Users Guide

One Moon Scientific, Inc.

dataChord Spectrum Miner uses various Open Source libraries. For details on the libraries see Appendix I.

Revision History
Revision 0.914 Jan 2013

Acknowledgements

Table of Contents

Welcome to Integrated NMR Analysis
I. Basic NMR Analysis
1. Overview of dataChord Spectrum Miner
Introduction
Overview
Quick Start
2. Loading NMR Spectra
Finding Local Files
Retrieving files from the server
Searching for Files
The Files Table
3. Display, Phasing and Baseline Correction of Spectra
Using the Icon Bar
Using the Crosshair Cursor
Using the Selector Cursor
Status/Control Bar
Phase Correction of Spectra
Phasing GUI
Phasing 2D Spectra
Baseline Correction of Spectra
Baseline Correction Options
Adjusting the chemical shift reference position
4. Analyzing and Integrating Regions
Controls
Table
Normalization
5. Processing NMR Spectra
Processing Controls
Acquisition Info Tab
Transform Tab
Linear Prediction Tab
Apodize Tab
Phase Tab
Solvent Tab
Baseline Tab
Extract Tab
Script Tab
6. Automated Spectrum Analysis
Sequence of Processing Steps
Process NMR Data
Locate NMR Signals in the Spectrum Process NMR Data
Categorize Signals and Format Output
The Peak Table
The Results Display
7. Manual Correction of the Analysis
Referencing the Spectrum
Problem: The spectrum has the wrong reference
Getting the Correct Number of Peaks
Problem: The analysis picked many peaks that just seem to be noise
Problem: There are real peaks that did not get picked
Getting the Peak Type Correct
Problem: There are peaks that were picked that are not included in the results string.
Problem: There are peaks with normalized integrals of zero in the results string.
Problem: There are peaks included in the results string that should not be there.
Peak Normalization
Problem: Peaks that I am sure correspond to two protons have an n value in the peak table (and results string) of 1.
Getting the Multiplet Structure Right
Problem: There are extra peaks on the shoulder or near this peak that I don't want included in the multiplet.
Problem: Two separate, but non-overlappling, multiplets (or individual peaks) have been inappropriately combined into a single multiplet.
Problem: This peak is obviously a triplet (or doublet or quartet etc.), but is labeled in the peak table and results string as a singlet (or something else that is not correct).
Problem: Correct number of peaks in multiplet, but it has the wrong label.
The Peak Analyzer
Regions
Peak Add and Delete
Multiplet Peaks
Couplings
8. Using Molecules
Loading Molecules
Retrieving molecules from a corporate database.
SMILES
Assigning Atoms to Peaks
9. Generating a Report
Displaying Peak Markers
Displaying Spectrum Annotations
Templates
10. Comparing Spectra
Loading Multiple Spectra
Controlling the View of Multiple Spectra
Using Multiple Spectrum Types
11. Creating and Using Spectral Display Windows
Adding Spectral Display Windows
Using the Graphical Interface
Using Tcl Commands
Using Spectral Windows
Display Modes
The Spectrum Icon Bar
Cursors
Crosshair Correlation
Keypad Navigation
Spectral Attributes Dialog
The File Panel
The View Panel
The Graph Panel
The Plot Panel
The PeakPick Panel
The Peak Display Panel
The Peak Attributes Panel
The Analysis Panel
Spectral Display Menu
Managing Spectral Display Windows
Spectrum Synchronization
Preserving the Spectral Window State between Sessions
II. Data Mining of Multiple NMR Spectra
12. Loading Sets of Spectra
Descriptive Table File
Retrieving and Matching Spectra
Scanning for Data
Using the Data Table
13. Selecting and Grouping Spectra
Selector
Grouper
14. Measuring Spectra
Aligning and Normalizing Spectra
Measuring Spectrum Intensities
Plotting Measured Intensities
Box Plots
Column Math
15. Patterns and Trends
Introduction
Principle Components Analysis
Non-Negative Matrix Factorization with Sparseness Constraints
Covariance Analysis
16. Using Reference Spectra
Local Reference Files
Configuring Reference Spectra
III. Appendix
17. Appendix I Open Source Software

List of Figures

1.1. The dataChord Spectrum Analyst Window
2.1. Local Files Menu
2.2. Network Files Interface
2.3. Search Interface
2.4. textflyout.png
2.5. filescontrol.png
11.1. Windows laid out in a 2x3 matrix
11.2. One Dimensional Spectrum
11.3. The Spectrum Attributes...File...Add panel (cut for space considerations)
11.4. Removing a dataset in Spectrum Attributes...File...Remove The Colors... Button The
11.5. The Spectrum Attributes...File Display panel
11.6. The Spectrum Attributes File panel Colors submenus
11.7. A standard color palette
11.8. Preset color schemes for background, axes, and cursors - but not peaks
11.9. Color Schemes in Spectrum Attributes for overlaid spectra (arrows indicate selected schemes)
11.10. The effects of different settings in Spectrum Attributes - Plot
11.11. The Spectrum Attibute Peak Pick pulldown menus
11.12. Immediate effects of picking peaks in the Peak Pick panel and spectrum display
11.13. Peaks on an HSQC spectrum
11.14. The Spectrum Attributes Peak Attributes panel, with pulldown menus
11.15. Application of the "Extract/Replace" button in the Spectrum Attributes...Analysis panel
11.16. Toolbars available in the Extracted Spectrum window

List of Tables

2.1. Date Formats
3.1. Baseline
3.2. Solvents and Chemical Shift Reference Compounds
5.1. Processing
5.2. Parameters
5.3. Parameters
5.4. Parameters
5.5. Parameters
5.6. Autophase parameters
5.7. Phase Parameters
5.8. "Data Combination
5.9. Time Domain Polynomial
5.10. Frequency Domain Peak Suppression
5.11. Gap Smoothing
5.12. Baseline Model
5.13. Baseline Region
5.14. Baseline Model
5.15. Mode
5.16. Processing
11.1. Cursor Correlation
17.1. Open Source Software