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EnviroLab Processor — Quantitation Wizard

A guided path through setting up and running a quantitation batch.

1 Calibration

Step 1: Calibration

Compound panel 21 compounds · m/z fixed · L2..L9 concs editable

The compound panel and L2..L9 calibration concentrations live in the database. m/z is fixed (the analyst's quantifier per compound — the instrument method defines this once and it doesn't change). The L2..L9 concentrations are default values; edit them in the cells below and click Save concentrations. Retention times are derived from MOCCA2 on the L1 sample and stored per-batch in istd_defaults (see the panel further down).

Showing L2..L9 only. L1 is the ISTD-only sample (rendered as a separate card in the chromatogram grid below). It is not a calibration level, so it does not appear in this table.
Name Quant m/z (Da) Qual ions ISTD L2 L3 L4 L5 L6 L7 L8 L9
ISTDs (deuterated internal standards) (5)
Naphthalene-d8 [ISTD] 136 108.0, 137.0 —
Acenaphthene-d10 [ISTD] 164 162.0, 160.0 —
Phenanthrene-d10 [ISTD] 188 94.0, 80.0 —
Chrysene-d12 [ISTD] 240 236.0, 120.0 —
Perylene-d12 [ISTD] 264 260.0, 265.0 —
Surrogates (1)
p-Terphenyl d14 [Surr] 244 243.0, 242.0 —
Analytes (target PAHs) (15)
Acenaphthylene 152 151.0, 153.0 Naphthalene-d8
Naphthalene 128 127.0, 129.0 Naphthalene-d8
Acenaphthene 153 154.0, 152.0 Acenaphthene-d10
Fluorene 166 165.0, 164.0 Acenaphthene-d10
Anthracene 178 176.0, 179.0 Phenanthrene-d10
Benz (a) anthracene 228 226.0, 229.0 Phenanthrene-d10
Fluoranthene 202 200.0, 203.0 Phenanthrene-d10
Phenanthrene 178 176.0, 179.0 Phenanthrene-d10
Pyrene 202 200.0, 203.0 Phenanthrene-d10
Benzo (a) pyrene 252 250.0, 126.0 Chrysene-d12
Benzo (b,k) Fluoranthene 252 250.0, 126.0 Chrysene-d12
Chrysene 228 226.0, 229.0 Chrysene-d12
Benzo (g,h,i) perylene 276 277.0, 274.0 Perylene-d12
Dibenzo (a,h) anthracene 278 277.0, 276.0 Perylene-d12
Indeno (1,2,3-cd) pyrene 276 277.0, 274.0 Perylene-d12

Standard chromatograms

One TIC per calibration level from the most recent uploaded batch, so the analyst can confirm the standards look right before moving on to sample quantification. Levels with no matching standard in the batch are shown as "no data".

Workflow: The L1 card at the top is the ISTD-only sample (concentration 0.01). It contains only the deuterated internal standards — no target analytes — and is not used in the calibration curve. Run Run on all standards on the L1 card first to identify the retention times of each ISTD, then those RTs are the anchor for matching the L2..L9 cal standards to their ISTD pairs.
Batch: /home/philip/workspace/envirolab-uploads/Agilent Good Run-5 — 9 cal standards found (rendered in 0.25s)
Integrate all standard peaks Runs MOCCA2 on every cal standard (L1..L9). The L1 card is the ISTD-only sample — use its peak table to anchor ISTD RTs before moving to L2..L9. ↗ Peak deconvolution (MCR-ALS / NMF)
MOCCA2: (saved defaults) Deconvolve:
L1 ISTD ISTD sample 003.D
Solvent delay: 2.0 min2m4m6m8m10m072k144k216k288kRetention Time (min)L1 — ISTD sample (003.D · 0.01)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L9 5 µg/L 011.D
Solvent delay: 2.0 min2m4m6m8m10m0357k714k1071k1429kRetention Time (min)L9 — 5 µg/L (011.D · 5)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L8 2 µg/L 010.D
Solvent delay: 2.0 min2m4m6m8m10m0164k328k492k656kRetention Time (min)L8 — 2 µg/L (010.D · 2)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L7 1 µg/L 009.D
Solvent delay: 2.0 min2m4m6m8m10m090k180k270k360kRetention Time (min)L7 — 1 µg/L (009.D · 1)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L6 0.5 µg/L 008.D
Solvent delay: 2.0 min2m4m6m8m10m077k154k231k308kRetention Time (min)L6 — 0.5 µg/L (008.D · 0.5)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L5 0.2 µg/L 007.D
Solvent delay: 2.0 min2m4m6m8m10m077k155k232k310kRetention Time (min)L5 — 0.2 µg/L (007.D · 0.2)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L4 0.1 µg/L 006.D
Solvent delay: 2.0 min2m4m6m8m10m070k140k209k279kRetention Time (min)L4 — 0.1 µg/L (006.D · 0.1)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L3 0.05 µg/L 005.D
Solvent delay: 2.0 min2m4m6m8m10m067k134k200k267kRetention Time (min)L3 — 0.05 µg/L (005.D · 0.05)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
L2 0.02 µg/L 004.D
Solvent delay: 2.0 min2m4m6m8m10m063k126k190k253kRetention Time (min)L2 — 0.02 µg/L (004.D · 0.02)
no peaks yet — click "Run on all standards" above.
Deconvolved components — zoom-synced with the TIC
Co-elution deconvolution: the panel below shows peaks that MOCCA2 found in the TIC (peak detection). For resolving overlapping peaks into their constituent compounds (e.g. "is this one peak or two co-eluting?"), MOCCA2 can do that natively — click Deconvolve peaks in the panel above and the per-card view below will show the resolved components. For a different algorithm (MCR-ALS via NMF, mass-spectrum aware), use the Peak Deconvolution (NMF) tool.
no deconvolution yet — click "Deconvolve peaks" above.
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