Dear Sir
I prepared a mobile phase (0.1% Water and 0.1% Acetonitrile) and it is used in LC-MS/MS analysis to identify phytochemical. I can not understand any difficulties during the test, but some literature strongly claims to use trifluoroacetic acid in the mobile phase because it has a strong inhibitory effect on the mass spectrometers negative ions.
I want to know from an expert. Is trifluoroacetic acid always shown a strong inhibitory effect on the mass spectrometer negative ions in LC-MS/MS analysis??
Thank you
TFA is not recommended for use with LC-MS methods. It often results in long-term contamination of the entire flow path of the instrument, column and source ($$$) due to its ability to bind to metals and plastics, then slowly leach off over time. It also is known to suppress MS ionization in various modes too (application dependent). Use of ion pairing agents such as TFA also result in changes to the surface chemistry of any HPLC columns used so be sure to: (1) label and column used with any ion-pairing reagent and (2) only use with specific samples, not for method development (use a new column for that).
If the acid is needed as part of the method (unrelated to the MS) to retain all of the peaks in the same form (ionized or non-ionized), then you still will need to use an acid in the method, but use something other than TFA.
Many LC-MS (ESI) methods benefit from the addition of an acid to enhance ion formation. Once of the most popular acids used is Formic Acid (which does not result in contamination of the system or suppress ion formation. In fact, it enhances it).
Additional info on suitable LC-MS acids can be found in this free article;
- "Popular LC/MS and HPLC Volatile Mobile Phase Modifiers"; https://hplctips.blogspot.com/2014/06/popular-hplc-volatile-mobile-phase.html
PS: I see that you wrote your mobile phase consists of: "mobile phase (0.1% Water and 0.1% Acetonitrile)". That does not make any sense and I think you may have made a typo. Perhaps you meant: (A) 0.1% TFA in WATER and (B) 0.1% TFA in ACN) ? If you method pH allows, perhaps try a more suitable acid such as Formic Acid (0.1%) for LC-MS applications, not TFA.
Ion pair agents are sticky and may produce irreproducible signal intensities at API sources. Consistent usage can decrease the ion intensities day by day due to its effects on limiting the charge transfers at APCI but also quenching the conductivity dependent ionization at ESI. Furthermore, I have read once it may also alter the Taylor cone formation during ionization.
Instead of the usage of TFA, when formic acid is insufficient, I would prefer DFA (ionhance) to get a bit higher sensitivity than TFA and for getting a similar resolution like TFA.
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