System is communicating

System is communicating

#1: My 
chromato-

gram is 
empty 

MASS SPECTROMETER (MS) TROUBLESHOOTING

B – Verify accuracy of MS method: Ensure the MS 
method is properly encoded to acquire the desired 
data and required reagents are prepared.

Solutions

Missing a solve for troubleshooting your instrument? 
Contact ptfionbaording@gmail.com

A – Inspect ESI capillary for clog and review 
source settings: Irregular and/or absent spray can 
be caused by a clog. Follow instrument 
manufacturer instructions to check for clogs and 
adjust source settings to ensure consistent spray.

C – Examine LC-MS for leaks and/or clogs: 
Investigate irregular pressure using an LC 
troubleshooting guide.

D – Check system for contamination: Move to 
issue #3: my blank files have a lot of signal.

*Some instrument allow you
 to remove the nebulizer to 
check spray performance. Others 
have windows into the source to view 
spray performance.

Are any 
mass signals 

present?

Yes
Check the system 

pressure at 
starting conditions

Pressure is Low or High

Pressure is Normal

See Solution ANo/Unsure Spray is absent or sputtering

Spray is consistent
See Solution B

*Check the 
stability of the 

ionization spray

See Solution D

See Solution C

#2: My 
observed 

mass values 
are shifted or 

inaccurate

#3: My blank 
files have a 
lot of signal

F – Re-calibrate mass spectrometer: Follow 
instrument manufacturer instructions to calibrate 
instrument (see Note 1). 

Did you verify 
MS calibration 

before 
acquisition?

No/Unsure

No

See Solution F

Yes

Are you acquiring 
any reference 

mass data?

Is this vial full and 
correctly applied in 

the MS method?

No/Unsure

Fill vial and 
see Solution BYes

No/Unsure Are low mass 
ions most 
affected?

Yes/Unsure

See Solution E

E – Perform check on detector voltage: Follow 
instrument manufacturer instructions to perform 
detector voltage check. 

Yes

#4: ***The 
instrument has 

stopped 
communicating!

Do MS peaks 
have normal 

distributions?

Notes

Note 1: Rebooting computer and/or mass 
spectrometer can help improve calibration 
application.

Yes/Unsure
No

See Solution G

G – Re-tune mass spectrometer: A tune of mass 
spectrometer voltages can help ensure correct 
mass value assignments. 

Does the signal in 
the blanks 

appear to be 
related to any 

injections 
preceding the 

blank? No/Unsure

Yes

Reboot computer 
connected to the MS 

and acquisition 
software 

***Instrument manufacturers 
have specific processes for 
shutting down mass 
spectrometers.

See Solution H
H – Use stronger needle wash: Needle washes 
that clean the autosampler between injections can 
help reduce carryover. Alternatively, consider 
running additional blanks between samples.

Has column been 
cleaned and was 

it stored properly? 
No/Unsure

Yes

**Run system 
with 100%B then 
100%A through 

column
**To avoid dirtying the mass spectrometer, 
send LC to waste during wash.

Signal persists
I – Re-make mobile phases: Follow the mobile 
phase making procedure outlined in Reverse Phase 
Metabolomics SOPs. Ensure all reagents are LC-MS 
grade, or equivalent. 

See Solution I

System is NOT 
communicating

Follow instrument 
vendor guidelines for 

soft system reboot

System is NOT 
communicating

Follow instrument 
vendor guidelines for 
hard system reboot

J – Reduce extra programs on MS computer: Try 
to reduce activities not related to acquiring MS 
data to reduce reboot requirements (see Note 2). 

Note 2: It is recommended to recalibrate MS after 
every reboot and re-start data acquisitions. 

See Solution J

See Solution J


	Slide 2