Chain of custody explained in peptide analysis
Chain of custody in peptide analysis: traceability from sample to laboratory result
Independent peptide analysis often focuses on the final analysis result. A laboratory report may contain information about, for example:
- molecular identity;
- HPLC purity;
- peptide content;
- residual moisture;
- endotoxins;
- sterility testing;
- possible degradation products.
However, the reliability of an analysis result depends not only on the laboratory technique used.
It must also be clear:
Which sample was examined, where did it come from, and what happened to it between sampling and analysis?
The documented route of a sample is referred to as chain of custody. In Dutch, this is often translated as:
- sample chain;
- chain of custody;
- documented sample traceability.
A well-documented chain of custody connects the original product with the final laboratory report.
When this connection is missing, a technically correct analysis result may still be difficult to link to the batch for which the report is used.
In this blog, we discuss how chain of custody works, which details are important, and why independent laboratory analysis only provides maximum value when sample identity, batch number, packaging, shipping, and receipt are carefully documented.
What does chain of custody mean?
Chain of custody is the chronological record of:
- origin of a sample;
- sample identification;
- transfer between the parties involved;
- storage;
- transport;
- receipt;
- laboratory processing.
The aim is to support the identity and traceability of the sample throughout the entire analysis process.
A chain-of-custody record can answer questions such as:
- Who selected the sample?
- Which batch did the sample come from?
- When was the sample packaged?
- What identification was on the vial?
- When was it shipped?
- When did the laboratory receive it?
- Under which laboratory code was it registered?
- Which analyses were performed?
Why is chain of custody important?
A laboratory examines the sample that is submitted.
The laboratory cannot automatically determine whether the sample is representative of:
- a complete production batch;
- all vials with the same label;
- an earlier delivery;
- a batch produced later.
Therefore, a clear connection is needed between:
- product;
- batch number;
- submitted sample;
- laboratory record;
- analysis report.
The better this connection is documented, the stronger the traceability.
What is sample identity?
Sample identity describes what material was examined.
Important details may include:
- product name;
- peptide code;
- nominal quantity;
- batch number;
- lot number;
- vial number;
- production date;
- internal sample ID.
A general description such as “peptide sample” provides little information.
A specific description with batch number supports a clearer connection.
What is the difference between a batch number and a sample ID?
A batch number usually identifies a production lot.
A sample ID identifies the specific sample selected for analysis.
A single batch can contain multiple samples.
For example:
- batch:
PEP-2026-041; - sample 1:
PEP-2026-041-A; - sample 2:
PEP-2026-041-B.
This allows multiple vials from the same batch to be tracked individually.
Why is batch linkage necessary?
An analytical result initially applies to the sample examined.
When the sample can be demonstrably traced to a specific batch, the result can be used as information about that batch.
Representativeness depends, among other things, on:
- sampling method;
- batch homogeneity;
- number of samples examined;
- production consistency.
A report without a clear lot number is more difficult to link to specific stock.
What is representative sampling?
Representative sampling means that the selected sample provides as reliable a picture as possible of the batch being examined.
This may be influenced by:
- batch size;
- production process;
- filling process;
- position of the vial in the batch;
- number of selected vials.
A single random vial can provide valuable information, but does not automatically fully describe every vial.
For critical quality assessments, multiple samples may be examined.
Who selects the sample?
The sample may be selected by:
- manufacturer;
- supplier;
- quality department;
- independent third party;
- laboratory.
The method of sample selection affects independence and representativeness.
When a supplier selects a single sample, the analysis is performed independently by the laboratory, but the sample selection is not necessarily independent.
This distinction is important.
What is independent sampling?
With independent sampling, a third party or laboratory selects the sample without the supplier determining in advance which vial will be tested.
This can strengthen the control of selection bias.
Possible forms include:
- random selection;
- stock sampling;
- on-site sampling;
- sealed transfer.
The required approach depends on the quality objective.
What is selection bias?
Selection bias occurs when the selected samples may not be representative of the entire batch.
For example, when only preselected vials are tested.
This does not automatically mean that the result is incorrect.
This means that the representativeness of the sample must be assessed separately.
What information is included on a chain-of-custody form?
A chain-of-custody form may contain:
- submitter's name;
- product name;
- peptide identity;
- batch number;
- sample ID;
- number of vials;
- nominal quantity;
- sampling date;
- shipping date;
- requested analyses;
- storage conditions;
- transfer details;
- signatures or digital confirmations.
Not every laboratory uses the same form.
Why is the shipping date important?
The shipping date helps reconstruct the timeline.
This can be used to assess:
- how long the transport took;
- when the sample reached the laboratory;
- how much time elapsed between sample collection and analysis.
This may be relevant for stability-sensitive samples.
What role does transport play?
During transport, a sample may be exposed to:
- temperature fluctuations;
- vibrations;
- light;
- delay;
- mechanical stress.
The impact depends on:
- peptide;
- lyophilized or dissolved form;
- packaging;
- transport duration;
- storage conditions.
Transport details may therefore be part of the chain of custody.
What is a sealed sample?
A sealed sample is packaged in a way that makes unauthorized opening detectable.
Possible means include:
- tamper-evident tape;
- numbered seal;
- secure sample bag;
- sealed transport container.
A seal supports the integrity of the transfer.
What does tamper-evident mean?
Tamper-evident means that possible opening or tampering can be detected.
Tamper-evident packaging does not necessarily prevent every form of access.
The main purpose is to make changes to the packaging detectable.
Why can photos be useful?
Photos can provide additional documentation of:
- vial;
- label;
- batch number;
- sealing;
- packaging;
- condition at shipment.
A photo does not replace a formal chain-of-custody record, but it can support traceability.
What happens when the sample arrives at the laboratory?
Upon receipt, the laboratory may check:
- packaging;
- number of samples;
- visible damage;
- sample label;
- requested analyses;
- consistency with the submission documents.
An internal laboratory code is then usually assigned.
This code is used during the analysis process.
Why does a laboratory use an internal code?
An internal code supports:
- sample management;
- data recording;
- analysis planning;
- reporting;
- archiving.
The internal laboratory code must be traceable back to:
- original sample;
- batch number;
- submitter;
- analysis report.
What is sample accessioning?
Sample accessioning is the formal process of registering a received sample in the laboratory system.
This may include:
- checking the packaging;
- verifying the label;
- recording sample data;
- assigning a laboratory ID;
- recording storage conditions;
- analysis planning.
A careful accessioning process reduces the risk of mix-ups.
How is sample mix-up limited?
Laboratories can use various measures:
- unique barcodes;
- internal sample IDs;
- digital records;
- duplicate checks;
- separate storage;
- controlled work procedures.
The exact quality procedures vary by laboratory.
What is an audit trail?
An audit trail is a verifiable record of changes and actions.
For example, a digital laboratory system can record:
- who entered the data;
- when data were modified;
- which analysis was performed;
- when results were approved.
An audit trail supports transparency and data integrity.
What is a LIMS?
LIMS stands for:
Laboratory Information Management System
A LIMS is used to manage:
- samples;
- laboratory codes;
- analytical tasks;
- results;
- reports;
- audit trails.
A LIMS can support traceability within the laboratory.
How is the sample stored before analysis?
The storage conditions must be appropriate for the type of sample.
Possible conditions include:
- controlled room temperature;
- refrigerated storage;
- deep-freeze storage;
- protection from light.
Important data include:
- storage temperature;
- storage duration;
- packaging;
- date of analysis.
Why is the sample's condition important?
A lyophilized sample and a dissolved sample have different stability characteristics.
Therefore, the following must be clearly recorded:
- physical form;
- amount;
- solvent, where applicable;
- concentration, if known.
Uncertainty can affect the interpretation of results.
What happens during sample preparation?
Before analysis, the sample may be:
- weighed;
- dissolved;
- diluted;
- filtered;
- divided among analysis tubes.
Each step must be performed according to a documented method.
Possible sources of variation include:
- pipetting deviations;
- incomplete dissolution;
- material loss;
- adsorption to surfaces;
- dilution errors.
Why is documenting sample preparation important?
An analytical result depends not only on the instrument.
Sample preparation can also affect the outcome.
Therefore, laboratories can record:
- amount used;
- solvent;
- dilution factor;
- equipment used;
- performing analyst;
- time of preparation.
Chain of custody and HPLC analysis
In HPLC, the prepared sample is examined chromatographically.
The chain of custody must preserve the connection between:
- original vial;
- laboratory ID;
- prepared solution;
- HPLC injection;
- chromatogram;
- final report.
This makes it possible to determine which chromatogram belongs to which sample.
Chain of custody and mass spectrometry
The same principle applies to mass spectrometry.
The recorded data must link the mass spectrum to:
- sample ID;
- batch number;
- analytical method;
- measurement date.
A spectrum without reliable sample linkage has limited traceability.
What is data integrity?
Data integrity means that data are:
- complete;
- correct;
- traceable;
- protected;
- being verifiable.
Laboratory quality often involves principles such as:
- assignability;
- readability;
- timeliness;
- originality;
- accuracy.
Reliable analysis requires both technical measurement quality and reliable data recording.
What is an independent laboratory?
An independent laboratory performs analyses without being part of the production organization that made the product.
This can contribute to:
- a more objective assessment;
- external verification;
- additional quality control.
However, independent analysis does not automatically mean that the entire sample chain is independent.
The way the sample was selected and submitted remains relevant.
What should be included in a laboratory report?
A useful report preferably contains:
- sample name;
- sample ID;
- batch number;
- analytical method;
- analytical result;
- analysis date;
- laboratory data;
- any specifications;
- responsible review.
Depending on the analysis, the following may also be added:
- chromatograms;
- mass spectra;
- calibration data;
- measurement uncertainty.
Why is a QR code not sufficient?
A QR code can provide access to a digital report.
The QR code does not by itself prove:
- that the report belongs to the correct batch;
- that the sample was representative;
- that the chain of custody is complete;
- that the report has not been incorrectly linked.
The content and batch linkage remain important.
Chain of custody and COA
A Certificate of Analysis can provide valuable information about an examined batch.
The reliability of the connection is stronger when it is clear:
- which sample was tested;
- which batch it came from;
- how it was shipped;
- when it was received;
- which laboratory ID was used.
A COA without a batch number or clear sample identification provides less traceability.
Can a single test result guarantee an entire batch?
No.
A laboratory result directly describes the sample examined.
The extent to which the result says something about the entire batch depends on:
- representative sampling;
- production consistency;
- batch homogeneity;
- number of samples examined.
An analysis provides important quality information, but is not an absolute guarantee for every individual vial.
Why are retests important?
A retest may be performed when:
- a result is unexpected;
- additional verification is needed;
- stability over time is being investigated;
- a new analytical method is being applied.
For a retest, it must be clear:
- whether the same sample was used;
- whether a new vial was selected;
- which batch the sample came from.
What is a retain sample?
A retain sample is a preserved reference sample from a batch.
This sample may later be used for:
- retesting;
- stability studies;
- investigation of deviations;
- comparison with previous results.
Retain samples must be clearly identified and stored under documented conditions.
Scientific limitations
A well-documented chain of custody supports traceability but does not automatically prove:
- batch homogeneity;
- complete product quality;
- sterility;
- biological activity;
- long-term stability.
Separate quality studies are required for this.
Chain of custody primarily describes the reliability of the connection between the sample, analysis, and report.
Summary
Chain of custody is the documented path of a sample from selection to the laboratory report.
Important components include:
- product name;
- batch number;
- sample ID;
- sample selection;
- packaging;
- sealing;
- shipment;
- receipt;
- laboratory record;
- analysis;
- reporting.
A laboratory result can only be reliably linked to a batch when it is clear which sample was actually tested.
Independent laboratory analysis and independent sample collection are not the same.
For strong traceability, sample identity, transfer, storage, analytical data, and reporting must be logically connected.
Research Disclaimer
Peptidera’s research peptides are offered exclusively for Research Use Only (RUO) and are intended for laboratory research and analytical applications.
Not intended for human or animal consumption, diagnostic use, therapeutic application, or self-administration.
-
ISO/IEC 17025:2017
The international standard for the competence, impartiality, and consistent operation of testing and calibration laboratories. This standard also addresses sample management, technical records, measurement traceability, and reliable reporting. -
WHO guidelines for sample collection and laboratory analysis
WHO documentation emphasizes that samples must be transported to laboratories in a controlled manner, while preserving the chain of custody and the condition of the sample. -
USP Supply Chain and Detection Technology Toolkit
USP describes sample collection, chain-of-custody documentation, secure storage, and sample retention as essential conditions for reliable test results. -
USP General Chapter <1079>
Covers risks and control measures for storage and transport within controlled distribution chains. This is relevant to temperature recording, sample transport, and maintaining product quality.
Related internal blogs:
- PB-0229 — Batch Numbers and Traceability for Peptides
- PB-0230 — Peptide Purity and HPLC
- PB-0231 — Mass Spectrometry for Peptides
- PB-0232 — Certificate of Analysis for Peptides
- PB-0240 — Stability Studies for Peptides
Internal link suggestions:
- Link to PB-0229 on batch numbers and lot traceability
- Link to PB-0232 on COAs and batch-specific analytical results
- Link to PB-0230 on HPLC analysis
- Link to PB-0231 on mass spectrometry
- Link to PB-0240 on retain samples and stability studies
- Link to the Peptidera page with independent certificates of analysis
- Link to the research peptide collection