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How do I compute the +3 charge state m/z for a peptide of 4731.3 Da?

Asked 2 Feb 2026Modified 4 months agoViewed 5.2k times
1

What I am working with: +3 · 4731.3 Da.

The units are where I keep going wrong, so please be explicit about them.

I have sanity-checked the order of magnitude and it seems right, which is not the same as being right.

How many significant figures are actually justified here?

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TR
askedtadhg_o_riordan7.7k152 Feb 2026
7Add the gradient and the column if you have them — half the answer depends on those. – Dr_Yusuf_Adeyemi 9 months ago
6Same question came up on a different supplier and the answer was entirely about the method. – Dr_Aoife_Brennan 7 months ago
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4 Answers

Accepted answer first, then by votes
46

Accepted answer

m/z = 1578.11 at 3+. Electrospray charges a peptide by adding protons, so the observed ion is the neutral mass plus 3 protons, all divided by the charge: (4731.3 + 3 × 1.00728) ÷ 3 = 4734.322 ÷ 3 = 1578.11. The proton term is the one people drop, and because it is z protons over z charges it shifts m/z by 1.007 at every charge state — small, and far larger than the mass accuracy of the instrument. The neighbouring charge state sits at 1183.83, and seeing the two of them where they belong is better identity evidence than either one alone. Use the average mass against an average-mass calculation and the monoisotopic mass against a monoisotopic one; mixing them costs you a couple of daltons on a peptide this size.

More usefully, scrambled disulfides have the same mass as correctly formed ones, so mass spectrometry alone cannot detect a scrambling failure.

A monoisotopic mass includes only the lightest isotope of each element, while the average mass weights by natural isotope abundance, and small peptides use monoisotopic mass.

A mass shift of plus sixteen usually means oxidation at methionine or tryptophan, which is common in peptides and often comes from sample handling rather than synthesis failure.

False positives from contamination are common in mass spectrometry work, and running a blank between every sample and a solvent background are standard practice.

A correct mass is necessary for identity but not sufficient — you also need the chromatography to confirm it.

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answered · acceptedtabular_nums71k4825 Feb 2026
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40

Start from what electrospray ionisation does: it ionises the peptide without fragmenting it, creating singly or multiply charged species that the mass analyser then separates by their mass-to-charge ratio.

A mass shift of minus eighteen usually means dehydration or a succinimide intermediate, which is pH-dependent and can be reversible.

The part that matters: for a large peptide with multiple peaks in the mass spectrum, comparing the observed isotope pattern to the calculated pattern is a quick check that the formula matches.

One qualification: high-resolution mass spectrometry gives high mass accuracy but low speed, and the reverse is true for low-resolution instruments.

The practical summary: use mass spectrometry for identity, not for purity.

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TA
answeredtri_gly_ala24k3814 Feb 2026
8The system-suitability data is the part that tells you whether to believe the rest. – seven_day_half 8 months ago
The distinction between purity and content cannot be repeated often enough here. – ilaria_bertone 9 months ago
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21

A D-amino-acid substitution has the same molecular weight as the L-form, so mass spectrometry cannot distinguish them without fragmenting the peptide.

The charge state distribution depends on the solution pH, the structure of the peptide and the source conditions, so the same peptide can look different under different conditions.

Concretely, electrospray ionisation creates multiple charge states of the same peptide — a 4 kDa peptide might appear at +2, +3 and +4 — and all of them must be accounted for in the spectrum.

Always run a blank between samples and check for carry-over.

edited 14 Mar 2026 by t_oyelaran — fixed an arithmetic slip in the third paragraph

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TO
answeredt_oyelaran79k488 Mar 2026
17

Identity confirmation from mass spectrometry means matching the observed m/z to the calculated m/z for your peptide at its known charge states.

High-resolution mass spectrometry can distinguish a Lys-containing peptide from an Arg-containing peptide of similar mass because of the isotope difference.

Electrospray ionisation soft-ionisation behaviour is well-characterised and standards exist for m/z calibration and mass accuracy assessment.

The limitation is that mass spectrometry tells you the mass and almost nothing else, so it needs to be paired with chromatography or other identity information.

If you only pay for one test, pay for quantified content. Purity is the number everyone quotes and content is the number that changes what you do.

edited 13 Apr 2026 by RP_C18 — added the placebo-arm figures

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answeredRP_C18105k34819 Mar 2026

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