Answer first
Intact-mass analysis asks whether the measured molecular mass agrees with an expected value. Sequence-level evidence asks where fragments or other observations support the proposed order and modification context. They are related but not interchangeable conclusions.
Where this framework helps
- Defining identity evidence for a modified or longer peptide
- Reviewing whether a mass report answers the project question
- Planning orthogonal evidence for research-standard qualification
Limits to keep visible
- Mass agreement can be consistent with more than one structural explanation.
- Fragment coverage varies with sequence, modification, instrument, and workflow.
- This guide does not prescribe a universal sequence-coverage threshold.
Intact mass is a whole-molecule comparison
The result compares an observed mass or deconvoluted mass with the expected molecular form. The packet should state which form is expected, including relevant modification and composition assumptions.
Fragment evidence adds localization
A fragment-level workflow can support portions of a proposed sequence or modification pattern. The report should state the method, interpretation approach, observed evidence, and unresolved regions instead of reducing the result to a single pass label.
Use orthogonal evidence deliberately
Identity confidence is stronger when independent evidence addresses different failure modes. The appropriate combination depends on the material and intended research use, not a fixed marketing checklist.
Primary and official sources
References used for this page
- ICH Q2(R2): Validation of Analytical ProceduresInternational Council for Harmonisation
Visible FAQ
Questions research teams ask
Is a mass match a sequence confirmation?
No. It supports agreement with an expected molecular mass. Sequence confirmation requires evidence that addresses sequence order or localized structural features at the depth the project needs.
Should every peptide request LC-MS/MS?
Not automatically. The need depends on the research question, analyte, available workflow, risk, and whether other identity evidence is sufficient for the intended purpose.
What should a mass report identify?
It should identify the sample and lot, expected molecular form, method or acquisition context, observed result, calculation or deconvolution basis, and the conclusion's limitations.