You can export data from your profiled spectra for further analysis, bin the spectra for analysis by more traditional techniques, or create images of your spectra for use in publications and presentations.
When you have finished profiling a spectrum or set of spectra, you often need to get the resulting data into a spreadsheet or statistical analysis package. Batch Export lets you create a text file containing all of the relevant details from profiled spectra, in formats that you can easily open in software like Microsoft Excel or Umetrics SIMCA-P.
| Menu Location | Tools > Batch Export... |
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How do I export data from one or more spectra?
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Start the Batch Export wizard.
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Select the type of data that would you like to export. You can export concentrations in various units, other profiling results like profiled areas, matched clusters and transform summaries, or annotations like stars, pins and custom colors.
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Choose the source spectra to export, and specify a target folder and filename for the exported text file. You can specify the currently open spectrum, other individual spectrum files or one or more folders containing spectrum files as the source.
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Choose a save location and file format. You can export as comma-separated text (.csv), as tab-separated text (.tsv), or as an excel spreadsheet (.xlsx).
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Choose the compounds for which you would like to export data. You can use custom compound sets that you have created in Library Manager to filter the output to specific compounds, or you can export all profiled compounds in all of the spectra.
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Choose additional data that you would like to include in the exported file. Additional data can include spectrum pH values, Chenomx compound IDs for the exported compounds, or InChI or SMILES strings for the exported compounds.
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Choose the default layout (files in rows and compounds in columns) or transposed layout (compounds in rows, files in columns) for the output file, depending on how you intend to use the file.
Tips and Tricks
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You must export Areas rather than Concentrations when working with compounds that have a region-based Fit Style (see “Compound Details”)
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To filter the exported compounds without modifying the source spectra, create a Compound Set or Smart Compound Set in Library Manager, and only export compounds in that Compound Set.
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Use the default layout to export files that you intend to open with statistical analysis packages. Use the transposed layout to export files that you intend to open in a spreadsheet program, or if you prefer the transposed layout.
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If you intend to open the exported file in Microsoft Excel 2003 or earlier, limit the number of compounds to less than 253 for the Default layout, or the number of files to less than 253 for the Transposed layout, since these versions of Excel do not support large numbers of columns.
When collaborating with other people on projects, you may want to quickly compare Compound Tables while profiling. Export Compound Table creates a copy of the current compound table in a format which can be easily imported into any modern spreadsheet program.
| Menu Location | File > Export > Compound Table... |
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How do I export my current compound table from this spectrum?
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Click File > Export > Compound Table.
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Choose a save location and file format. You can export as comma-separated text (.csv), as tab-separated text (.tsv), or as an excel spreadsheet (.xlsx).
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Click Save.
Tips and Tricks
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If there are blank cells, there will be corresponding blank values in the exported data (this can happen if the table contains compounds that are missing from your compound library or if you export columns that can have empty cells, like "author", "pulse sequence", or "compound comment")
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The "Status" column will never be exported, even if it is visible in the table.
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The Starred and Pinned columns will export as "Yes" or "No" for each cell, and the Color column will export as a hex RGB value, such as 0000FF for each cell. Cells that have no color assigned will all export as the "default" color for that cell, i.e. the color that the cells compound appears when displayed on the graph.
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You can add/remove columns, reorder columns, or click on the header of any column to change the table sort order. The columns you chose to appear in your Compound Table will be exported, and the order of the rows and columns in the exported file will be in the same order as your Compound Table.
Related Topics
When you collaborate with other people on a project, you may have different compounds in
your library than your collaborator has in theirs. Exporting profiled compounds creates a
compound pack (.pack) containing the set of actual compound signatures
that you used to profile the project, including compounds that have been annotated with
stars, pins, or colors. You can exchange compound packs with other
users of Chenomx NMR Suite, and import new packs via Library Manager. This is one way to be
certain that you and your collaborator are always profiling spectra for that project using
exactly the same collection of compound signatures.
| Menu Location | File > Export > Profiled Compounds... |
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How do I export a compound pack from the current spectrum?
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Open the Export Profiled Compounds dialog.
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Enter a name for the exported compound pack. The name you enter is used to label the associated Compound Set when the compound pack is imported into another library via Library Manager.
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Click OK.
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In the resulting file chooser, locate the folder in which you would like to save the compound pack.
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In the File Name field, type the new name for the compound pack file. The specified name can be different from the name of the compound pack itself, but you may prefer to keep them the same.
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Click Save.
Tips and Tricks
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If you want to export all of the compounds in a compound set, regardless of whether they have been fit in a particular spectrum, use Export as Compound Pack in Library Manager.
When you are profiling a series of spectra from the same study, the spectra are often quite similar to one another. While it is possible to profile each spectrum from scratch, it can be more efficient to copy a profile from an earlier spectrum in the series and adjust it to match the current spectrum. Importing profiles is an important technique for profiling large series of similar spectra efficiently.
| Menu Location | File > Import Profile... |
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How do I import a profile from another spectrum?
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Open the Import Profile dialog.
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Select a profiled spectrum (
.cnx) from which you would like to import the profile. -
Click Import.
Tips and Tricks
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When you import a profile, the imported data completely replaces any profile of the current spectrum that you may have done before the import.
Related Topics
Statistical approaches to analyzing large numbers of spectra often involve data reduction methods like spectral binning to reduce the number of variables that must be considered. Spectral binning divides spectra into a series of regions, or bins; subsequent analysis involves the integrated area of these bins instead of the raw spectral data. Profiler lets you perform spectral binning on collections of spectra, exporting the results to an excel document (.xlsx) and to tab-delimited text (.tsv) that is easily read by spreadsheet programs and statistical analysis software packages.
| Menu Location | Tools > Spectral Binning... |
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How do I bin spectra?
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Start the Spectral Binning wizard.
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Choose the source spectra (
.cnx) for binning, and specify a target folder for the resulting binned data. You can specify a series of spectrum files or one or more folders containing spectrum files as the source.If you would like to repeat a binning session that you have previously saved, you can specify a binning configuration file (
BinningConfiguration.xml) to import.A binning configuration file is automatically created each time you calculate binning results.
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Choose a binning method to apply to the specified spectra. You can use a defined bin size in ppm or a defined number of bins. You can also use bins based on the transform windows of the compounds in a Compound Set ("targeted binning").
If you would like to reuse a predefined set of bins, you can specify a bin definition file (
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Choose regions of the spectrum to exclude from binning, if desired. You can specify any regions of the spectrum using start and end values in ppm.
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Choose a binning target. You can bin spectra based on the sum line (standard binning) or the subtraction line (residual binning).
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Choose a normalization method. You can normalize the bins relative to the total area under each spectrum line or to units of standardized area (sa). Note that 1 sa is the area under a theoretical DSS methyl peak at 0.50 mM in each spectrum.
Tips and Tricks
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Binning can take a long time, especially on older computers or particularly large datasets. If you have never tried binning before, try a small dataset of five or ten spectra first, before moving on to larger datasets. The time needed for the smaller dataset will help you to more accurately estimate the time needed to complete a binning session.
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If you choose one or more folders as the source, binning includes spectra both directly in the specified folders and in subfolders of the specified folders.
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Binning based on number of bins divides the spectrum into the specified number of bins after excluding the regions that you have defined, if any.
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To do residual binning, each of the source spectra must have been analyzed in Profiler and must contain at least one compound with a defined concentration.
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Excluding regions from a binning dataset can help you to remove the influence of interfering or confounding signals, such as solvent peaks.
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Normalization based on total area gives the area of a particular bin as a fraction of the total area of all bins, except area in any of the excluded regions that you may have defined.
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Spectral binning is subject to several numerical limits:
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Each binning session can include a maximum of 5000 spectra.
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The range that you define when using number of bins or size of bins as a binning method must be at least 1 ppm wide, and can be as large as 1998 ppm (-999 to 999 ppm).
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You can specify a maximum of 100000 (one hundred thousand) bins or a minimum of 1.
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You can specify a minimum bin width of 0.00001 ppm and a maximum bin width equal to the width of the range that you have chosen. For example, if you are binning across a range of 2 to 10 ppm, your maximum bin width is 8 ppm.
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Related Topics
| Menu Location | File > Send to Processor |
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As you work with a spectrum in Profiler, you may notice that the phase correction, baseline correction or other aspects of the spectrum's lineshapes are not properly adjusted. Similarly, you may import a spectrum directly into Profiler, only to realize that it requires phase correction, baseline correction, or additional pH or CSI calibration. Send to Processor closes the current spectrum in Profiler, and opens it in Processor, retaining any changes you have made in Profiler.
Tips and Tricks
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Any changes that you have made in Profiler are retained when you send the spectrum to Processor, and will be visible if you bring the spectrum back into Profiler. However, you still need to save the spectrum, either in Processor or Profiler, to permanently save those changes to the spectrum file.
Related Topics