Analytical Methods — Cross-Cutting Comparison
This note compares every analytical technique referenced across the Chemistry library on the axes that determine which to reach for at the bench or in the QC lab: sensitivity (LOD), selectivity (matrix tolerance), throughput, sample destruction, in-situ vs ex-situ, quantitative vs qualitative, depth profiling, spatial resolution, mass range, elemental vs molecular, structural vs compositional, and cost per sample. Use the tables to triage; use the decision tree to pick by sample-type and question-type.
See also
1. Twelve families
SEPARATION MASS SPEC SPECTROSCOPY STRUCTURE / MICROSCOPY
GC Q-TOF NMR X-ray crystallography
HPLC/UHPLC Orbitrap IR (FTIR/ATR) cryo-EM
IC FT-ICR Raman electron diffraction
SEC/GPC TIMS UV-Vis SEM/TEM
CE triple-quad Fluorescence AFM/STM
2D-LC ion trap (IT) CD SAXS/WAXS, SANS
SFC MALDI-TOF XRF/XPS/EELS/EDS
ICP-MS EPR (ESR)
GC-MS AA, ICP-OES
LC-MS/MS
THERMAL SURFACE ELECTROCHEM PARTICLE/COLLOID
DSC BET porosimetry CV/LSV DLS, zeta
TGA Hg porosimetry EIS NTA
DMA AFM/STM GCD SLS
DTA LEED AUC
ITC Auger SAXS
2. Sensitivity, selectivity, throughput — the gross axes
Family LOD (representative) Selectivity (matrix) Throughput (per sample) Sample destruction NMR (¹H, 600 MHz)mM high (chemical-shift unique) 5–60 min (1D), hours (2D) non-destructive UHPLC-MS/MS pg–ng/mL very high (m/z + RT) 2–10 min partial (mobile-phase consumed) HPLC-UV µg/mL medium 10–30 min partial GC-MS pg/mL very high 15–45 min partial FTIR (ATR) mg medium 30 s non-destructive Raman mg (resonance ng) medium seconds non-destructive UV-Vis µg/mL low (broad bands) seconds non-destructive ICP-MS ppt (10⁻¹² g/g) very high (elemental) 2 min destructive (digest) ICP-OES ppb high 1 min destructive (digest) AA (atomic absorption) ppb (flame) – ppt (GFAA) high (element-specific) 30 s – 2 min destructive XRF ppm medium seconds non-destructive XPS atomic % high (1–10 nm surface) minutes non-destructive (vac) MALDI-TOF fmol (proteins) high seconds partial SAXS mg/mL (proteins) structural, not chemical 5–60 min non-destructive DLS µg/mL (particles) size only 1 min non-destructive DSC mg thermal events only 30 min partial (melted) TGA mg mass loss 30 min destructive CV (cyclic voltammetry)µM (analyte) redox-specific minutes partial Cryo-EM nmol protein structural days non-destructive X-ray crystallography mg crystal structural, atomic resolution days–weeks non-destructive (post-crystallization) AFM/STM atomic nanoscale only 5–60 min/image non-destructive DSC + microcalorimetry (ITC) µM–mM binding binding thermodynamics 2–4 h non-destructive
3. What question are you asking?
Question type First-line technique(s) What molecule is this? (unknown identity) LC-MS/MS, GC-MS, NMR (1D + 2D) How pure is this? HPLC-UV/DAD, qNMR (ERETIC, PULCON), elemental analysis (CHNS) What functional groups? FTIR, ¹H/¹³C NMR What polymorph / crystal form? XRPD, ssNMR, FTIR, Raman What molecular weight (small molecule)? HRMS (Orbitrap, Q-TOF, FT-ICR) What molecular weight (polymer)? SEC/GPC, MALDI-TOF, light scattering (SLS) What MW distribution (Đ) of polymer? SEC/GPC w/ multi-detector (RI + LS + viscometer) What absolute MW (no calibration std)? SEC-MALS, AUC, mass spec What is the elemental composition? ICP-MS (trace), ICP-OES (major), XRF (in-situ), AA (single element) What metal in this catalyst residue? ICP-MS (ppt sensitivity for Pd, Pt, Ru, Os, Rh) What stereochemistry / chirality? chiral HPLC, CD, NMR w/ chiral shift reagent, VCD What protein binds what? SPR (Biacore), BLI (Octet), MST, ITC What is the crystal structure? single-crystal XRD (Cu/Mo Kα), neutron diffraction (H positions) What is the protein structure? X-ray, cryo-EM, NMR (< 30 kDa) What is the powder structure? XRPD + Rietveld refinement What is the surface composition (top 1–10 nm)? XPS, AES, TOF-SIMS What is the surface area / porosity? BET (N₂ at 77 K), Hg porosimetry (large pores) What is the particle size distribution? DLS (1 nm–10 µm), NTA (10 nm–1 µm), SEM (any), laser diffraction What is the morphology? SEM, TEM, AFM What is the thermal behavior? DSC (transitions), TGA (decomposition), DMA (mechanical vs T) Is there a glass transition? DSC, DMA (DMA is more sensitive — frequency-dependent tan δ peak) What is the heat of reaction? DSC (mg), reaction calorimetry RC1 (g–kg) What is the binding affinity Kd? ITC (any), SPR (proteins on chip), MST (label-free), BLI What concentration of analyte X in matrix Y? LC-MS/MS w/ stable-isotope internal standard Is this drug stable? HPLC-UV degradation profile, ICH Q1A forced-degradation studies Is there an impurity at 0.05% level? UHPLC-MS w/ ELS / CAD, qNMR What is the diffusion coefficient? DOSY-NMR, DLS, FRAP, pulsed-field-gradient NMR What is the dynamic / motion timescale? NMR (T1, T2, NOE), neutron scattering (QENS) What is the electron transfer rate? electrochemistry (CV w/ scan-rate dependence), EIS What is the protein conformation in solution? SAXS, CD, NMR (HSQC for fingerprint), AUC What is the protein aggregation state? DLS, AUC, SEC-MALS, MP (mass photometry)
4. Spatial and depth resolution
Technique Lateral resolution Depth resolution / probing depth Optical microscopy 200 nm (visible) surface (~λ) Confocal fluorescence 200 nm × 200 nm × 500 nm optical section ~500 nm Super-resolution (STED, PALM/STORM) 10–50 nm 10–500 nm SEM 1–10 nm 0.5–5 µm TEM 0.05 nm (atomic) ~100 nm sample thickness EDS in SEM ~1 µm ~1 µm EDS in TEM ~1 nm ~thickness EELS in TEM ~1 nm ~thickness AFM 1 nm laterally, 0.1 nm Z top monolayer only STM atomic top atom layer XPS 10 µm (lab); 50 nm (synchrotron PEEM) 1–10 nm (escape depth) Auger AES 50 nm 1–5 nm SIMS (dynamic) 50 nm–1 µm sputter-depth-profile, no inherent depth limit LEIS mm beam, atomic Z resolution top monolayer (very surface-sensitive) XRD mm (lab); µm (microbeam) µm–mm (Bragg depth) Raman / Confocal Raman 1 µm 1 µm (confocal section) FTIR microscopy 5–10 µm varies (ATR: ~1 µm; transmission: through-thickness) LA-ICP-MS 5–50 µm sputter-depth profile MALDI imaging 5–50 µm top layer DESI imaging 50–200 µm top layer
5. Mass-spec instrument tiers
Instrument Mass accuracy Resolution (FWHM) Mass range Throughput Use Single quad (unit-mass) ± 0.5 Da 1000–2000 < 4000 Da high screening, GC-MS quant Triple quadrupole (QqQ) ± 0.1 Da 1000–2000 < 3000 Da very high (SRM/MRM) API quant, drug metabolism, environmental Ion trap (linear / 3D) ± 0.1 Da ~1000 < 4000 Da medium MSⁿ of unknowns, proteomics screening Q-TOF < 2 ppm 30 000–60 000 < 40 000 Da high unknowns ID, drug metabolism, food/environment, proteomics Orbitrap (Q Exactive, Exploris, Astral) < 1 ppm 60 000–1 000 000 < 6000 Da medium-high proteomics, metabolomics, intact protein, top-down FT-ICR (Bruker SolariX) < 100 ppb > 1 000 000 (7 T+) < 30 000 Da low (minutes/spectrum) petroleomics, NOM, ultra-high MS TIMS (Bruker timsTOF) < 2 ppm 50 000 + IM ~80 < 20 000 Da very high (4D: m/z, RT, mobility, intensity) proteomics (PASEF), lipidomics, drug MALDI-TOF / TOF-TOF ± 0.05% 10 000–50 000 < 500 000 Da very high proteins, peptides, polymers (MALDI is best for polymers up to ~50 kDa), bacteria (Bruker MALDI Biotyper) MALDI-FT-ICR < 100 ppb > 1 000 000 < 50 000 Da medium imaging mass spec, ultra-high accuracy ICP-MS (Q, TOF, MR) unit 300 (Q), 10 000 (HR) < 250 (elements) high trace metals, isotope ratios
The 2024–2026 generation: Bruker timsTOF Ultra 2 (proteomics workhorse, PASEF + dia-PASEF), Thermo Orbitrap Astral (200 Hz duty cycle, single-cell proteomics), Waters BioAccord SELECT SERIES MRT (multi-reflecting TOF), Sciex ZenoTOF 8600 , Agilent 6495D triple-quad LC/MS (Pesticide method automation), Bruker scimaX MRMS (FT-ICR 7T/15T).
6. Cost per sample — order-of-magnitude
Technique Cost / sample (USD, US lab 2025) FTIR-ATR $2–10 UV-Vis $2–10 HPLC-UV $15–40 GC-MS $30–80 LC-MS/MS (Q-TOF or Orbitrap) $50–200 NMR (¹H 1D) $30–80 NMR (2D HSQC/HMBC) $100–300 NMR (ssNMR, ¹³C CP-MAS) $200–500 ICP-MS (multi-element panel) $60–200 ICP-OES $40–120 AA (single element) $15–40 XRF (XRD-handheld) $10–30 XPS $200–800 TGA / DSC $50–150 Raman $30–100 BET (multi-point N₂) $200–500 Mercury porosimetry $400–800 DLS (multi-angle) $60–150 Cryo-EM (collection + reconstruction) $5000–20000 (academic core) Single-crystal XRD $300–1500 (per structure) XRPD + Rietveld $150–400 Mass photometry (Refeyn) $30–60 SAXS (lab) $200–500 SAXS (synchrotron) “free” but trip + prep $2000+ Synchrotron XRD (single-crystal) “free” but trip + prep $5000+ ITC (Microcal PEAQ) $100–250 ELISA $5–30 / well SPR (Biacore) $150–400 MST (NanoTemper) $80–200
7. Hyphenated / coupled techniques — when one instrument isn’t enough
Coupling What it adds Typical use GC-MS retention + mass environmental, forensic, metabolomics LC-MS/MS retention + mass + fragmentation quant in matrix LC-MS-IR (Bruker IR detector) adds IR for FG ID impurity ID where ms-only is ambiguous LC-NMR (or LC-NMR-MS) adds NMR structure rare, very specialized HPLC-CAD universal quant detector (charge aerosol) counterion + non-UV impurities GC-IRMS (isotope ratio) adds δ¹³C, δ²H food authenticity, doping, climate ICP-MS hyphenated (LA-ICP-MS, HPLC-ICP-MS) speciation arsenic species, Cr(III)/Cr(VI) SEC-MALS-RI-viscometer absolute MW + Đ + branching polymer characterization DSC-microcal (modulated MDSC) reversible vs non-reversible Cp polymer Tg vs cold crystallization separation TGA-MS / TGA-FTIR evolved gas analysis polymer / pharma decomposition pathways Raman + FTIR (Tornado/Bruker) complementary FG pharma polymorph screen Cryo-EM + cryo-ET tomography of single particles structural biology, organelles Pump-probe TA + Raman excited-state dynamics photochem, photovoltaics EPR-DNP-NMR electron-nucleus polarization transfer, 100× sensitivity low-abundance ¹³C, ¹⁵N at solid-state
8. Quantitative chemistry — what can you actually trust?
Technique Typical % RSD Caveats qNMR (PULCON, ERETIC) < 1% needs clean spectrum, integration discipline HPLC-UV w/ external standard 1–3% UV depends on molar absorptivity HPLC w/ internal standard 0.5–1% need IS that doesn’t co-elute LC-MS/MS w/ stable-isotope IS 5–15% matrix effects, ion suppression ICP-MS w/ standard addition 1–5% matrix-matched calibration essential Karl Fischer (water) 0.5–2% only water content Elemental analysis (CHNS) 0.3% absolute sealed-tube combustion TGA 1–5% reproducibility-driven GC-MS w/ SIM 5–15% matrix effects ELISA 10–30% cross-reactivity, plate effects
9. The “method validation” frame (ICH Q2(R1) / Q14)
For any quantitative method intended for GMP, ICH Q2(R1) requires:
Specificity — separate analyte from impurities, degradants, excipients.Linearity — R² > 0.99 typical, residuals random.Range — typically 80–120% of nominal.Accuracy — recovery 98–102%.Precision — repeatability (intra-day), intermediate (inter-day), reproducibility (inter-lab).Detection / quantitation limit — LOD = 3σ/S, LOQ = 10σ/S.Robustness — small parameter changes don’t break the method.
ICH Q14 (2024) adds analytical procedure development — explicitly endorses Analytical Quality by Design (AQbD) with design-of-experiments, prior knowledge, and analytical control strategy.
10. Modern (2024–2026) frontier
Ion mobility (TIMS, FAIMS, SLIM) — adds a fourth dimension to LC-MS, separates lipid isomers and protein conformers that share RT and m/z.Native MS (Robinson, Heck) — intact protein complexes by gentle ESI; 2024-era instruments (Bruker scimaX MRMS, Thermo Q Exactive UHMR) push into MDa range.Cryo-EM single-particle — sub-2 Å resolution routine (formerly only crystallography); Janelia/MRC-LMB workflow democratized.Cryo-electron tomography (cryo-ET) — 3D in-cell structure of native complexes.MicroED (electron diffraction) — micron-sized crystals (formerly too small for XRD) now usable; Tamir Gonen + Brett Krause 2018+ revolutionized small-molecule structure determination.Mass photometry (Refeyn) — single-molecule MS at the bench; protein-protein binding stoichiometry in minutes.Single-cell mass spec (Slavov lab MS-SCoPE; Bruker timsTOF) — proteomics on individual cells.Hyperpolarized NMR (DNP) — 10⁴-fold signal enhancement; commercially Bruker Daresbury DNP-NMR.Imaging MS at single-cell resolution — MALDI-2, DESI, SIMS NanoSIMS Cameca.Online process analytical technology (PAT) — Raman, NIR, FTIR for continuous manufacturing process control (FDA encouragement under PAT initiative 2004+, accelerated 2020+).AI-aided structure elucidation — DP4, MestreLab, NMR-prediction services (Mnova/MNova-AI, ACD/Labs).
11. Decision tree — pick by sample + question
What type of sample?
├─ Pure compound (organic small molecule)
│ ├─ ID confirm → NMR (1D + HSQC/HMBC) + HRMS
│ ├─ Purity (chromatographic) → HPLC-UV w/ DAD + ELSD/CAD
│ ├─ Polymorph / crystal form → XRPD + DSC + ssNMR / FTIR / Raman
│ ├─ Stereochemistry → CD, VCD, chiral HPLC, NMR w/ chiral shift
│ └─ Single-crystal structure → SCXRD (Cu Kα or Mo Kα)
├─ Mixture / matrix (food, environmental, biological)
│ ├─ Quant of known compounds → LC-MS/MS w/ SIM IS or GC-MS-SIM
│ ├─ Untargeted profiling → LC-HRMS (Orbitrap) or GC-Q-TOF
│ └─ Elemental trace → ICP-MS
├─ Protein
│ ├─ Identification → MALDI-TOF, LC-MS/MS (peptide ID)
│ ├─ Intact mass → native MS, MALDI-TOF
│ ├─ Stoichiometry → SEC-MALS, MP, AUC, native MS
│ ├─ Structure → X-ray crystallography (mg, crystals), cryo-EM (< 1 µg), NMR (< 30 kDa)
│ ├─ Conformational change → SAXS, HDX-MS, NMR
│ ├─ Binding affinity → ITC, SPR, BLI, MST
│ └─ Aggregation → DLS, AUC, SEC-MALS, MP
├─ Polymer
│ ├─ MW + Đ → SEC/GPC w/ multi-detector (RI + LS + viscometer)
│ ├─ Tacticity → ¹³C NMR (pentad analysis)
│ ├─ End groups → MALDI-TOF, ¹H NMR
│ ├─ Thermal → DSC + TGA + DMA
│ ├─ Crystallinity → XRD + DSC
│ └─ Surface composition → XPS, ToF-SIMS
├─ Solid catalyst / surface
│ ├─ BET surface area + porosity → N₂ at 77 K (BET), Hg porosimetry for macropores
│ ├─ Phase ID → XRD + Rietveld
│ ├─ Surface composition → XPS, AES, ToF-SIMS
│ ├─ Morphology → SEM (cheap), TEM (atomic)
│ ├─ Active site → in-situ DRIFTS, in-situ XAS (XANES + EXAFS, synchrotron)
│ └─ Single-atom imaging → HAADF-STEM
├─ Nanoparticle / colloid
│ ├─ Size distribution → DLS (intensity-weighted), NTA (number-weighted), SAXS
│ ├─ Composition → ICP-MS (after digestion), TEM-EDS
│ ├─ Surface charge → zeta potential
│ └─ Aggregation → DLS + zeta, AUC
└─ Battery / electrochemistry sample
├─ Capacity / cycling → GCD
├─ Impedance → EIS (Nyquist + Bode)
├─ Reaction mechanism → CV at scan-rate variation
├─ Cathode/anode composition → ICP-OES + XPS
└─ Cell-level operando → operando XRD, neutron, Raman
Adjacent
NMR depth — nmr-spectroscopy-deep for instrument generations, pulse sequences, ssNMR, DNP, in-vivo MRS.Spectroscopy reference tables — spectroscopy-reference-tables for IR group frequencies, NMR shift tables, UV-Vis chromophore tables.Polymer characterization — polymer-chemistry §MW averages + tacticity + crystallinity sections.Surface chemistry — surface-and-interface-chemistry for adsorption isotherm + zeta + contact angle.Electrochemistry — electrochemistry for CV/EIS/GCD theory.Materials characterization — materials-chemistry cross-references electron microscopy + XRD on solid samples.Engineering-side characterization — ndt-methods for non-destructive testing of structural materials (radiography, ultrasonics, MPI).Biology-side characterization — cryo-EM, AUC, SPR also appear in the Biology library.
When to pick what
The fastest narrowing: identity → MS + NMR ; purity → HPLC ; structure → X-ray crystallography (if you have a crystal) or cryo-EM (if you don’t) ; elemental → ICP-MS for trace, ICP-OES for major, XRF for in-situ ; surface → XPS for top 10 nm, BET for area ; thermal → DSC for transitions + TGA for decomposition ; particle size → DLS for ensemble, SEM for individual ; binding → ITC if you have mg quantities, MST/BLI/SPR if you don’t . The single most common mistake in 2020s analytical workflows is collecting LC-MS data when LC-UV would suffice (faster, cheaper, simpler quant) or shooting NMR at a polymer when you needed SEC (NMR cannot give Đ). Match the question to the technique.