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8.What salt form should I use?
Peptides are usually delivered as TFA salts. If residual TFA would be problematic for your experiment, we recommend other salt forms such as acetate and hydrochloride. These salt forms are usually 20-30% more expensive than the regular TFA salt because of the peptide loss that takes place during the salt conversion and the greater amounts of raw materials required.
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Peptide Purity is the percentage target sequence amongst the total quantity of peptides. Because peptide bond formation in synthesis is not 100% efficient, not all polypeptide chains are the target sequence. Some chains may not go to completion, or amino acids may not properly bond on certain chains. These deleted sequences make up a certain percentage of peptides in your mixture. We analyze and purify crude peptides using Reverse Phase HPLC in conjunction with Mass Spec Analysis to attain the desired target sequence purity.
After your peptide is purified and lyophilized, the white peptide powder will contain some non-peptide components such as water, absorbed solvents, counter ions and salts. Net peptide content consists of the actual percentage weight of peptide in your final product. This number varies, anywhere from 50 to 90 percent, depending on the purity, sequence and method of synthesis and purification. When calculating the concentration of peptide solution for biological assays or other sensitive peptide experiments, it is essential that you account for peptide content. Peptide concentrations can be determined by subtracting away the non-peptide weight determining the volume of solvent in which to dissolve. For example, when using 1mg of final product to make a 1mg/ml solution of peptide with a content of 80%, you would use 800ul of solvent instead of 1000ul.
Peptide content is not an indication of peptide purity; these are two measurements. Purity is determined by HPLC and indicates the presence/absence of contaminating peptides with undesired sequences. Net peptide content only gives information on the percent of total peptide versus total non-peptide components independently of the presence of multiple peptides. Net peptide content is accurately found by performing amino acid analysis or UV spectrophotometry.
It is difficult to determine the actual peptide concentration based on the weight of the lyophilized peptide. Lyophilized peptides may contain 10-70% water and salts by weight. More hydrophilic peptides generally contain more bound water and salts compared to hydrophobic peptides.
If the peptide has a chromophore in the sequence (W or Y residues), peptide concentration can be conveniently determined based on the extinction coefficient of these residues.
The following steps can be used for the calculations:
Molar extinction coefficients of chromophoric residues at 280 nm at neutral pH using a 1-cm cell:
Tryptophan 5560 AU/mmole/ml
Tyrosine 1200 AU/mmole/ml
The extinction coefficient of each chromophore in the peptide sequence is generally considered to be additive, that is, the overall molar extinction coefficient of the peptide depends on the types and number of these choromophoric residues in the sequence.
Calculations: mg peptide per ml = (A280 x DF x MW) / e, where A280 is the actual absorbance of the solution at 280 nm in a 1-cm cell, DF is the dilution factor, MW is the molecular weight of the peptide and e is the molar extinction coefficient of each chromophore at 280 nm
Hypothetical example: A 50X diluted solution of a peptide with the sequence GRKKRRQRRRPPQQ (MW = 1847) reads 0.5 AU at 280 nm in a 1-cm cell. To calculate the original peptide concentration in the stock peptide solution:
Mg peptide/ml = (0.5AU x 50 x 1847 mg/mmole) / [(1 x 5560) + (2 x 1200)] AU/mmole/ml = 5.8
Cautions:
Any absorbance calculation assumes that the peptide is unfolded and the chromophores are exposed, which is usually the case in short, soluble peptides. If there are doubts about the solubility or the folding of the peptide, it is advisable to make the measurement under denaturing conditions (e.g., 6M GdnHCl or 8M urea). Obviously, these peptide solutions will be rendered useless, unless the denaturants are removed.
If the sequence does not have Trp or Tyr, the only practical option is to do amino acid analysis.
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