Profiler provides you with a variety of tools to identify and quantify compounds in your spectra. The Profiler selects compounds from your Library, sets concentrations, determines peak locations, and finds and using extended information about compounds that you would like to profile.
The Compound Table summarizes the results of your profiling work in the active spectrum and lists the compounds that are available to profile. The Compound Table lists both Potential (Maximum) Concentration in the right hand column as well as Measured/Profiled Concentration in the left hand column. You must select at least one compound set in the Compound Sets view to see any compounds in the Compound Table.
The currently selected compound in the Compound Table is the active compound in the Spectrum Graph, where you can adjust its shape, position, and concentration. Select a compound without a concentration in the Compound Table, a preview line for the compound appears in the Spectrum Graph, scaled vertically to suit your current zoom level. You can click on the preview line to begin profiling that compound; its concentration will be set to match the height of the preview line.
Filter the current contents of the Compound Table using Quick Searches for compound names, comments, compound IDs, regions of the spectrum, or specific locations in the spectrum.
Select more than one compound from the Compound Table by holding down Ctrl (Cmd in Mac OS X) and clicking additional compounds. If you would like to select a range of compounds, click on the first compound and then hold down Ctrl-Shift (Cmd-Shift in Mac OS X) and click on the last compound. Apply colors, pins, or stars to multiple compounds simultaneously.
Available units of concentration include millimoles per litre (mM), micromoles per litre (μM) and milligrams per decilitre (mg/dL).The maximum allowed concentration for any compound is 5000 mM (5 M). When you select mg/dL as the concentration unit, the maximum value varies per compound, since the units incorporate the molecular weight of the compound. However, the maximum value is always equivalent to 5000 mM.Concentrations in mg/dL are only available for compounds whose molecular weight has been specified in the compound's Reference Card, and the accuracy of such concentrations depends on the accuracy of the molecular weight provided. The molecular weight has already been correctly specified for all compounds in the default Chenomx Reference Library.
Tips and Tricks
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After typing in the Quick Search box, press the down arrow key to navigate to the Compound Table.
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Set custom display colors for compounds, pin compounds so that they are visible even when they are not selected and toggle stars on compounds to generally mark them for future reference.
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Hover the mouse cursor over some parts of the Compound Table, tooltips appear containing more details. For example, hovering over the optional matched clusters column for a compound shows you which clusters are matched.
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Set compound concentrations directly in the Compound Table, by double-clicking on a compound's concentration cell and typing in a value.
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Right-click on a compound's row in the table. Operations accessible through the context menu include scaling concentrations, automatically fitting the compound to the spectrum, and clearing fits, custom colors, stars or pins.
There are many columns available for display in the Compound Table. Display any number of the available columns, (at least one visible) and drag column headers in any order. Sort the Compound Table on any column by clicking its column header. Click the header again to reverse the sort order.
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Copy the contents of a cell to the Clipboard by right-clicking on the cell and select Copy [cell name] to Clipboard. Paste the contents as text to any other program.
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Compounds modified from their default state (including fits, custom colors, pins and stars) will appear in the Profiled Compounds set, and appear in bold in the Compound Table.
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Press Delete with one or more compounds selected in the Compound Table to clear all fits, custom colors, pins and stars for the selected compounds.
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To make more space for the Compound Table, you can hide the Spectrum Thumbnail by clicking View > Show Spectrum Thumbnail.
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The Cluster Navigator enables fast navigation among clusters of an active compound. The Navigator appears in the top left corner of the Spectrum Graph as an ordered list of the approximate positions of all the clusters, in ppm. Click on a cluster position and navigate to an optimal view of the cluster.
Tips and Tricks
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Use the Q and E keys to display the next or previous cluster.
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Clusters that appear green in the Cluster Navigator are 'matched', meaning they closely match the spectrum line as determined by comparing the sum line (red) and the spectrum line (black) near each cluster.
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Click on a cluster and drag along the Cluster Navigator to display multiple clusters in the Spectrum Graph.
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Transform windows appear alongside compound signatures to guide profiling by restricting the frequency range that you can adjust each cluster. All Chenomx Reference Compounds have had transform windows set to allow the flexibility to fit most common biofluids. You can choose to have the transform windows enforced, preventing you from moving any cluster outside its transform window, or not enforced, allowing you to move any cluster beyond its transform window.
Edit transform windows
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In the Edit menu, check Enforce Transform Windows to lock.
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On the Edit menu, clear Enforce Transform Windows to allow clusters beyond transform windows.
Tips and Tricks
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View the size of the transform that has been applied to any cluster by hovering the mouse cursor over it. The transform size appears in the top right corner of the Spectrum Graph, and visually as a thick blue line connecting the starting position of the selected cluster and its current position.
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When you move a cluster outside its transform window, its transform adjustment triangle turns red. The Transform column in the Compound Table will also indicate whether the compound has any clusters that have been moved beyond their transform windows
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Clusters that are outside their transform window appear in the Transforms column of the Compound Table as Outside Windows. Note that you may need to turn on the Transforms column in the Compound Table.
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When you move a cluster outside its transform window, the adjustment triangle on the horizontal axis of the graph turns red. Also, when you hover over the cluster of its triangle, the visual indicator for the adjustment is red, as is the text in the top right corner of the Spectrum Graph describing the extent of the adjustment.
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Transform windows for pH sensitive compound signatures (including those found in the Chenomx Reference Library) are determined in part based on the pH uncertainty for the current spectrum. If you find that you frequently need to override the transform windows for a spectrum, user Processor to check the accuracy of its pH calibration, and consider increasing its pH uncertainty value.
Scale Concentrations lets you modify the concentrations of profiled compounds in the current spectrum by a common multiplication factor. You can use this to compensate for dilution effects, errors in CSI concentration or other systematic influences on compound concentrations.
| Menu Location | Compound > Scale Concentration... |
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How to Scale Concentrations of one or more compounds by a common factor
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Select one or more compounds in the Compound Table, and in the Compound menu, click Scale Concentrations..., or go to Edit menu, click Select All, and then in the Compound menu, click Scale Concentrations....
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Enter the multiplication factor. To increase concentrations, use a factor greater than one. To decrease them, use a factor less than one.
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Click OK.
Tips and Tricks
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You cannot enter a multiplication factor that would result in a concentration higher than 5000 mM for any compound.
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If you set the multiplication factor to zero, all of the profiled compounds are set to 0 mM.
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Scale Concentrations does not affect compounds with unknown concentrations (--).
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If you want to scale concentrations for a specific compound or for all of the profiled compounds in a group of
.cnxfiles, use the Batch Edit feature.
Profiler can propose the pH of the sample by analysing the position of the fit peaks clusters that are pH sensitive and report an optimized pH value that would best explain the location of each.
The pH analysis is carried on based on 3 different selection modes:
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the cluster(s) that are specifically selected for a given compound
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the set of compounds selected in the compound table
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if no clusters or compounds are selected, then it analyzes the entire list of profiled compounds.
Compounds with no concentration and clusters with 0 net intensity or without pH-defined chemical shifts are ignored.
The results of the analysis of each clusters/compounds are presented in a scrollable list, with compounds in the first column, cluster ID in the second, best pH value in the third, the valid compound pH range in the fourth, and the pH sensitivity of the cluster in the last column. The sensitivity is reported as the change in ppm around ± 0.1 unit of pH around the global optimum pH that is proposed.
Only the clusters with a sensitivity of ≥ 0.001 ppm are used in the calculations and reported in the list.
The reported optimized pH is the value that minimizes the weighted amount of transforms that would need to be applied to the listed clusters to explain their current position. The listed sensitivity values are used as weights.
It is possible to change the pH of the spectrum directly in the interface. Upon pH change, the clusters transforms are automatically recalculated to preserve the initial positions of the clusters.
When working with multiple compounds, it can become difficult to distinguish which compounds are contributing which parts to an overlapped region. Set custom colors, 'pin' a compound to ensure it remains visible, or 'star' a compound to label it for later analysis. 'Remember' compounds applies your compound selection from one spectrum across the remaining spectra in your project, which can be useful when using a feature such as 'Fit Automatically'.
| Menu Location | Compound > Assign Color... |
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How do I set a custom color for one or more compounds?
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Select one or more compounds in the Compound Table.
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In the Compound menu, click Assign Color... and select your desired color. Alternatively, if your Compound Table has a Color Column open, click in the Custom Color column (
) to access the color chooser.
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Click one of the preconfigured colors in the color chooser, or click More... to choose from a larger selection of colors.
| Menu Location | Compound > Pin to Graph |
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How do I pin one or more compounds?
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Click the pin for the compound in the Pinned column (
) of the Compound Table.
Or
Click the pin next to the compound's line in the Legend (
).
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Select one or more compounds in the Compound Table and, in the Compound menu, click Pin to Graph.
| Menu Location | Compound > Add Star |
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How do I star one or more compounds?
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Click the grey star for the compound in the Starred column (
) of the Compound Table.
Or
Select one or more compounds and, in the Compound menu, click Add Star.
| Menu Location | Tools > Remember Selection |
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How to 'Remember' compounds from my current spectrum to work with in other spectra
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Select one or more compounds.
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In the Edit menu, click Remember Selection.
| Menu Location | Tools > Restore Selection |
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How do I re-apply selected compounds to a new spectrum?
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Open the spectrum that you want to select your compounds in.
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In the Edit menu, click Restore Selection.
Tips and Tricks
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You can use this feature to quickly select a number of known compounds in the Compound Table to be fit automatically.
| Menu Location | Compound > Clear > Color |
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| Menu Location | Compound > Clear > Pin |
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| Menu Location | Compound > Clear > Star |
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How do I clear a color/pin/star from one or more compounds?
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Select one or more compounds in the Compound Table.
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In the Compound menu, click Clear > Color/Pin/Star
Tips and Tricks
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Set or clear custom colors for compounds visible in the Legend by clicking on the colored box beside the compound in the Legend.
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Setting a custom color/pin/star for a compound adds it to the Profiled Compounds set, even if you have not fit the compound.
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Custom colors/pins/stars are stored with the spectrum when you save it as a
.cnxfile. The colors you select are still associated with the compounds when you next open the file, until you clear them. If you want to set the color of a specific compound in a group of.cnxfiles, use the Batch Edit feature. -
You can export custom colors/pins/stars to a file using Batch Export.
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