Chromatography Forum

I developed a method on the Agilent 6430 LCMSMS recently and during development had a baseline of near 0 in height. Performed ~100 injections and no problem detecting my LOQ standard ~2000 area response. When I tried to validate the method the sensitivity on the low end completely disappeared with the baseline ~10000 height. I started troubleshooting and switched to a brand new column, prepared fresh mobile phases, flushed the HPLC with flushing solution and ran IPA overnight.

The next day the problem was still there and I noticed that with no flow from the LC using this method the baseline is consistent between 5000 and 10000 height, with the occasional drop to zero for 30 seconds but spike back up again. We just had an OQ/PM performed on the instrument so I can't imagine the second quad being dirty.

My method is:
MRM: 193 to 115 m/z, 142 fragmentor, 23 collision energy
ESI source: 325 degrees C, 60 psi nebulizer, 4000V capillary, gas flow 12 L/min
Flow:1 mL/min
Injection volume: 5uL
MPA: 0.1% formic acid in DI water
MPB: 0.1% formic acid in MeOH
Gradient: 45%A to 95%B over 4 minutes with reequlibration
Diluent: MeOH
Column: Agilent SB-Phenyl, 4.6x150 mm, 3.5 um

Does anyone have any ideas what is causing this increase in baseline noise? Please let me know if you need more information.

Thanks in advance.

have you looked at source gases? maybe your bottle/generator is the source of contamination....

Are there any frits, inline filters, guard columns that could be gummed up? I recently (on the 6460) had a plug in the filter frit that sits right behind where the tubing from the LC connects to the MS box. Perhaps you had some particulates collected, which would then exhibit some sort of retention behaviour of their own and slowly bleed out a contaminant.

Please let us know if and when you do find resolution. Sometimes the Agilent folks are good to call up and mull over ideas with, as they may spot patterns that you aren't aware of. For example I was having trouble getting auto-tune to complete successfully, and when I sent a screenshot to a tech, he immediately identified the problem as a rare contaminated batch of calibrant solution.

The gas does not seem to be the problem because we actually use nitrogen tanks and the tank has been changed since the problem started.

I have talked with the agilent folks and they seem to think there might be a voltage issue inside the machine or a loose connection. We just had our PM performed so this is likely. I will update this post once I learn more.

The machine appears to run fine in Negative mode.

Similar problem here.
The detector was 6490 (demo version) and hplc 1290.
Every 30 seconds signal fall down to 0 than after 5 seconds raise to normal level.
The problem occur on high masses on low everything looks fine. They didnt fix it in
our lab so i dont know what happens...but iam sure it was something with electronics.

Duno how looks your check procedure.
Would be easy for us if you write everything you do to find the "bug".
What about manual tune window any noise level with and without solvent introduce to ms/ms


p.s.
sry my english is bad

Agilent will be in tomorrow to service the instrument, so I will then find out more, hopefully!

Pepter in the manual tune tab there is a lot of baseline noise in the Q1 and Q2 scan, with and without flow. The check tune passes. But I think that is because the abundances are so high it doesn't matter. My issue is with the LOQ levels.

I will keep you updated, when I find out more.

Did service solve your problem ?

Not yet.

The instrument was vented and the voltages were adjusted and capillary coil was replaced. This seemed to solve the problem, but then it started again.

It may be faulty gas filters? Even though they were just replaced during the PM. We will get some new ones in today to see if this solves the problem.

Is there anything in a full scan that shows up readily? If you can find the mass of the contaminant(s), it might help you to locate the source of the contaminant.

A brand new capillary solved the problem. The instrument has been running for a few days with no reoccurance of the "noise".

Hmm ... strange was contaminated or platinum ends scratched ?

The appearance of the old capillary was fine.