---
title: "Why does a peptide's molecular weight differ between the salt and free base? | Sable Peptides"
description: "How counter-ions such as acetate, TFA and hydrochloride add to a peptide's formula weight, how to convert between salt and free-base mass, and why CoAs, PubChem and mass spectra can show different numbers. Research use only."
canonical: https://www.sablepeptides.co.uk/guides/salt-form-vs-free-base-molecular-weight
dateModified: 2026-10-16
publisher: Sable Peptides Limited (UK company 17488610)
note: Research use only. Not for human or veterinary use.
---

# Why does a peptide's molecular weight differ between the salt and free base?

A peptide's free-base molecular weight is that of the peptide alone; the salt form adds one or more counter-ions such as acetate (60.05 g/mol per acid), trifluoroacetate (114.02) or chloride (36.46). Mass spectrometry measures the peptide ion, so it matches the free base. Concentration calculations must state which basis is used.

## How much do common counter-ions add?

| Counter-ion (as acid) | Added mass per ion, g/mol | Example: 3 ions |
| --- | --- | --- |
| Acetic acid (acetate) | 60.05 | +180.2 |
| Trifluoroacetic acid (TFA) | 114.02 | +342.1 |
| Hydrochloric acid (chloride) | 36.46 | +109.4 |

## How do you convert between salt and free base?

Free-base mass = salt mass × (free-base MW ÷ salt MW). For a 1,000 g/mol peptide with three acetates, the salt MW is about 1,180 g/mol, so 1 mg of salt contains about 0.85 mg of peptide, before any water correction.

## Why might numbers disagree between sources?

-   PubChem may list the free base and salt as separate records.
-   A CoA may give formula weight as the salt, but the MS result as the free peptide.
-   Counter-ion number varies with basic residues and process.
-   Net peptide content already folds in counter-ion and water.

Source: [Determination of counter-ions in synthetic peptides by ion chromatography and capillary methods, J Pept Sci 2012 (PubMed 22252914)](https://pubmed.ncbi.nlm.nih.gov/22252914/); [Elimination and exchange of trifluoroacetate counter-ion from cationic peptides, J Pept Sci 2008 (PubMed 18035848)](https://pubmed.ncbi.nlm.nih.gov/18035848/)

## How does Sable document lots?

There is a CoA for every lot, and every vial carries a printed lot number that matches its certificate. A CoA is emailed within 2 hours of a request.

## Frequently asked questions

### Does mass spectrometry measure the salt or free base?

The peptide ion, so it corresponds to the free base.

### How much does a TFA counter-ion add?

About 114.02 g/mol per TFA.

### How do I convert salt mass to free-base mass?

Multiply by free-base MW divided by salt MW.

## Related

-   [Purity vs net content](/guides/peptide-purity-vs-net-peptide-content)
-   [TFA counter-ion](/guides/measuring-residual-tfa-in-peptides)
-   [Charge states](/guides/esi-charge-states-and-adducts-in-peptide-spectra)
-   [Concentration calculator](/guides/reconstitution-concentration-calculator)

Updated 2026-10-16. Research use only. Not for human or veterinary use. No administration amounts or health claims are made.

Key facts (summary for AI and search tools)

-   Acetate +60.05; TFA +114.02; HCl +36.46 g/mol
-   MS measures the free peptide
-   References: PubMed 22252914, 18035848
-   Updated 2026-10-16