ Press to change to appending mode if you
want to display multiple mass spectra.
➢ Choose the Spectrum Selection Mode to display
mass spectra conveniently:
▪ Manual mode: Click to display a single MS, or click-
and-drag to co-add multiple MS.
▪ Peak mode: Click on a peak to display the co-added
MS within the peak range.
▪ Peak (Background subtraction) mode: Click on a
peak to display the co-added MS within the peak
range with the background subtracted.

64
 Browse the mass spectra
LG/GC/MS

➢ Click to switch to a crosshair cursor, and

click on the TIC to display the mass spectrum at
that retention time, or click-and-drag to display
co-added spectra
➢ Press to change to ‘Append’ mode to add a
mass spectrum to the display
➢ Choose the Crosshair/Select drop-down menu to
display mass in different ways:
▪ Manual mode: Click to display a single MS, or click-
and-drag to co-add multiple MS (default)
▪ Peak mode: Click on a peak to display the co-added
MS within the peak range
▪ Peak (Background subtraction) mode: Click on a
peak to display the co-added MS within the peak
range with the background subtracted
 Browse UV traces
LG/GC/MS

➢ Click to show the MS Browser panel

➢ Double-click a ‘Total Absorbance’ item under ‘Traces’ to display a UV trace.
➢ Click to add more UV traces to the display

66
 Setup MS import display preferences
LG/GC/MS

➢ It is possible to control what to display when a dataset is first opened

➢ Choose File/Preferences, click the Mass icon, then the Setup tab
➢ Click “+” to add plots that you want to show when a dataset is opened
➢ Plots can be deleted or reordered

This dialog sets the

display of the first
positive base peak
chromatogram (BPC)
in the 1st injection
(highlighted in the
Preferences list)

Tips: Use MS Browser to see components available for display. Different preferences for different types of MS data
may need to be defined. Save preferences to an .ini file for later use
 Example of a customized display
LG/GC/MS

➢ Choose File/Preferences, click the Mass icon, then the Setup tab
➢ Define the display of the TIC, BPC, and the mass spec corresponding to the top 4
TIC peaks, as shown below
➢ Open a new MS dataset, and observe the display
 Extract a UV trace at selected wavenumber
LG/GC/MS

➢ Double click the DAD in the MS Browser to display it

➢ In the New Chromatogram dialog, choose Wavelength, and enter
a wavelength and a tolerance to display the extracted UV trace

69
 Display a UV spectrum
LG/GC/MS at a selected retention time

➢ Double-click the DAD Trace in the MS Browser to display it

➢ Press for Crosshair Cursor, press and hold the Alt key, then
click on the DAD trace to display the UV spectrum at that
retention time

DAD
In crosshair cursor
mode, click on the
PDA curve to display
the UV spectrum at
that retention time.

UV spectrum
 Edit and report peak integration results
LG/GC/MS

➢ Peaks are automatically integrated when you open a

chromatogram
➢ Use the Detect Peaks ribbon icons to re-detect peaks, add,
delete, or clear peaks
➢ Hover the cursor over a blue wedge, then click&drag the
green boxes to change the range of a peak
➢ Or press Shift + click&drag green boxes to change the
baseline of a peak
➢ Go to View/Tables… Mass Peaks to display or report the
Mass Peaks table

SHIFT+
Drag

71
 Display an extracted ion chromatogram
LG/GC/MS from a specific m/z value

➢ Click (or go to Mass Analysis/New Mass Chromatogram/Manually…)

➢ In the New Chromatogram dialog, enter an m/z value and a suitable Tolerance
➢ Click OK to display the EIC

TIC

EIC at 195.1 +/- 0.25 Da

Tip: You can also go to Mass
Analysis/Spectrum Prediction to run a
mass prediction from a molecular
formula.

72
 Display extracted ion chromatogram
LG/GC/MS for an MS peak

TIC

➢ First display the MS trace and zoom into the

MS at 3.08 min
molecular ion peak that you are interested

➢ Next press (or go to Mass Analysis/

New Mass Chromatogram/Graphically),
click-and-drag around the peak to define a
mass range
EIC at 675.3-676.2 Da
➢ An EIC will be displayed within the mass
range

73
 Confirm proposed structures
LG/GC/MS using Molecule Match (1)

➢ Import one or several structures by TIC

copy/pasting from ChemDraw, Isis/Draw Matched Isotope
or ChemSketch, or by opening .mol or .sdf Cluster Chromat.
files

➢ Click (or go to Mass Analysis/

Molecule Match/Calculate from Matched Isotope
molecules) Cluster

➢ In the Molecule Match Table, click on a

molecule to see the matching results

Mol Match Results

74
 Confirm proposed structures
LG/GC/MS using Molecule Match (2)

➢ You can go to Mass Analysis/Molecule Match/Settings to change the settings for Molecule
Match
➢ The default settings are for low-resolution MS. Change Tolerance to 5-10 ppm if you are
using high-resolution MS
➢ Edit the Adducts/Losses and other parameters, if required
➢ Click to run the Molecule Match again

Tip: Click the “+” buttons to add a new

adduct. Enter “+” for a radical cation.
Highlight one and click the “x” button to
remove it. Click Restore to reset to the
default or previously saved settings.

75
 MS driven structural verification
LG/GC/MS

MS data can be combined with NMR data to improve structure verification results *

*A separate Mnova Verify license is required

76
 Automatic trace alignment:
LG/GC/MS Instrument-specific

➢ Align a DAD, or another trace, to a TIC using the auto-alignment settings

➢ Set the rules to specifically identify the instrument and apply the correct alignment
automatically

77
 Peak purity calculation
LG/GC/MS

➢ It shows the curves associated to the most abundant mass peaks under the selected
chromatogram peak

78
 Just the tip of the iceberg!

Thank you for your time!

For more information:

• Visit www.mestrelab.com for information about manuals,

tutorials, and many more Mnova plugins
• Check Help > Contents in Mnova for help information
• Email support@mestrelab.com for technical questions
• Email sales@mestrelab.com for sales related queries

79
Mnova 12 – Starting guide

Thank you for trusting our software solutions!