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FC-MS from Teledyne Isco. Combi Flash ® a Name You Can Rely On. Goals:. Sources of issues Approaches to resolving problems Overview of “chemical” issues. Troubleshooting: Divide et imperia !. I have a problem!. I don’t see my peak!!. “Chemical”. Mass Spectrometer. Fluid Interface.

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FC-MS from Teledyne Isco

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FC-MS from Teledyne Isco

CombiFlash®a Name You Can Rely On


  • Sources of issues

  • Approaches to resolving problems

  • Overview of “chemical” issues

Troubleshooting:Divide et imperia !

I have a problem!

I don’t see my peak!!


Mass Spectrometer

Fluid Interface

CombiFlash System

“Stupid” items

Start with the simple things!

  • Carrier solvent bottle full? Primed?

  • Correct carrier solvent?

  • MS enabled?

  • Chemistry

  • Probe gas lines?

  • Probe?

  • Clean cone?

  • Nitrogen pressure?


Got peaks?

Check flow into probe

“Stupid” things

Method Development injection




  • Chemical issue

  • Clog before or in MRA valve


Inject compound(s) known to work- MS injection

  • Method development screen

  • Verifies MS working

  • Verifies most functions of Fluid Interface

  • Limits location of clog (if one exists)

Trouble shooting flow chart

Flow = 0.5 or 0.2 mL/min?

Works now?

Clean probe and test injection again

Check flow into probe




  • Clog between pump and probe

  • Leak between pump and probe

Run known sample on CombiFlash

MRA- Continued

  • Check flow into probe- 0.2 mL/min or 0.5 mL/min

  • Check Pulse Dampener pressure reading- verify flow

Mass Spectrometer

  • Use 0.5 or 1 mL glass syringe

  • Full with fluid, push fluid through probe

  • This cleans clogs, make sure flow is straight (if not, bent tip)

Trouble shooting

Sample run Ok?

Run known sample on CombiFlash

Clean Capillary




Call Tech Service

Fix CombiFlashissue

Run known sample on CombiFlash

  • Last of the “simple things”

  • If this works, system working fine

  • Even Test Mix A checks Rf-200

MS- Capillary

  • Shut down MS completely

  • Shut off roughing pump

  • Remove cone- watch o-rings!!!

  • Use 1/16” HPLC fittings

  • Use methanol to purge plug

  • Sonication in MeOH or DCM may be needed too

Chemical Issues- weak or no Molecular Ion

  • Compound doesn’t ionize

  • Needs different ionization mode

  • Compound breaks down

  • Compound forms adduct [M+MeOH + H], [M+Na]

Case Study

  • λmax 200-220 nm

  • [M+1] = 141 Da expected

  • Solvent system Hexane/EtOAc

  • User advised to use a range of masses, would get weak peak @ m/z 123

Chemical Case Study

Not charged- not seen. Major product (loss of another hydrogen between methyls

Very minor product- charged, m/z=122 or 123 (depending on loss of H)

H+ binds to non-bonding electrons on oxygen

Good leaving groups

  • -NH2 (leaves as ammonia)

  • -OH (leaves as water)

  • COOH (leaves as CO2)

  • Look for increase in conjugation

  • Look for easily formed, stable molecules


  • Bond to the molecule- usually detected as [M+H+Adduct]

  • May be more intense than [M+1]

Adduct List

Adduct example & sources

  • Solvent

  • Glassware

  • Syringe

Adducts- potential confusion

  • Sample dissolved in methanol- use method development, [M+MeOH+H] observed. Purification in hexane/ethyl acetate- will you see adduct?

  • Sample run on LC-MS mobile phase water/MeCN, [M+MeCN+H] observed. Purification in hexane/ethyl acetate- will you see adduct?

  • Use a range that covers [M] through [M+adduct]

Compound won’t ionize


  • Use method development screen, use positive or negative mode

  • Try APCI (if using electrospray)

  • Carrier solvent?

Routine maintenance

  • Cleaning cone

  • Vacuum pump oil

  • Detector (Tech service task- after at least a year)

Cleaning cone

  • Put MS into Stand-by

  • Wait 5 minutes for cool-down

  • Unplug

Cleaning Cone

  • Remove probe

  • Remove housing

Clean the cone

  • Clean the cone with solvent and a wipe

  • Note o-ring & plug

  • Replace housing

Replace probe

  • Replace probe- note switch on top of housing

  • Replace probe carefully so tip isn’t damaged!


  • Desolvation gas

  • Nebulization gas

  • APCI gas (APCI probe)

  • Plug in probe electric

  • Replace solvent inlet line

  • What could possibly go wrong?


  • Tuning files on CombiFlash system

  • Contain probe/analyzer/ detector parameters for a particular MS unit

  • MS and CombiFlash are “paired”

  • Don’t swap an CombiFlash without its MS!

Mismatched tune files- one symptom:


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