Calculation of peaks named with their RRT

Juwe

Dear all,

I have a problem with my testing for related substances. I created a CF (Peak, Real) which should divide the amount (calculated by Empower) through a value given in a second custom field. It works fine for all peaks listed in the component tab. But it doesn`t work for all unknown peaks as long as they are named with the RRT by selecting the API in the field „RT Reference Used to Name Unnamed Peaks by RRT". If I leaf this field empty the corrected amount of all peaks is calculated in my CF.

Is it not possible to perform further calculations with peaks named with the RRT, or did I make a mistake when creating the CF?

Thanks in advance!

Empower2019

Make your API peak a default peak in the processing method, then process the channel again and see, you should then get values for your CF for all unknown peaks. This presumes you only have 1 API in the sample.

Juwe

I have set my API as default peak in the PM. But the CF shows only results if the field „RT Reference Used to Name Unnamed Peaks by RRT" is empty.

Empower2019

Do you have the peak type of the second custom field set to All and not Founds Only? I think the Use Reference Peak to name unknowns actually populates the peak into the Component Editor so its no longer officially an unknown. I think the Amount field might be screwing this up because you don't really get amounts for unknowns unless you specify a curve reference. Try applying the method set to populate all the Unknown RRTs then set a curve reference of the API against these peaks and apply method set again to see if you get values.

Cant think of another way to do this.

Juwe

Yes, I have set the peak type to All.

The thing I don`t understand is the following: The amount is calculated for all peaks even the API is selected for „RT Reference Used to Name Unnamed Peaks by RRT", whereas the value in my CF appears only if the field „RT Reference Used to Name Unnamed Peaks by RRT" is emtpy.

Here the formula from my CF: Amount/CConst1

Empower2019

You say in Post 1 that the CF is Amount/value from another CF. What is this other CF?Are there 2 CFs in total?

Juwe

I tried both version.

1) Amount/Factor  (--> Factor is the second CF)

Then it occurred to me that I could also enter the factor in the PM in the field CConst1.

So I changed my CF into: Amount/CConst1

Unfortunately, none of the both versions lead to results if the field „RT Reference Used to Name Unnamed Peaks by RRT" isn`t empty.

MJS

Like Empower2019 is getting at, I'm a bit confused by your actual fields.  You said a second custom field in your first post and then in your last post this morning you reference CConst1.  CConst1 can only be specified if the peak is listed in the component table as each component can have a different value, so it wouldn't work for auto-named components.

Can you share some screenshots of your custom fields?  What is the mathematical formula you are trying to address in them?

Empower2019

An unnamed peak cant pick up on CConst1 since its not in the component editor like a  named peak would be along with RT, Peak Match etc. Is it possible you could set up a Sample Real CF called Factor and put this factor in the sample set so for all unknowns its going to divide amount by whatever is in Factor? This presumes factor is a fixed value? The only way I was able to calculate amounts for unknowns was to make my main active peak a default peak in the processing method.

After doing this, any amounts and indeed any custom fields can also calculate for unknowns.

Juwe

Thanks a lot for your comments. I have some screen shots attached which show that the CF is calculated only if the field „RT Reference Used to Name Unnamed Peaks by RRT" is emtpy. Thanks!

Empower2019

Thanks for the screenshots. It doesn't look like CConst1 is the issue then if you managed to get amounts for unknowns. I thought it might be the internal standard causing an issue but I cant see anything obvious from your screens. Is it possible to just not have the unknown peaks named as RRT Unk...etc?
Setting the Idoethane as default will also calculate any RRT values for unknows using this peak as reference so can you just go back to your custom field and leave the "RT Ref to use.." field blank?

You can still report values for your custom field in a report method and throw the field RT Ratio (which is another term for RRT) alongside the peak retention time so you essentially have the same info for the unknowns (amount and RRT) alongside your know peaks. Summaries can be performed on these values too and you can split peak tables into knowns and unknowns per sample. I suspect this feature forces a name in the Empower database so the peaks aren't technically unknown, this feature is probably only useful for amounts of unknowns and RT but not further CF calculations. 

Dan_Ramlose

I think I'm having the same issue and I've taken it up w/ others @ Waters already.
For unknowns, I get amounts etc. so long as I do NOT specify a RT Reference (but there's no peak names RRT~x.xxx). If I specify a RT reference in the PM, I get peak names but nothing else! Basically, I think my Empower installation is suffering from a day-one problem. I hope it goes away when we update to FR5, probably next month. Waters hasn't made any progress on it as far as I know.

Empower2019

I wonder is this a known issue which is mentioned in Service Notes for Empower 3?

Dan_Ramlose

Not that I've been able to find...

Juwe

@Dan_Ramlose: Unfortunately, I have to disappoint you. We have the FR5 installed...

I have also send an iRequent to Waters, but no feedback yet.

Empower2019

I had the same issue with graphing data over multiple sample sets, I think that thread is still on page 1, sometimes Waters aren't great at all for getting back to you about issues, then you read in the Service Notes that your issue is a known bug that's now fixed in a later version. There may be a fix for your issue Juwe but the only one I can see is to not name the unknown peaks RRT...etc as my previous post. 

Neil

Hello - perhaps I do not see all of your component table but I am not sure how you got amounts calculated for the unknown peaks.  The internal standard peak will only work for those components listed in the component table.  What I did was using your idea of a default peak, I set the default pk start and default pk end time to include the unknown peak.  I got both the amount and the cf to work for the unknown peak with the RT Ref Peak Used to Name Unnamed peaks by RRT populated.  Perhaps I am missing something in what you did but please come back to me and let me know how you got the amount calculated for the unknown peak with the internal standard.
Neil

Neil

Hello again - I got it to work without using the Default Peak start and end times.  I think I have replicated what you did and both the amount and cf are working.  Perhaps you should email me directly and we can sort this one out.  neil_j_lander@waters.com.
Neil

Empower2019

Would  you mind sharing how this is done please, especially in relation to an internal standard? Might be useful for other people in the same situation. 

Dan_Ramlose

Neil - please discuss with Don Trinité as he has worked on this issue and has a copy of one of my projects that demonstrates how unknowns are not calculated if assigned a RRF via Retention Reference in a PM but do get calculated if no Ret. Ref is selected. Working together, you may be able to find a solution and close a ticket

As I understand it, the default peak start/end times are included to allow for different unknowns to use different default peaks.

Thanks,
Dan

Neil

Hi Dan- will do.
Neil

Neil

Hello - I have a solution for the original question in this chain and received confirmation that it works.  The original custom field was something like:
Amount/CConst1*100/Label_Claim.  I made 2 modifications.  First I used the CCalRef1 field for the main peak.  Then I modified the custom field to point to both the CConst1 and Label_Claim for the main peak.  The  new custom field looks like this:
(Amount/CCalRef1[CConst1])/CCalRef1[Label_Claim]*100.  Now all peaks including the ones with RRT have an amount calculated and a result for the custom field.
Neil