Guide to CLIC Expressions

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tjanke
Posts: 23
Joined: July 27th, 2012, 10:48 am

Guide to CLIC Expressions

Post by tjanke »

What are CLIC Expressions?

CLIC expressions are an important part of GC Image that allow users build rules for selecting and filter blobs. This gives users the ability to quickly find the parts of the chromatogram they are interested in. CLIC expressions are also used to build filtered images, constrain template matching, and give custom statistics in the blob table.

For more details on building, running, and saving CLIC expressions, see the references section below.

References:
tjanke
Posts: 23
Joined: July 27th, 2012, 10:48 am

Re: Guide to CLIC Expressions

Post by tjanke »

How do I build and run my first CLIC expression?
  • Start GC Image
  • Open the exampleMS.gci file provided with GC Image
  • Filter > Correct Baseline
  • Filter > Detect Blobs
  • Edit > CLIC Expression
  • In the main expression text area type retention(1) > 3
  • Set the Data Type to Blob
  • Click the Select Blobs button
Congratulations. You have built and run your first CLIC expression. If you look back at the chromatogram, all blobs that appear after 3 minutes in the column 1 dimension should be selected.
tjanke
Posts: 23
Joined: July 27th, 2012, 10:48 am

Re: Guide to CLIC Expressions

Post by tjanke »

How do I get the intensity of a spectra peak in CLIC expression?

This can be done using the intensity function. To retrieve the intensity of a spectrum at m/z 57, we would type intensity(57).

An example use for this would be to only select blobs where the intensity is over a certain amount. We could get all blobs where the intensity at m/z 57 is greater than 1000 by using the following expression: intensity(57) > 1000

In addition to giving a single m/z value, a range can be specified. If you wanted to retrieve the total intensity from m/z 50 to m/z 100 you would use the following expression: intensity("50-100")

In addition to the intensity function, the percent and relative functions are also available. These 3 functions will mirror the values seen in the MS Viewer. Intensity, Percent Intensity, and Relative Intensity can all be seen in the MS Viewer depending on which is selected.
tjanke
Posts: 23
Joined: July 27th, 2012, 10:48 am

Re: Guide to CLIC Expressions

Post by tjanke »

How can I select blobs using base peak?

You can do this using the massrank or ordinal functions. If we want to select all blobs with a base peak of 57, we could use either of the following examples:
massrank(1) = 57
ordinal(57) = 1
tjanke
Posts: 23
Joined: July 27th, 2012, 10:48 am

Re: Guide to CLIC Expressions

Post by tjanke »

How do i reference library search results in CLIC?

There are a few functions that reference library search results. Here are some examples:

hitlist("benzene") < 5 - If benzene is in the top 5 of the hit list, the blob will be selected.
hitmatch("benzene") > 800 - If the NIST match factor for benzene is greater than 800, the blob will be selected.
hitrmatch("benzene") > 800 - If the NIST reverse match factor for benzene is greater than 800, the blob will be selected.
hitprobability("benzene") > 70 - If the NIST match probability for benzene is greater than 70 percent, the blob will be selected.
tjanke
Posts: 23
Joined: July 27th, 2012, 10:48 am

Re: Guide to CLIC Expressions

Post by tjanke »

How do I compare spectra in CLIC?

The match function can be used to compare spectra. An example CLIC expression is match("43,96;57,100;71,37;85,20") > 600.

The important part of this expression is the mass spectrum given to match against. In this case it is "43,96;57,100;71,37;85,20". This example spectrum was created manually. Another way to get a spectrum is to copy it from the MS Viewer. To do this:
  • View a spectrum in the MS Viewer
  • On the MS Viewer toolbar select Copy to Clipboard > Spectrum String > Full Spectrum
  • On the GC Image menu bar: Edit > CLIC Expression
  • Paste the spectrum into the MS field.
This MS field can be reference using the "<MS>" tag within the expression. So our expression would change to match("<MS>") > 600.

There are a number of functions that can be used to compare spectra. These are generally standard ways of doing vector comparison. They are:
  • AbsoluteValue
  • FirstDerivativeAbsoluteValue
  • Correlation
  • FirstDerivativeCorrelation
  • Euclidean
  • LeastSquares
  • FirstDerivativeLeastSquares
  • DotProduct
  • Match
  • RMatch
tjanke
Posts: 23
Joined: July 27th, 2012, 10:48 am

Re: Guide to CLIC Expressions

Post by tjanke »

How do I use HRMS data in CLIC?

Version 2.5 introduces accurate mass support in CLIC. There are two options to create accurate mass CLIC expressions.


The first is to specify a tolerance in addition to the desired mass.

Here are some examples:
Ordinal( 56, 0.05 ) - get the ordianl value of the most intense spectral peak of the from the MS range of "55.95 - 56.05" in the raw spectrum
Intensity( 56, 0.05 ) - get the intensity of the from the MS range of "55.95 - 56.05" in the raw spectrum


The second option is to use the "A" functions in combination with the MS Data Binning setting in the Multi-Channel options. These functions inclue:
AOrdinal(), AIntensity(), ARelative(), and APercent()

Examples:
MS Data Binning is Dynamic Bin with a tolerance of 0.05
AOrdinal( 56 ) - get the ordianl value of the most intense spectral peak of the from the MS range of "55.95 - 56.05" in the raw spectrum
AIntensity( 56 ) - get the intensity of the from the MS range of "55.95 - 56.05" in the raw spectrum


If you wish to get the accurate mass for a given rank, there are two options:
MassRank( rank, "accurate" ) and AMassRank( rank ) - these will both given the accurate mass of the spectral peak with the given intensity rank.

Example of the difference:
MassRank( 1 ) - 130
AMassRank( 1 ) - 130.01238
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