Exchanging Out TFA from Synthetic Peptide Preparations: Why it’s Important and How to do it Effectively

Trifluoroacetate (TFA) counterions intrinsic to synthetically prepared peptides can interfere with physicochemical characterization of the peptidic material and can alter the results of downstream biological assays. Accordingly, it is important that purified peptides be free of TFA salts; nevertheless, investigators new to peptide analysis may not be fully aware of the effects of TFA, and because the ion pairing is extremely strong, requiring an additional ion replacement step to remove TFA from the crude or purified peptides, commercially available peptides contain varying levels of TFA contamination. In this case study, we show how TFA salts hamper peptide analysis by FTIR spectroscopy. Subsequently, we present a detailed method by which TFA can be exchanged for HCl, with the goal of increasing the reproducibility and accuracy of peptide-based assays.

Why removing TFA from synthetic peptides is relevant

The majority of synthetic peptides are still manufactured by solid-phase procedures. Due to the cleavage and standardized purification steps, the resulting product usually contains TFA salts. TFA binds to the free amino termini as well as the side chains of positively charged lysine, histidine, and arginine residues. This ion pairing is strong and requires an additional ion replacement step to remove TFA from the crude or purified peptides. Thus, in general, commercially available peptides contain varying levels of TFA.

The presence of TFA in the peptidic material not only interferes with physicochemical characterization but also affects biological studies. Several investigations have documented the influence of TFA on peptide structure. For example, characterization of synthetic beta-amyloid peptide has shown the strong influence of TFA counterions on the physicochemical properties of these peptides (Shen, 1994). In particular, it has been shown that TFA can change the secondary structure, solubility, and aggregation propensity of synthetic amyloid beta peptides, and even affect the ultimate size, flexibility, and geometry of amyloid beta fibrils (Hilbich, 1991; Burdick, 1992). Therefore, it is not surprising that even small amounts of TFA can alter results of in vivo studies (Cornish, 1999; Ma, 1990) and that TFA present on peptidic material hampers sample characterization by FTIR spectroscopy. TFA has a strong infrared (IR) absorption band at 1673 cm⁻¹, significantly overlapping or even completely obscuring the amide I band of a peptide (Surewicz, 1988 and 1989). The TFA salt has to be removed from the peptide in order to be able to use IR absorption spectroscopy for physicochemical characterization or concentration determination of the peptide. In addition, bound TFA can alter the apparent mass of a peptide as determined by weighing. A single TFA molecule bound to a peptide is equivalent to adding an amino acid (113 Da) to the sequence. For this reason, peptide preparations reported as being “>98 percent pure (by HPLC)” often have true peptide content of only around 70 percent.

How to remove TFA from synthetic peptides

Excess, unbound TFA can be easily removed from a synthetic peptide preparation by freeze-drying; however, removal of the TFA counterions that are in direct contact with positively charged peptide residues is more challenging. Several exchange procedures can be found in the literature, including: 1) high-performance liquid chromatography (HPLC) separation; 2) ion exchange chromatography; and 3) adding a strong base to selectively render the peptide insoluble so that the TFA salt-containing supernatant can be removed.

A convenient and popular procedure involves mixing the peptide with a solution of an acid stronger than TFA and a freeze-drying step. Here, we present a detailed protocol, adapted from the method reported by VV Andrushchenko and colleagues (J Pept Sci. 2007), for replacement of TFA counterions by hydrochloric acid (HCl).

How to remove trifluoroacetic acid (TFA) from synthetic peptides using HCl

1. Dissolve the peptide in Milli-Q water aiming at final concentration around 1 mg (weight) per 1 mL of solvent.

NOTE: Phosphate buffer (50mM phosphate and 100mM NaCl) can be used instead of Milli-Q water

NOTE: Save around 10 µL or more for comparative mid-infrared analysis by Direct Detect spectrometer*.

2. Add 100 mM HCl to the peptide solution to achieve the final HCl concentration between 2 mM and 10 mM.

NOTE: HCl concentration below 2 mM may result in incomplete TFA exchange.

NOTE: Depending on peptide sequence concentrations above 10 mM might result in irreversible changes to the peptide.

3. Allow the solution to stand at room temperature (RT) for at least a minute.

4. Freeze the solution in liquid nitrogen.

5. Lyophilize overnight or until all liquid is removed.

6. Re-dissolve the sample in HCl solution.

7. Freeze the solution in liquid nitrogen.

8. Lyophilize overnight or until all liquid is removed.

9. Repeat steps 6 to 8 at least two times.

10. After final lyophilization step re-dissolve the peptide in Milli-Q water at around 2 mg (weight) per 1 mL of solvent.

11. Use 10 µL of the final sample for analysis in the Direct Detect spectrometer to determine the degree to which TFA has been removed.

Monitoring TFA removal using IR spectrometry.

IR spectrometry can be an accurate, convenient, nondestructive way to monitor TFA removal. Use the Direct Detect mid-infrared spectrometer (Figure 1) for this procedure. First, obtain a peptide standard, dissolved in water and initial concentration estimated by amino acid analysis. Using serial dilutions of this standard, generate a standard curve and calibrate the spectrometer as directed in the user guide. To monitor TFA content in the samples from step 11, spot samples in triplicate, using water as a blank, on assay-free cards and analyze them in the spectrometer. Because the analysis requires only 2 µL per spot, only a minimal amount of peptide is consumed.

In conclusion, monitoring and removing TFA contamination from peptide preparations is helpful for drawing conclusions about the relationships between the structure of a peptide and its chemical/biological properties. Even analysts without specialized expertise in peptide biochemistry or spectroscopic analysis can easily perform the method outlined here.