10 Replies Latest reply on Sep 19, 2017 5:53 AM by james_jenkins

    What effects 219 peak width on standard autotune?


      On my 5975 MS, the peak width for 219 on the standard autotune runs low. My range is 0.45 to 0.65. The 69 and 502 run above 0.50 but the 219 consistently runs 0.47 and below. Cleaning and maintenance are performed regularly. Filaments have been changed, repeller and drawout plate have been replaced, new PFTBA used, new autotune downloaded from Agilent hotline. My even older 5973 has no problems. Any suggestions?

        • Re: What effects 219 peak width on standard autotune?

          Ion peak width and shape is related to the way the quadrupole functions and is tuned and not source cleanliness.


          Have you reconfigured the system or loaded new software since it was installed?


          The first thing to check is the quad dc polarity.  There is a sticker on the analyzer that shows the optimum polarity determined by factory tests.


          In the program Agilent GCMS Configuration the quad dc polarity must match the sticker.



          So in this explanation, my DC polarity does not match the sticker.  I would need to select Negative, save the configuration, which overwrites the default tune files, and then retune the instrument.   I posted a document here in the Agilent Customer Community explaining DC Polarity  (Quadrupole DC Polarity - what it means and how to check it )  .



          If that matches, then we have other questions:

          Are the tune ion peaks shaped correctly?  Are they split or fronting?


          How many samples have been run on this system? 

          What is the tune EM value?  How old is the Electron Multiplier?     <this is a customer replaceable consumable part, like tires on a car. If it is more than a couple of years old, you need to purchase and install a new one.



          In the tune, it shows:

          219 width.jpg

          Notice that there is a Wid219 number.  The AMU Gain and Offset numbers above it set the ion peak width for the entire range, and this number shows the compensation for the mid mass if the line is not perfectly linear.  Also, notice that this tune report shows that the Pw50 -- the Peak Width at 1/2 height -- is 0.60 amu.  This is the peak width that autotune (ATUNE.U) is trying to achieve.


          Would you be willing to post a picture of your tune report?  That will speed this up.  The other way to handle this would be to call 1-800-227-9770 option 3,2,2


          GCMS Phone Tree.png


          We have technical people ready to answer your questions from 8am to 5pm in your local time.

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          • Re: What effects 219 peak width on standard autotune?

            See attached Standard Autotune.

              • Re: What effects 219 peak width on standard autotune?

                Standard Spectra Autotune.   The Standard Spectra Autotune attempts to tune the MS so that the final PFTBA spectrum looks like those in the NIST library.  This should improve library search match scores.  On an Agilent GCMS system with an HED, or a newer one with an extractor source, the tune algorithm has to detune the source parameters to lower the 219 and 502 sensitivity that our instrument improvements over the years have increased.


                STUNE is a compromise. It gives up sensitivity to gain library match scores. 


                You run the transferline at 285, but the source at 230.  The very hot transferline tip is next to the cooler source body.  Best source thermal stability would mean that they should both be at or nearly the same temperature.  Higher source temperatures reduce the high mass sensitivity somewhat. Since you are running STUNE, that is a good thing. I would recommend trying your application with the source set to 285.  Please retune after changing the source temperature.


                There are only 74 peaks in the spectrum scan.  The typical amount it something like 100-200 or so.  The EM Gain is fine.  How old is the EM? How many samples have been run on this system? 


                The ion peak shapes are tilted to the right a bit and not symmetrical.


                Load STUNE.U, change the quad polarity to NEG, save the tune, run STUNE, and let's look at it.  The quad polarity can affect the total transmission of the quad and it also affects ion peak shapes.  It could be that the quad would prefer to be in NEG now.


                Would you please run an ATUNE and upload it as well?  We can troubleshoot issues much better with ATUNE as it is trying to maximize sensitivity and not detune it like STUNE does.

              • Re: What effects 219 peak width on standard autotune?

                See attached A tune


                EM changed last year. We don't run a lot of samples.


                Bill Dieffenwierth

                St. Vincent's Med Center


                  • Re: What effects 219 peak width on standard autotune?

                    A beautiful autotune, so there is nothing wrong with the MSD.  In fact, it is really clean with low background and very low air/water.  The ion peak shape is nice, too. Symmetrical with no tilt. The 503 isotope peak is nice here, too, because it is high enough abundance.


                    Go to Tune and Vacuum Control.  Make sure that STUNE.U is loaded (it's name is in the top border bar).  Go to File, Save As, and save STUNE.U with a new name, like STUNE_Backup.U or something. That way if you make a change you don't like you can go backwards.  Then File, Open, STUNE.U.

                    Open Tune, then Tune Wizard...


                    Notice here at the bottom it says "Sets all parameters and criteria saved in the tune file."   STUNE is a canned Target Tune than can be edited.  The next window that will pop up is:


                    Don't change anything, just click OK.  The next window is:



                    Notice that the 69 target abundance is 250,000.  Autotune wants 400-600,000.  Increase this a bit to, say, 325,000 or so.    

                    The next line is Peakwidth Target.  Increase this to 0.6 amu. 

                    Then click OK.   The next window is:



                    Just click OK.   Then a normal Windows File Save window will pop up for you to save STUNE.U.


                    Then run Standard Spectra Tune again and let's see how that goes.   These changes will increase the amount of ions making it out of the source and through the quad with a very slightly higher allowable peak width and turn up the EM to get them a bit larger, too.   It should improve the adjustability so that STUNE can detune it a bit easier....hope that makes sense!

                    • Re: What effects 219 peak width on standard autotune?

                      I'll also say it is fun to ask someone how many samples they run.  Some people say that they hardly use it....and that means that they run it every day, but only two sequences of samples because their coworker runs theirs 24x7.   Some people say that they hardly use it...and that means that they run one sample every other week.  


                      The reverse is also true.  "Oh, I run my system a lot!"  can mean ....a lot to them, so ten samples a month or a week or a day or an hour!   I have a customer who has a system that has run 300,000 samples over the last five years or so.  Now that is a lot of samples!

                    • Re: What effects 219 peak width on standard autotune?

                      We run around 1600 samples a year between two instruments (5975 and a 5973). Probably more of those are run on the 5975.We run ethy acetate as a cleanup between each sample.

                      Have no problems with our 5973's tunes. We purchased that one in 1999.


                      Bill Dieffenwierth

                      SVMC Jacksonville, FL

                      • Re: What effects 219 peak width on standard autotune?

                        I changed the parameters under Tune Wizard. Attached are the Standard tunes for Feb 27 and 28th. the 69 peak width is slightly higher but the 502 is now on the high end. The first Stune I did after changing the parameters the 502 peak width was at .69.

                        I haven't changed the quad polarity or reset the source from 230 to 285 yet.


                        Bill Dieffenwierth

                        SVMC Jacksonville,FL

                        • Re: What effects 219 peak width on standard autotune?

                          Hi wdief001,

                          I went ahead and flagged the “Correct Answer” on this post.  If you still need help though, please let us know and we would be happy to continue working with you.