Why Pharma Is Different — and Why That Catches People Off-Guard
Most automation engineers approach their first pharma project with reasonable confidence. The engineering is familiar. The software tools are the same. The site looks like other industrial sites they have worked on. What they are not prepared for is that pharma adds an entire parallel workstream — a validation lifecycle — that runs alongside the engineering and must be managed with the same rigour as the technical delivery itself.
In non-pharma industries, documentation is generated as a byproduct of design. You build the system, then write it up. In pharma, documentation is a deliverable in its own right. A Validation Plan must be approved before testing begins. A URS must be frozen before design. Test protocols must be reviewed and approved by QA before execution — not after. Every deviation from expected test results must be formally logged, investigated, and closed. None of this is optional, and none of it is absorbed into the engineering timeline automatically. If you treat it as overhead, it will overwhelm you.
The mistakes below are not theoretical. They are patterns that appear on first pharma projects with enough regularity that experienced pharma engineers can predict them by week three of a contract. The good news: every one of them is preventable with the right preparation.
Mistake 1 — Starting Without a Validation Plan
The Validation Plan is the governing document for the entire validation effort. It defines scope, roles, document structure, acceptance criteria, and the conditions under which the system will be considered validated. Without it, every subsequent document is produced without an agreed framework — and when QA reviews your IQ protocol two months later, they have no baseline to measure it against.
Draft and get the Validation Plan approved before any design documents are issued. It does not need to be exhaustive — it needs to be agreed. A two-week delay at the start to align the VP is far cheaper than a three-week remediation exercise when QA rejects your IQ because it does not match any pre-approved scope.
VP-SYS-001 includes a phase-gate table covering eight lifecycle phases from Planning through to GMP Lifecycle support, a full deliverable register with approval columns, and a pre-built acceptance criteria table. It gives you the structure to agree upfront — without starting from a blank page.
Mistake 2 — Treating the URS as a Formality
Many first-time pharma SIs produce a URS that reads like a marketing brochure — "the system shall monitor temperature and trigger alarms." This is not a testable requirement. It cannot be traced to a test case. It tells QA nothing about thresholds, response times, alarm priorities, or what happens when the requirement is not met. A URS that cannot be tested is not a URS — it is a wishlist.
Every requirement in the URS must be testable, unambiguous, and traceable. Apply the simple test: could you write a pass/fail test case directly from this sentence? If not, the requirement is not finished. Each requirement needs a unique ID so it can be picked up in the Traceability Matrix and linked to its corresponding test case in the IQ, OQ, or PQ.
Mistake 3 — Mis-classifying the GAMP Category
The GAMP 5 software category determines the depth of validation required. Category 4 (configurable commercial software) requires configuration specification and testing. Category 5 (custom software) requires full source code review, software design specification, and unit testing evidence in addition to everything Category 4 requires. Getting this wrong does not just affect documentation — it affects the entire testing scope and can invalidate completed work if QA catches the mis-classification late.
Classify the GAMP category formally in the Validation Plan before design begins, and get QA agreement on it. Any system with bespoke code — custom function blocks, purpose-written scripts, application-specific logic — is Category 5. A standard PLC platform with custom application code is Category 5, not Category 4. When in doubt, apply the stricter category. Downgrading later requires QA justification; upgrading does not.
Mistake 4 — Building Without a Traceability Matrix
A validation package without a Traceability Matrix has no way to demonstrate that every user requirement is addressed in design and verified in testing. At audit, the question is always the same: "Show me where this requirement is tested." Without a TM, the answer is a manual trawl through every test protocol hoping to find the relevant test case — an answer that tells the auditor you do not have a controlled validation process.
Start the Traceability Matrix as soon as the URS is baselined and maintain it as a live document throughout the project. Every URS requirement gets a row. As design documents and test protocols are produced, the corresponding design reference and test case ID are added. The TM is not a document you produce at the end — it is the spine that holds the validation package together.
An FDA inspector reviewing a validated system will typically start with the URS, then ask to see the TM, then pull a sample of requirements and trace them forward to test evidence. If the TM does not exist, or if traceability gaps exist, this is an observation — and observations on validated systems can stop production. It is not bureaucracy. It is the mechanism by which the regulator knows the system does what the client said it would.
Mistake 5 — Making Changes Without Change Control
On a conventional automation project, engineering changes are informal. A verbal instruction from the client, a quick programme edit, a revised panel drawing — normal. On a pharma project, any change to a baselined document or to a system that is in or past FAT must go through formal change control. That means a written request, an impact assessment, approval before implementation, and a record of what was changed and when. Ad-hoc changes to validated systems are one of the most common audit findings on pharma sites — not because engineers are being careless, but because they do not know the rules have changed.
Establish the change control threshold at the project kickoff and make sure everyone on site knows it. A practical rule: once the Validation Plan is approved and the URS is baselined, every change to scope or design requires a CCR. Not a conversation. A written, numbered, approved request. This protects you as much as it protects the client — undocumented changes are a commercial liability as well as a regulatory one.
Mistake 6 — Not Logging Test Deviations
Test execution on a pharma project is not a trial-and-error process. When a test case fails, you cannot simply fix the underlying issue and re-run the test as if the first attempt did not happen. The failure must be formally logged as a deviation — with a description of what was observed, a root cause investigation, the corrective action taken, and QA approval of the closure. The re-test is then a separate, formally numbered execution. Without this process, the test protocol record is incomplete and the system's validation status is questionable.
Before test execution begins, establish your deviation logging process and make sure the execution team understands it. Every person executing test cases must know: if the result is not as expected, stop and log it before taking any corrective action. The deviation log is not a sign of a bad project — it is evidence that your validation process works. QA expects deviations on complex systems. What they do not expect is a clean test record on a system that was clearly modified during testing.
Mistake 7 — Skipping Supplier Assessment
Under GAMP 5, the system integrator is responsible for demonstrating that their sub-suppliers — PLC vendors, SCADA platform providers, instrument manufacturers, control panel builders — operate under a quality management system appropriate to the GMP risk of the supplied product. This is not just about ISO certification. It is about understanding whether the supplier's development processes, change control practices, and software quality controls are adequate for use in a validated system. Skipping this assessment is a gap that will appear in any client audit of your work.
Conduct and document a supplier assessment for every critical supplier before their products enter the validated system. For major platform vendors (PLC, SCADA), a desktop assessment based on documentation review is often sufficient. For custom software or firmware suppliers, a more detailed audit may be required. The output is a Supplier Assessment Report with a formal conclusion — approved, conditionally approved, or rejected.
Mistake 8 — Handing Over Without a Validation Summary Report
The Validation Summary Report is the document that closes the validation lifecycle. It summarises all testing completed, all deviations raised and resolved, all outstanding items and their risk assessment, and provides the formal conclusion that the system is validated for its intended use. Without a VSR, the client's system is never formally validated — it is commissioned but not validated. Many first-time pharma SIs finish testing, hand over their test protocols, and consider the job done. The client's QA team does not agree.
Budget time for VSR production in your project plan from the start. The Validation Summary Report requires input from all completed test protocols, the deviation log, and the change control log. It cannot be written until testing is complete, which means it often falls in the last two weeks of a project when everyone is under pressure. If it is not planned for, it will be the bottleneck that delays handover. Allow at least three days for drafting, QA review, and approval.
The Underlying Pattern
All eight of these mistakes share a root cause: treating the validation lifecycle as something that happens after the engineering, rather than something that runs in parallel with it from day one. The Validation Plan needs to be agreed before design starts. The URS needs to be testable before FAT protocols are written. The Traceability Matrix needs to grow as documents are produced, not assembled retroactively at closeout. The deviation log needs to be active before the first test case is executed.
The V-Model framework is not an academic model — it is the practical structure that prevents these failures. The left side of the V (design documents) and the right side of the V (test protocols) mirror each other. Every design decision on the left generates a test obligation on the right. When both sides are built in parallel and connected by the Traceability Matrix, none of the eight mistakes above can happen silently.
The best time to prepare for these mistakes is before the project kicks off, not during delivery. That means having your document templates ready — Validation Plan, URS, Risk Assessment, Traceability Matrix, IQ/OQ/PQ protocols, deviation log, change control log, and VSR — so that when the project starts, the structure already exists. The engineering will fill those templates. What you cannot afford is to be building the document structure from scratch while the engineering is already running.
What Experienced Pharma Engineers Do Differently
Engineers who have delivered multiple pharma projects develop a set of default behaviours that prevent these mistakes from occurring. They start every project with a VP kickoff meeting where scope, roles, and document structure are agreed before anything else. They write URS requirements with test cases already in mind — if they cannot imagine the test, the requirement is not finished. They maintain the Traceability Matrix as a shared document that is updated every time a design document or test protocol is issued.
They treat the change control threshold as a hard boundary, not a guideline. They log deviations as a matter of professional practice, not reluctantly. They budget validation effort explicitly in project quotes — not as a percentage of engineering cost, but as a separate itemised workstream with its own day count. And they finish every project with a VSR that gives the client's QA team a clean package to file.
None of this is mysterious. It is process discipline applied to a regulated environment. The engineering skills transfer directly from non-pharma work. What needs to change is the project management mindset — and the earlier that change happens, the less expensive your learning curve will be.
| Mistake | When It Hurts | Consequence |
|---|---|---|
| No Validation Plan | QA review of first protocol | No agreed baseline — entire package questioned |
| Vague URS | Traceability Matrix build | Cannot link requirements to tests — TM gaps |
| Wrong GAMP category | OQ scope agreement | Test scope underestimated — rework required |
| No Traceability Matrix | Audit or QA review | Cannot demonstrate coverage — observation risk |
| Undocumented changes | Ongoing — any audit | System validation status uncertain |
| Deviations not logged | Test protocol review | Test records incomplete — re-execution required |
| No supplier assessment | Client QA audit of SI | Gap in GMP supply chain documentation |
| No VSR | Handover | System never formally validated — no GMP release |