Mass Spec will not Autotune
Applies to MS in general
What could be my problem?
There could be several things that would cause your Mass Spec not to Autotune. The
most common conditions that typically cause Autotune problems and are easily
corrected are listed in scenarios below. By following these suggestions most Autotune
problems can be corrected, providing that no hardware-electronics problems exist.
• Vaccuum
• Perform and evaluate air and water check
• Calibration valve and calibrant
• Perform and evaluate autotune report
What should i observe or do?
Vacuum
One thing that should be checked constantly when operating the Mass Spec is
the vacuum, and should be the first thing you check when having or suspecting
problems. When everything is working as designed, the vacuum, depending on
-5
model and configuration, should be in the range of 5X10 to approximately
-6
5X10 range in the vacuum manifold, as measured by the Gauge Tube and
Gauge Controller.
This document is believed to be accurate and up-to-date. However, Agilent Technologies, Inc. cannot assume responsibility for the use of this material.
The information contained herein is intended for use by informed individuals who can and must determine its fitness for their purpose.
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If your mass spec has a front and rear vacuum chamber, make sure that the
vacuum is checked in both places. Typically if there are two vacuum chambers, the
Rear chamber's vacuum will be anywhere from slightly better than the front to as
much as a decade better, meaning if the front vacuum reading is in the 6 range
then the rear should be in the 7 range.
What to do if vacuum is bad:
1) Verify That The Pumping System Is Operating
Check that the oil level is correct in the sight glass of the foreline and auxiliary
pumps, (your system may not have an auxiliary pump). Then confirm that the
pump or pumps are running and that the HIVAC PUMP is operating. The HIVAC
pump could be a diffusion pump or turbo pump, depending on the particular
system in use. You can typically verify diffusion pump operation by observing the
heat being put off by the diffusion pump heaters, but DO NOT physically touch
these pumps because they get very hot and will burn you badly. Turbo pump
operation usually can be verified by the low-level high frequency winning sound, or
by a turbo speed indicator gauge, if installed. If the mechanical pump or pumps
(foreline, auxiliary or rough pump) are not running, verify that the pump circuit
breaker is on, (if there is any doubt, reset the breaker by placing it in the OFF
position then back to the ON position). If the foreline and auxiliary pump restarts,
observe to see if the system will complete the pump down sequence. If the system
completes the pump down sequence and the vacuum is okay, the system may
have shut down because of some voltage glitch. If the pump(s) do not start, they
may be seized or there could be a electronics problem in the Mass Spec that is
preventing power from being applied to the pump or pumps. If this is so, Agilent
on-site service is recommended.
2) Pumping System Is Okay But Vacuum Is Still Bad
In this case the best way to troubleshoot the problem is to split the system in half.
You do this by removing the column from the injection port and capping it off by
pressing that end into a septum. If your column is 0.25mm id or smaller and at
least 10 meters long, you should be able to remove the column without venting the
system. If the column is .32mm id or larger it is recommended that the column be
at least 30 meters long to prevent a venting accident.
CAUTION: If in doubt vent the MASS SPEC.
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This procedure separates the Mass Spec from the GC. With the column capped off
the Mass Spec should pump down quickly. If the vacuum problem still exists, the
next step requires you to use the vent procedure and vent the Mass Spec. After
the Mass Spec has been vented, cap off the Mass Spec interface with a blank
ferrule, (i.e., a ferrule without the hole), then pump the system down.
If the vacuum problem still exists, there is a problem at the Mass Spec, and you
may at this time elect to check all other fittings in the vacuum manifold that can
leak to the outside of the manifold.
3) If the Mass Spec won’t Pump Down at All
(Diffusion pumps will not turn on or turbo pumps won’t come up to speed) -
Check for foreline pressure, if it's excessive (greater than 300 milli-torr) then more
than likely there is a leak at the Mass Spec or the Foreline/Rough pump is not
coming online. If your system has Diffusion pumps, check the O-rings at the
bottom of the diffusion pump. O-rings at bottom of diffusion pumps (typically two
(2) per pump) will become hard and brittle, preventing them from sealing. This is
especially true if the problem occurred after shutting down the system and allowing
the pumps to cool. The O-RINGS in question are typically located at the bottom of
the diffusion pumps beneath caps (2 per pump) on the drain/fill spouts. The O-
rings over time will become hard and brittle, because of the harsh environment
they have to operate in, (mainly the high temperatures). When the system is
cooled down everything contracts, causing the O-rings to break their seal with the
cap and the drain/fill spout. When you attempt pump down again the O-rings are
not pliable enough to re-seal and the foreline pressure remains too high to allow
the diffusion pumps to turn on. When replacing these O-rings, make sure that you
replace all of them at the same time, typically 2 per pump.
NOTE: It’s especially important to change these O-rings if the mass spec has
been running for a long time and has been shut down for maintenance.
These O-rings operate in an harsh environment and will become brittle
and non-pliable over time.
4) Verify manifold o-rings or copper gaskets are in good condition and that the o-ring(s)
or copper gaskets are seated properly in their groove.
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NOTE: The manifold O-RING or COPPER GASKETS should be inspected for
cuts, flat spots, deeply grooved gaskets and general good condition. The
O-ring \ gasket grooves should be checked for cleanliness, there should
be no signs of dirt or debris in the O-ring \ gasket groove. The O-ring \
gasket, O-ring \ gasket groove and the sealing surface of the manifold
can all be cleaned with a lint free cloth, dampened with isopropyl alcohol
or methanol.
If Vacuum Is Good But Problem Still Exists
5) Perform Air and Water Check
If your vacuum is looking okay, at this point we can proceed to performing An Air
and Water Check. This check can be done in several ways, depending on what
software product and revision you running, it could be possible to run the Air and
Water Check by selecting it from a menu in the software. Another way is to simply
perform a spectrum scan from manual tune, then evaluate the spectrum scan to
determine what percentage the air (ion 28 and 32) and water (ion 18) are, relative to
ion 69. In performing the spectrum scan MAKE SURE THE CALIBRATION VALVE
IS OPEN.
What to look for in the Air & Water Check:
When evaluating the spectrum scan, you should not see any ion below (less than)
mass 69, that is higher than 10 percent of the abundance of mass 69. That means if
there is ion 18 (water), ion 28 (nitrogen), ion 32 (oxygen) or any other background
ion, they should be below 10 percent of the mass 69 abundance. You may also
want to check the overall background of the spectrum against backgrounds that you
have had in the past to verify if the current background is significantly different
(usually higher) than before. High background can be a sign of a source of
contamination.
Masses 18, 28 and 32 being higher than normal could indicate a leak, but only if the
abundances are of the correct ratio. In other words if you have a true leak, the
resultant spectrum will be representative of the atmosphere's make-up. In the event
of a leak you should have ions 28 (nitrogen), and 32 (oxygen). The ratio of ion 28 to
ion 32 should be approximately 4:1, or four times more nitrogen than oxygen, you
will also have mass 18 (water) in some amount representative of the humidity at the
time. These are the signs of a true leak. If you have a single abnormally high ion, for
instance ion 28 is high or ion 18 being high individually, this is not a leak but more
likely a sign of contamination, either from the gas source (tank) or chemical filter
traps that have become saturated.
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If Autotune parameters and peak ratios seem normal, but abundances appear low
across the spectrum with a high multiplier voltage, (2600 to 3000 volts), that’s
usually a strong sign that the multiplier is going bad and in need of being replaced. If
you have a multiplier that was taken out before, you may elect to try it just to verify
the problem, (assuming that the old multiplier is not in bad condition).
If A Leak Is Suspected
Split the system in half by removing the column from the injection port of the GC
and capping off (plugging) the column, by pressing the injection port end of the
column into a septum. If the leak was in the injection port then the indications of the
leak should go away while the column is capped off.
NOTE: If your column is at least 30 meters long or longer and .25mm id or
smaller, you should be able to remove the column without venting the
system. However don't take your time plugging off the column. If you’re
not sure, VENT.
If the problem still exists, then the Mass spec should be vented, (using the vent
procedure). Remove the column and cap off the Mass Spec interface by using a
blank (no-hole) ferrule.
CAUTION: DO NOT OPEN THE Mass Spec until MS temperatures, (Source and
Quad), are below 60 deg. C.
After capping the Mass Spec, pump the system down and verify if the problem is
corrected. If the problem is corrected, you should vent the Mass Spec and reinstall
column using a new ferrule at the Mass Spec Interface.
CAUTION: Never use an all graphite ferrule at the mass spec interface, this
ferrule should be 85 percent vespel and 15 percent graphite.
It's recommended to pump the system down in stages to continuously monitor if the
problem is corrected. To pump system down in stages simply reinstall column into
Mass Spec interface, using a new ferrule, and cap of the injection port end of the
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column with a septum as described above. Pump the system down long enough to
determine that the system is okay. Then remove the septum from the end of the
column and install the column into the GC injection port and re-verify that the
system is still okay. Use the guidelines given above to determine if you need to vent
the Mass Spec before removing the septum from the column.
If you are still experiencing a problem, Agilent technical support or on-site service is
recommended!
6) Calibration valve and calibrant (PFTBA)
Make sure that the calibration valve is operational and that the calibration vial is
filled with the calibrate, PFTBA. An indication that the valve is working properly is
that, when the valve is turned on, (at the beginning of a tune or scan), there should
be a notable jump in pressure when monitoring manifold pressure.
7) Perform And Evaluate Autotune (standard spectra tune)
If the system will complete the Autotune without generating a system error, the
autotune report could provide information that will help you isolate your problem.
Even if the Mass Spec can not complete the tune, the resultant error message that
is typically generated will often be an excellent guide to determining the actual
source of the problem.
If an error message is displayed during tune operations, stop and seach the
Technical Support Assistant for that particular error.
What to look for
There is a lot of info on the Autotune report, which can make it confusing, but we
can make it simple by narrowing it down to what’s important for us to make a
determination on how the system is performing. First look at the 3 principal peaks of
the Autotune, 69, 219 and 502. Observe their peak shapes and their peak width.
Peak shape should be smooth and symmetrical, and peak widths are typically in the
0.5 amu range. Next look at the absolute abundance of ion 69, it should be in the
range of approximately 150,000 to 450,000 counts for the absolute value of ion 69.
Absolute abundance could be different depending on exact hardware and software/
software revisions in use.
Relative to ion 69, ion 219 should be 35 percent or greater, and 502 should be
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2 percent or greater. Isotope ratios will vary, but typically they are in the range of 1,
4, and 10 per cent for ions 69, 219 and 502 respectively. Repeller voltage should be
relatively low, between approximately 4 to 8 volts.
Multiplier or EM voltage should be reasonable, depending on EM age, between
1400 and 2600 volts, (the maximum is 3000 volts), as the multiplier voltage
surpasses 2600, it's anybody's guess as to how long it will last. There are several
indications that you could expect as the source gets dirty. Typically the 502 ion will
start to decrease before any other ion, and the 502 peak becomes jagged in
appearance.
If Autotune parameters and peak ratios seem normal, but abundances appear low
across the spectrum with a high multiplier voltage, (2600 to 3000 volts), that’s
usually a good sign that the multiplier is going bad and in need of being replaced.
If you have a multiplier that was taken out before, you may elect to try it just to verify
the problem, "assuming that the old multiplier is not in bad condition. Since
multiplier voltage does not increase to compensate for low 219 or 502 ion
abundance, the EM or multiplier voltage may or may not increase unless the 69 ion
abundance has dropped below its target abundance mentioned above. If all or some
combination of the above symptoms appear, typically it's an indication that the
source is in need of good cleaning.
If tune problems still exist after cleaning the source, there is no other error message
being displayed, and all other suggestions have been investigated, Agilent technical
support or on-site service is recommended.
8) Remember, If An Error Message Is Displayed …
If an error message is displayed during the tune process, Search the Technical
Support Assistant for that particular error message.
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