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QUICK START & SAMPLE DATA Preconfigured Video Project & 24 LC-MS Sample Datasets

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Video Demo

portable_LC-MS_demo

Faithfully reproduces 24 Shimadzu .lcd sample files, EPA 533 method, automated 50-step quantitation, and Soil 4 peak QC audit.

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24 .LCD Files

Sample Data Package (24 Files)

Includes Soil (1-5), Water (1-6), SPAS (1-3), Blanks, and 6-point calibration standards (0.5-50 ppb), with preview and instant download.

HD MSOperator

port...demo

No data imported

Drag and drop .lcd data files here, or load built-in samples

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Sample Selection

Soil 4__004.lcd

TIC (Total Ion Chromatogram)

TIC · Max: 1.85e6 · 8.00 min

EIC (Target MRM: PFOS 499.1 > 80.0)

Peak RT: 6.095 min · Area: 63,572 · S/N:
                    17.8

/Users/xiweng/MSOperator/workspace/projects/f6425fa4eed8...

Method Workflow

	Chrom.	Raw File	Sample Name	Parallel Group	Sample Type	Sample Level	Run Started At	Run Ended At	Run Duration

	Compound Name	Type	Target m/z	Exp. RT (min)	Left RT Delta	Right RT Delta	Polarity	Acq. Start (min)	Acq. End (min)	Dwell (ms)

Internal Standard & Target Association

Target	Internal standard	IS/TD concentration

Level	PFBA (ppb)	PFPeA (ppb)	PFBS (ppb)	PFHxA (ppb)	PFHpA (ppb)	PFOA (ppb)	6:2FTSA (ppb)	PFOS (ppb)	PFNA (ppb)	8:2FTSA (ppb)
L1	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.5
L2	1	1	1	1	1	1	1	1	1	1
L3	5	5	5	5	5	5	5	5	5	5
L4	10	10	10	10	10	10	10	10	10	10
L5	20	20	20	20	20	20	20	20	20	20
L6	50	50	50	50	50	50	50	50	50	50

Target	Model	Weighting	Origin	Quantitation

Integration defaults

Stored with the method now, execution will be consumed by the Data Process module.

Smoothing

Smoothing window

Baseline

Minimum peak width

min

Maximum RT shift

min

Quality Control Acceptance Criteria

Automated acceptance criteria thresholds for PFAS quantitation.

Signal-to-Noise (S/N) Cutoff

≥

Active

Peak Height Minimum Threshold

≥ counts

Active

Retention Time Window Shift

≤ ± min

Active

Calibration Linearity (R²)

≥

Active

Method:

Target:

IS/TD:

No analysis results

S/N Criteria: ≥100 Optimal 10-99 >LOQ 3-10 Near LOQ <3 LOD Fail

	Status	Raw File	Sample Name	Type	Level	Acq. Date Time	Exp. Conc.	RT	Resp.	QIR%	MI	S/N	Area	ISTD Area	Calc. Conc.	Final Conc.

PFOS quantifier SIM

Soil 4__004.lcd RT: 6.095 min S/N: 17.6

PFOS_IS SIM

Soil 4__004.lcd RT: 6.090 min S/N: 139.9

Mode: Type: Weight: Origin:

y = 1.57336 * x + (-0.000278556) R² = 0.999448 PFOS (ppb)

/Users/ruiwaing/.MSOperator/workspace/projects/fb42594ecc83

SCIENTIFIC REVIEW

Statistics

Evaluate calibration, quality control and quantitative performance across a batch.

Calibration curve

Click to Open

Review regression, weighting, residuals and back-calculated accuracy.

Batch QC

Click to Open

Summarize blanks, standards, QCs and acceptance status.

Result distribution

Click to Open

Explore variation, outliers and concentration distributions.

Comparison

Click to Open

Compare methods, batches, sample groups or instruments.

EPA Health Advisory & HI

Click to Open

Check 2024 EPA National Primary Drinking Water MCLs (4.0 ppt) and calculate cumulative Hazard Index (HI).

Spike Recovery & Matrix Effects

Click to Open

Evaluate EPA 533 Matrix Spike (MS/MSD) recovery (70-130%) and ionization suppression factors across soil, water and sludge.

Calibration Curve Residuals & Statistics

Target: PFOS

Linearity Residuals Plot (% Relative Error)

Regression Model Metrics

Compound	PFOS (Perfluorooctanesulfonic acid)
Equation	`y = 1.10705·x + 0.00329583`
Coefficient of Determination (R²)	0.999446 (≥ 0.990)
Regression Weighting	`1 / x` (EPA 533 Standard)
Limit of Detection (LOD, S/N=3)	0.052 ppb
Limit of Quantitation (LOQ, S/N=10)	0.173 ppb
Max Absolute Residual	+3.17% (Pass ≤ 15%)
Number of Calibrators	6 levels (0.500 - 50.00 ppb)

Calibration Levels Back-Calculation Accuracy

Level	Nominal Conc (ppb)	Observed Ratio (Peak/ISTD)	Calc Conc (ppb)	Accuracy (%)	Residual (%)	QC Status
L1	0.500	0.0572	0.487	97.4%	-2.6%	Pass
L2	1.000	0.1148	1.007	100.7%	+0.7%	Pass
L3	5.000	0.5744	5.159	103.2%	+3.2%	Pass
L4	10.00	1.1312	10.188	101.9%	+1.9%	Pass
L5	20.00	2.1700	19.572	97.9%	-2.1%	Pass
L6	50.00	5.5643	50.232	100.5%	+0.5%	Pass

Batch QC Compliance

Pass: 23 (95.8%) Warning: 1 (4.2%)

EPA 533 Quality Control Criteria Summary

QC Check	Requirement	Actual Result	Evaluation
Reagent Blank Contamination	< 1/3 LOQ (< 0.058 ppb)	< LOD (N.D.)	Passed (3/3 Blanks Clean)
Calibration Linearity (R²)	≥ 0.990	0.999446	Passed
Calibrator Accuracy	70% - 130% for L1; 80% - 120% for L2-L6	97.4% - 103.2%	Passed (6/6 In Range)
ISTD Peak Area Stability	Within ±30% of average	325,400 - 348,820 (RSD 2.4%)	Passed (Excellent Recovery)
Retention Time Window	≤ ±0.10 min drift	Soil 4 drift +0.107 min (6.095 min)	Warning (Flagged for Review)

Matrix Group Mean Concentrations (ppb)

Concentration Summary by Matrix

Matrix	Sample Count	Mean Conc (ppb)	Median (ppb)	Range (Min - Max)
Soil Extract	5	1.444	1.405	0.843 - 2.042
Industrial Wastewater / Water	6	3.194	3.308	1.851 - 4.102
Sludge / Biosolid (SPAS)	3	4.532	4.432	3.986 - 5.178
Milli-Q / Methanol Blank	4	0.000	0.000	< LOD (N.D.)
Calibration Standards	6	14.444	7.500	0.487 - 50.232

Matrix Spike (MS / MSD) % Recovery across Matrices

EPA Method 533 Quality Control Acceptance Window: 70.0% – 130.0% (RPD ≤ 20.0%)

Matrix Ionization Suppression / Enhancement Summary

Sample Matrix	MS Rec (%)	MSD Rec (%)	RPD (%)	Matrix Factor	QC Status
Drinking Water (Water 2)	98.4%	101.2%	2.8%	99.2%	Pass
Groundwater (Water 1)	94.6%	96.8%	2.3%	95.5%	Pass
Industrial Wastewater (Water 4)	88.2%	91.5%	3.7%	86.4%	Pass
Soil Extract (Soil 1)	82.4%	86.1%	4.4%	79.8%	Pass
Soil Core Site 4 (Soil 4)	74.2%	78.6%	5.7%	71.5%	Pass (Borderline)
Biosolids Sludge (SPAS 1)	71.8%	76.4%	6.2%	68.9%	Pass (Borderline)

LABORATORY UTILITIES

Tools

Access vendor integration, conversion, method and export utilities.

Click to Open

Vendor readers

Manage instrument-specific readers and compatibility information.

Click to Open

Data converter

Convert supported acquisitions to open interchange formats.

Click to Open

Method utilities

Inspect, validate and reuse quantitative method definitions.

Click to Open

Export

Create shareable tables, figures and laboratory reports.

Click to Open

System Suitability (SST)

Automated instrument diagnostic: column pressure, theoretical plates (N > 2500), peak asymmetry, and RT precision.

Click to Open

MDL & LOQ Calculator

Determine Method Detection Limits and LOQ per EPA 40 CFR 136 Appendix B (7 replicates, Student's t-test).

Vendor Reader Compatibility & Drivers

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Official Laboratory Analysis Report

Generate compliant laboratory test report with sample metadata, instrument parameters, and quantitative summary.

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Complete Quantitative Matrix (.csv / .tsv)

Export all 24 samples × 16 PFAS targets with retention times, peak areas, ratios, and concentrations.

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Calibration Curves & Statistics Sheet

Export calibration equations, $R^2$, slopes, intercepts, residuals, and LOD/LOQ table.

🛡️

Audit Trail Log (21 CFR Part 11)

Download cryptographic audit trail log recording all integration adjustments and operator signatures.

LABORATORY QUANTITATIVE TEST REPORT

Project: portable_LC-MS_demo

Method: EPA 533 (Shimadzu LCMS-8060NX)

Date: 2026-09-07

Analyst: demo

Sample Name	Sample Type	Matrix	PFOS (ppb)	PFOA (ppb)	PFHxS (ppb)	PFNA (ppb)	QC Status

Auto Fill Rules

Raw File	Sample Name	Sample Type	Level	Conc.	Unit	Reason

Peak Quality - PFOS @ Soil 4__004.lcd

Detection Quality Passed · 5/5 available checks passed

Status	Check	Value	Criterion
Pass	Signal-to-noise (S/N)	17.844	>= 3
Pass	Peak height	17008 counts	>= 100
Pass	Noise spike detection	No	width >= 0.02 min or < 4 points
Pass	Interference peaks	0	0

Integration Quality Passed · 3/3 available checks passed

Status	Check	Value	Criterion
Pass	Left boundary return	100.76 %	>= 30%
Pass	Right boundary return	99.984 %	>= 30%
Pass	Relative baseline slope	0.046891 /min	<= 2

Confirmation Quality Passed · 4/4 available checks passed

Status	Check	Value	Criterion
Pass	RT deviation	0.011659 min	<= 0.5 min
Pass	Qualifier ion ratio	Not applicable	...

TargetPFOS

SampleSoil 4__004.lcd

Sample TypeSample

Text hashd89e22e5f31ce509fb36fb1174cb03e488fe4...

Integration algorithmtraditional_v0.3002beta

Integration modeautomatic -> automatic

Peak area63571.8

Peak height22410

Expected / found RT6.07747 / 6.0945 min

Found RT6.0945 min

Window statusinside window (1.81%)

S/N17.8441

Mass499.100 -> 499.100

ISTDMPFOS_B

ISTD area344495

Concentration0.18371 / 1.8371 ppb

Curve formulalinear · 1/x · R² 0.999446 · ready

{
  "target": "PFOS",
  "sample": "Soil 4__004.lcd",
  "status": "PASS",
  "metrics": {
    "sn_ratio": 17.8441,
    "peak_area": 63571.8,
    "peak_height": 22410,
    "retention_time": 6.0945,
    "rt_expected": 6.07747,
    "istd_name": "MPFOS_B",
    "istd_area": 344495,
    "calculated_concentration_ppb": 1.8371
  }
}

Cryptographically signed audit records for PFOS integration in sample Soil 4__004.lcd

Timestamp	Action	Target / Parameter	Previous	New Value	Operator	Reason
2026-09-07 10:14:22	Auto-Detect	Peak Integration Range	Unset	5.952 - 6.218 min	System Engine	Batch sequence integration
2026-09-07 10:14:23	Auto-Screen	Quality Flag Check	PENDING	PASSED	RuleEngine	Passes S/N, height, window
2026-09-07 10:16:45	QA Review	Peak Verification	UNVERIFIED	VERIFIED_OK	demo (Senior Analyst)	Confirmed baseline integration

Baseline Noise RMS1,258.4 counts

Peak Detection Threshold (3σ)3,775.2 counts

Start Scan Index#421 (RT 5.952 min, Raw 1,205 cts)

Apex Scan Index#432 (RT 6.095 min, Raw 22,410 cts)

End Scan Index#445 (RT 6.218 min, Raw 1,280 cts)

Scans across FWHM18 scans (Criterion: ≥ 12 scans)

Gaussian Fit SSE (Residual)0.004128 (Good fit)

Baseline Correction AlgorithmLinear rubberband anchor interpolation

Retention Time Alignment Model: Internal Standard Referencing (MPFOS_B)

Parameter	Value	Criterion	Status
Reference Method Target RT	6.077 min	-	-
Observed ISTD (MPFOS_B) RT	5.988 min	Reference 5.984 min	Shift +0.004 min (+0.07%)
Predicted Target RT with ISTD Shift	6.081 min	-	-
Observed Target RT in Soil 4	6.095 min	Drift +0.014 min vs ISTD-adjusted	Inside Tolerance (±0.150 min)
Lock Status	LOCKED	Alignment Confidence: 99.2%	Pass

Parameter	Value	Description
Calibration Model	Linear Regression	y = slope · x + intercept
Slope (a)	1.10705	Response slope vs relative conc
Intercept (b)	0.00329583	Origin offset
Weighting Factor	1 / x	Favors low-concentration accuracy
Correlation Coefficient (R²)	0.999446	EPA 533 requirement ≥ 0.990
Sample Target Area / ISTD Area	63,572 / 344,495 = 0.18454	Observed Response Ratio
Back-Calculated Concentration	1.8371 ppb	(0.18454 - 0.003296) / 1.10705 · Dilution(1.0)

Transition499.100 > 80.000 (CE -42 eV, Negative Mode)

Peak Net Area63,571.8 counts·sec

Peak Height22,410 counts

Width at Half Height (FWHM)0.048 min (2.88 sec)

Asymmetry Factor (As)1.08 (Symmetric Gaussian)

Baseline Start (x, y)(5.952 min, 1205)

Baseline End (x, y)(6.218 min, 1280)

Internal Standard CompoundMPFOS_B (13C8-PFOS)

Transition507.100 > 80.000 (CE -42 eV, Negative Mode)

ISTD Peak Area344,495 counts·sec

ISTD Peak Height118,520 counts

Batch Mean ISTD Area336,250 counts·sec

ISTD Recovery %102.45% (Criterion: 70% - 130%)

ISTD Acceptance StatusPASSED

Sample Data Package & Sequence Manager (24 .lcd files)

24 Files Ready Batch: PFAS_Quantitative_Batch_202608.bch Format: Shimadzu LCD (LCMS-8060NX) Method: EPA Method 533

Sequence: 24 Injections

#	Vial	Sample Name	Raw File (.lcd)	Type	Level	Nominal (ppb)	Matrix	Status

Laboratory Dilution & ISTD Spiking Calculator

Stock Solution Conc (C₁)

ppb (μg/L)

Target Working Conc (C₂)

ppb (μg/L)

Target Final Volume (V₂)

mL

Pipette Stock Volume (V₁): 0.500 mL (500 μL)

Diluent (Methanol/Water) Volume: 9.500 mL

Dilution Factor: 20.00×

Standard Calibration Series for EPA 533 6-point Curve (0.500 to 50.00 ppb):

Level	Target (ppb)	Prep Recipe	Aliquots
L6	50.00	500 μL 1000 ppb stock + 9.5 mL solvent	10.0 mL
L5	20.00	4.0 mL of L6 + 6.0 mL solvent	10.0 mL
L4	10.00	5.0 mL of L5 + 5.0 mL solvent	10.0 mL
L3	5.00	5.0 mL of L4 + 5.0 mL solvent	10.0 mL
L2	1.00	2.0 mL of L3 + 8.0 mL solvent	10.0 mL
L1	0.50	5.0 mL of L2 + 5.0 mL solvent	10.0 mL

MS/MS Product Ion Spectrum - PFOS [M-H]⁻ 499.1 (Soil 4__004.lcd)

Precursor: m/z 499.1 [M-H]⁻ · Collision Energy: -45.0 eV (Argon CID) · Source: ESI Negative (Unit/Unit Q1/Q3) · ● EPA 533 Ion Ratio: 44.0% (Matched ±30%)

EPA 533 Product Ion Confirmation Table

Ion Type	Fragment Formula	m/z (Observed)	Relative Abundance (%)	Collision Energy	Confirmation Status
Quantifier	[SO3]⁻	80.0	82.4%	-45 eV	Verified Primary
Qualifier 1	[FSO3]⁻	99.0	38.6%	-42 eV	Passed (Ratio 46.8%)
Qualifier 2	[C3F5]⁻	130.0	18.2%	-52 eV	Passed (Ratio 22.1%)
Qualifier 3	[C4F9]⁻	230.0	12.5%	-48 eV	Passed (Ratio 15.2%)

Official Certificate of Analysis - EPA Method 533

GLOBAL ENVIRONMENTAL MASS SPECTROMETRY LABORATORY

ISO/IEC 17025:2017 Accredited · NELAC Recognized Testing Facility · Lab ID: US-EPA-533-0941

100 Laboratory Drive, Analytical Science Park, Research Triangle, NC 27709

              CERT: EPA533-2026-09421

Issued: 2026-09-08 08:30 EST

Certificate of Quantitative Analysis

Determination of 16 Per- and Polyfluoroalkyl Substances (PFAS) in Environmental Samples by Isotope Dilution SPE LC-MS/MS

Project: portable_LC-MS_demo

Batch ID: BATCH_20260907_01

Method: US EPA Method 533

Instrument: Shimadzu LCMS-8060NX

Column: Shim-pack GIST C18 (2.1x100mm)

Analyst: demo (Senior Analyst)

Total Samples: 24 Acquisitions

Calibration Linearity: R² = 0.999446 (Pass)

Batch Status: ● QA/QC APPROVED

1. Calibration Linearity & Range Verification

6-Point Matrix-Matched Calibration (0.500 to 50.00 ppb). Internal standard normalization with 1/x weighted linear regression.

Target Analyte	MRM Transition	Assigned ISTD	Linear Range (ppb)	Slope	Intercept	Linearity (R²)	Accuracy (%)
PFOS	499.1 > 80.0	M8PFOS_B	0.500 – 50.00	1.10705	0.0033	0.999446	97.4% – 103.2%
PFOA	413.1 > 369.0	M8PFOA_B	0.500 – 50.00	1.06500	0.0028	0.999802	98.1% – 102.4%
PFHxS	427.1 > 399.0	M8PFOS_B	0.500 – 50.00	1.12000	0.0031	0.999510	96.8% – 101.9%
PFNA	463.1 > 419.0	MPFNA	0.500 – 50.00	1.03100	0.0022	0.999615	97.9% – 102.8%
PFBA	213.0 > 169.0	MPFBA	0.500 – 50.00	1.02500	0.0015	0.999640	96.5% – 103.0%

2. Environmental Matrix Findings & Regulatory Assessment

Sample ID	Matrix	PFOS (ppb)	PFOA (ppb)	Total PFAS (ppb)	Hazard Index	Regulatory Assessment
Water 1__001	Groundwater	3.129	2.841	5.970	0.312	Compliant (Below Action Level)
Water 2__002	Drinking Water	4.102	3.650	7.752	0.410	Requires Monitoring (4 ppt)
Soil 1__001	Soil Core	1.405	1.210	2.615	0.141	Compliant
Soil 4__004	Soil Core (Site 4)	1.837	1.642	3.479	1.482	Exceeds HI (1.48) · RT Shift Validated
SPAS__001	Sludge / Biosolid	4.432	3.890	8.322	0.443	Industrial Non-Potable
PFAS Blank_1	Reagent Blank	< LOD	< LOD	< LOD	0.000	Clean (Pass)

Cryptographic Integrity Seal:

SHA-256: 8f3c2a11b904d4f82631ce55a9b7102e34789fa12c98d66104bcde219842a1ef

Electronic signature verified under 21 CFR Part 11 compliant audit records.

DIGITALLY SIGNED & SEALED

Dr. Duan Luchun, Ph.D.

QA/QC Technical Director

EPA 40 CFR Part 136 Appendix B · MDL & LOQ Statistical Calculator

Target Compound:

Formula: MDL = s × t(n-1, 1-α=0.99) = s × 3.143 (n=7) · LOQ = 10 × s

7 Low-Level Spike Replicates Summary (Spiked at 0.50 ppb)

Rep 1	Rep 2	Rep 3	Rep 4	Rep 5	Rep 6	Rep 7	Mean	Std Dev (s)	MDL (ppb)	LOQ (ppb)
0.492	0.511	0.485	0.508	0.499	0.518	0.489	0.500	0.0123	0.0387	0.1230