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name: interpret-chromatogram locale: caveman-ultra source_locale: en source_commit: 82c77053 fence_basis_commit: 82c77053 translator: "Julius Brussee homage — caveman" translation_date: "2026-04-24" description: > Interpret chromatogram (GC/HPLC) — verify system suitability, id peaks by tR + spectral match, integrate, calc figures of merit, assess peak quality → reliable quant. license: MIT allowed-tools: Read Grep Glob WebFetch WebSearch metadata: author: Philipp Thoss version: "1.0" domain: chromatography complexity: intermediate language: natural tags: chromatography, peak-analysis, resolution, integration, system-suitability

Interpret a Chromatogram

Systematic interpret GC/HPLC → system suitability, peak id, integration, param calc, peak quality → confident qual+quant.

Use When

• Review chrom data before reporting
• Verify system suitability passes before sample seq
• ID unknown peaks / confirm analytes by tR / spectral
• Troubleshoot peaks, baseline anomalies, integration artifacts
• Train analysts → interpret

In

Req

• Chromatogram: Digital/printed w/ time + detector axes
• Ref standard: tR + response of known analytes (same method)
• Method params: Column, mobile phase/carrier, temp/gradient, detector

Opt

• Spectral: UV-Vis (DAD), MS, or other → peak confirm
• Prior chroms: Historical data (same method) → trend
• Suitability criteria: Method / regulatory limits
• Prep details: Dilution, recovery, IS conc

Do

Step 1: Verify System Suitability

Confirm system in spec before interpret.

Parameter	Typical Specification	Calculation
Retention time RSD	<= 1.0%	RSD of tR over n >= 5 injections
Peak area RSD	<= 2.0% (assay), <= 5.0% (impurity)	RSD of area over n >= 5 injections
Tailing factor (T)	0.8-2.0 (USP), ideally 0.9-1.2	T = W0.05 / (2 * f) where W0.05 = width at 5% height, f = front half-width
Resolution (Rs)	>= 1.5 (baseline), >= 2.0 (regulated)	Rs = 2(tR2 - tR1) / (w1 + w2)
Theoretical plates (N)	Per column spec (e.g., >= 2000)	N = 16(tR / w)^2 or N = 5.54(tR / w0.5)^2
Capacity factor (k')	2.0-10.0 for primary analyte	k' = (tR - t0) / t0

1. Locate suitability injections (usually 5-6 replicates ref std at seq start)
2. Calc each param
3. Compare vs acceptance criteria
4. Any fail → system not suitable → don't proceed till fixed
5. Doc results in batch record

→ All params in spec → system fit for purpose.

If err: tR RSD fails → check temp instability, mobile phase prep err, column degrade. Tailing fails → inspect inlet liner (GC) / column frit (HPLC). Res fails → test mix → replace column if needed.

Step 2: ID Peaks

1. Compare peak tR vs ref std chrom
   • Acceptable: ±2% of ref tR (or ±0.1 min short runs)
2. Ambiguous → co-injection (spike): add std to sample, re-inject. Target peak increases w/o broaden/shoulder.
3. DAD HPLC: compare UV-Vis spectrum vs lib
   • Match index ≥ 990/1000 → positive ID
   • Check spectral purity across peak (front/apex/tail overlay)
4. MS: confirm molecular ion (m/z) + key frag ions vs ref
5. Flag unidentified → "unknown" w/ tR + rel response

→ All targets ID'd by tR match w/ spectral confirm where avail. Unknowns flagged w/ tR + area.

If err: tR uniformly shifted → systematic change (column age, temp drift, mobile phase err). Re-inject std → establish current tRs before re-eval.

Step 3: Integrate

1. Select mode:
   • Auto w/ data sys defaults → start
   • Manual only when auto demonstrably misplaces baseline / peak boundary
2. Set params:
   • Baseline sensitivity (slope / threshold)
   • Min area/height → reject noise
   • Peak width matches narrowest expected
3. Verify baseline:
   • Connects start+end of peak at true baseline
   • Overlap → valley-to-valley / perpendicular drop per method
   • Gradient: rising baseline → tangent/exponential skim
4. Check integration errs:
   • Split peaks as 2 when should be 1
   • Shoulder merged into main peak when should be sep
   • Noise spikes as peaks
   • Baseline thru peak (neg clip)
5. Record final params + any manual + justification in audit trail

→ All targets integrated, correct baseline, no artifacts, manual docs w/ rationale.

If err: Auto consistently mishandles peak shape → timed-events integration w/ custom params for that window. Never adjust to achieve desired result → adjustments must be sci justified.

Step 4: Calc Chrom Params

Calc for all reported peaks:

1. Resolution (Rs) adjacent:
   • Rs = 2(tR2 - tR1) / (w1 + w2)
   • Rs ≥ 1.5 → baseline sep; ≥ 2.0 → routine margin
2. Tailing (T) at 5% height:
   • T = W0.05 / (2f)
   • 1.0 symmetric; >2.0 → significant tail
3. Plates (N):
   • N = 16(tR / w)^2 baseline w, or N = 5.54(tR / w0.5)^2 half-h
   • Higher → better efficiency
4. Capacity (k'):
   • k' = (tR - t0) / t0, t0 = dead time (void vol / flow)
   • Ideal 2-10 → good sep + reasonable run
5. Selectivity (α) critical pair:
   • α = k'2 / k'1
   • α > 1.05 → adequate sep
6. Tabulate all, compare vs method spec

→ All params calc, tabulated, compared vs criteria. Critical pair res + plate count documented.

If err: Plates below spec → column may be degraded → test fresh std, compare historical. Params drift in seq → investigate instrument stability.

Step 5: Assess Peak Quality

1. Symmetry: Gaussian / near-Gaussian. Fronting (T < 0.8) → overload; tailing (T > 1.5) → secondary interactions / dead vol.
2. Baseline sep: Quant → critical pairs must be baseline-resolved. Valley no return → note % valley + assess accuracy impact.
3. Peak width consistency: Broader than expected (vs std) → on-column degradation, extra-column broadening, injection issues.
4. Spectral purity (DAD/MS): Purity index → inhomogeneity → co-eluting impurity likely. Consider method adj for better res.
5. Neg peaks / baseline disturb: Neg in UV → sample solvent absorbs more than mobile phase at λ → normal for solvent front, abnormal elsewhere.
6. Ghost peaks: In blank → carryover, contaminated mobile phase, column bleed. ID source before report.
7. Summarize quality + note limitations on reported results

→ Quality assessed per analyte. Anomalies (tail, co-elute, ghost) documented w/ data impact.

If err: Significant quality issues (co-elute confirmed by spectral impurity, ghost at analyte tR) → data may not be reportable. Flag, investigate root cause, re-run after corrective action.

Check

• Suitability params calc + in spec
• All targets ID'd by tR (± spectral)
• Unknowns flagged w/ tR + area
• Integration correct baseline, manual docs
• Res, tail, plates, k' calc for all peaks
• Quality assessed → no unresolved co-elute affecting quant
• Ghost + carryover evaluated via blank
• Results tabulated vs method acceptance

Traps

• Accept auto integration w/o review: Data sys misplaces baselines, esp shoulders, small peaks near large, gradient baselines. Visual review always.
• Confuse tR shift w/ new peak: Uniform tR shift (all move) → systematic change, not new compounds. Re-inject std → recalibrate before ID calls.
• Report peaks below noise: S/N < 3 (detection) / < 10 (quant) → don't ID / quant. Calc S/N explicit for trace peaks.
• Ignore solvent front: Void vol peak ≠ analyte. t0 correctly ID'd + excluded from reporting.
• Manual integration → target result: Adjust to pass spec = data falsification. Changes must be sci justified + audit-trailed.
• Neglect spectral purity: Clean peak can hide co-eluting impurity. Always check purity when DAD/MS avail.

→

• develop-gc-method — method dev for GC producing chrom
• develop-hplc-method — method dev for HPLC producing chrom
• troubleshoot-separation — diagnose problems found during interpret
• validate-analytical-method — formal validation of method generating data
• interpret-mass-spectrum — detailed MS interpret for GC-MS / LC-MS peak confirm