Blog Archives
TF 3.0 Export Results Grid to Excel and Copy Images to Clip Board
Sticking to new features in data review, we’ll continue with a simple workflow.
One of the many request that TraceFinder has received over the last year has been to have the ability to export the results grid directly to Excel instead of having a Custom Report generated.
In TF 3.0 all data grid results whether in the quantitative views or targeted screening section, export all data to Excel or CSV files directly.
No need to produce a custom report and navigate through the files menus to go get it.
Simply export and place the file where you want it.
Also a feature that has been requested is the ability to copy high definition images of chromatograms and such to the clipboard for use in papers, lab notebooks and presentations/posters.
We also did this in TF 3.0
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
Excel rules the world or at least it thinks it does…..
So, this week we’ve gotten a few questions on importing a sample list in CSV format.
There is an error that can occur if the csv file you exported and made adjustments to, is still open in Excel when you try to reimport it.
Unfortunately, the error message isn’t as descriptive as maybe it should have been, but it did give us a chance to post another answer to a “Ask A Guru” question
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
Need to just enter some compound info for the method… Ok here’s a solution
So at times we’ve had the request that chemist just want to enter in some compound data without having a rawfile to extract the spectra from.
And though TF gives you multiple ways of creating methods, some feel they just want to be able to add a compound and input their data by hand.
Though many workflows support doing this in using a CSV file and creating a method from importing that csv file into the CDS, sometimes that just may be too much.
So here is couple of CDS files that you can have on hand just to pull over and fill in place holder information.
One is for XIC/SIM type of experiments and the other is for SRM type of experiments.
https://dl.dropbox.com/u/13860428/Blank%20XIC%20Compound%20CDS.csv
https://dl.dropbox.com/u/13860428/Blank%20SRM%20Compound%20CDS.csv
Now that I have a CDS, what do I do with it?
Well, the end game of the CDS is to supply information that can be used to create methods and acquire data.
Here we’ll look at the Acquisition List side of the equation.
Here in the data we retrieved from a CDS or PMD file is stored.
Note that PMD files do not contain all instrument information but this can be added to a CDS and then adjusted.
From here you can select the export SRM data in the Method View tab and an Xml file containing the instrument specific data will be produced.
If you open this file in a text editor such as note pad it will contain the information in the Acquisition List in a format that can be imported into the Instrument Method editor.
If on the Batch View section or the final page of the Acquisition Mode wizard you select Auto-TSRM update this information is passed to the mass spec at the time of acquisition. This allows the user to collect only the data needed to be processed and allows for manual updates in the batch to be automatically loaded to the mass spec at run time. This does not monitor the RT of peaks and automatically update the mass spec controller, but allows for user input to occur in on place versus having to open the instrument editor for a second adjustment.
Compound Data Store or Compound Database – Kinda the same thing….
TF has the concept of bring in a data you know about compounds and storing it for later use.
This we call the Compound Data Store (CDS), but what’s in a name… Its a an XML file that contains information about the compound.
The picture above shows this data in excel. It contains information like the compound name, experiment type, collicion energy, retention time, fragments relationships.
Attached here is a copy of the csv template TEMPLATE.
This information can be edited in excel and uploaded into TF to add to a database or to alter the data base. The changes will be reflected in the TF CDS module.
Once the data is in the CDS, a method developer can utilize it to create processing methods which in turn can be used in syncing acquistion methods in the Master Method.
A blog post to come later this week will highlight the use of the information in the Auto-SRM feature.
A quick note is that the CDS is not automatically turned on at installation.
The user will have to configure the option and restart TF to take advantage of this feature.
Sample List???…. Do I need a Sample List??? Yes and here’s how to import one
So the basic element of data navigation and collection is a list of samples.
This list will identify the properties of the data collected and tell the system, what to do to and the names of the files collected or to be collected.
So TF has a couple of different ways to do this.
The first and easiest is to make a template of the defined sample grid you want to use. In TraceFinder, the user can define the columns that are displayed in both the data results and sample definition grids.
In Batch View or in the sample page of the Acquisition Mode/Wizard, right click the mouse in the grid and a menu dialog that opens up.
In that dialog , select “Export to CSV”. This will make a copy of the grid and the header lables is a file that can be opened by any editing grid application. The most common is Excel, but you could open in a text editor also.
Simply, open the file and for daily use just input sample information in the template and save as a daily/batch .csv file.
A LIMS system, can create a .csv file in this same format or even use a bar code reader to fill in certain fields even in Excel.
Once the sample input is done save the file as .csv and close the editor.
If the file is still open in Excel, MS Office will not let it be used by another program so TF can’t import it until it’s closed.
Right click in the grid and select “Import Samples”.
The Dialog below opens, then select the appropriate file.
The information contained in the CSV file will be inserted into the grid either at the end of the current data or where the index indicator is if that is the option selected in the drop down list below the browse section.
There is also a xml format that can be created fromat LIMS system that can be used, or if Xcalibur has previously been in use the .sld files can be utilized also. Any sample type that TF does not recognize will be set to the Unknown Sample type.
TraceFinder: Direct Knowledge 