problems inputting Authentic standards

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Lucas Schwartzenberg

May 28, 2014, 5:52:28 AM5/28/14
I'm trying to input new authentic standards by entering my known metabolites into the 'targeted'-sheet.
The list is complete, but strait up using the 'TOOLS -> Copy RTs to RTcalculator' just empties out the metabolite list on the RTcalculator sheet.

I've tried to figure out were things went wrong, one of which was to complete the steps on the 'targeted'-sheet in order.
Things seemed well enough until I came to step iii) Search in MS file(s).
Microsoft visual basic gives an error : "variable not defined"
It highlights 'groupsrowno =' and points to 'Sub zTargetedpeaks12()' but my experience with programing is to limited to derive anything from this.

Am I having these problems because I forgot to input something in the excel sheets, or is this a 'external software' related problem?

Darren Creek

May 28, 2014, 11:22:15 PM5/28/14
to Lucas Schwartzenberg,
Hi Lucas, 
Thanks for reporting this, and apologies for the bug. 

I think the best way to overcome this is to avoid step (iii) on the targeted sheet.  This was an old function to extract all EICs from LCMS data, but I think few people were using it and now the 'Extractmasschromatograms' function is not supported by mzmatch.R. 

The reason is because it is better to use xcms to extract peaks from you LC-MS data. You can do this using the standard functions (steps a-d) on the Settings page. Those functions will produce a txt file of all peaks which can be used as the input for step (iv) on the Targeted sheet.

Let me know how this goes. 

Note: the actual error you found in Excel can be fixed by deleting the words 'option explicit' from the very top of that VBA module - but this will only get you into R before it crashes again due to the reasons above.  You may wish to do this if you're trying to extract peak lists from an existing peakML file, but in general its best to use the functions on the 'settings' page to generate .txt peak lists. 

all the best,

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Dr Darren Creek
NHMRC CJ Martin Fellow / Lecturer
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences
Monash University, Parkville campus
381 Royal Parade, Parkville, Vic, 3052
Join us for the
International Metabolomics Society Conference, Tsuruoka / Japan, June 23 - 26, 2014

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