Sample types & QC roles • mrmhub

Manual

MRMhub uses the qc_type column in the analysis annotation to categorize samples by their analytical purpose. This label determines which samples are used for drift correction, batch correction, QC-metric calculation and calibration, and which are excluded from the reported study results. Assigning the wrong label therefore causes MRMhub to use the wrong samples for corrections, so the qc_type column should be checked before processing.

QC types (sample types)

The classification combines nomenclature from several sources: the standardized terms SPL, BQC, TQC, LTR and RQC were introduced by Broadhurst et al. (2018) for the use of system-suitability and quality-control samples in mass spectrometry assays, while the others (LQC, MQC, HQC, CAL, NIST, SST and the blank types) derive from traditional terminology in analytical and clinical chemistry.

QC type	Group	Description
`SPL`	Unknowns	Study sample (“unknowns”)
`BQC`	QC	Batch / Process QC
`PQC`	QC	Process QC (or Pooled QC); see `BQC`
`TQC`	QC	Technical QC
`EQC`	QC	Equilibration QC; injected to equilibrate the system and check that it is stable and performing as expected
`LQC`	QC	Low QC
`MQC`	QC	Mid QC
`HQC`	QC	High QC
`QC`	QC	General QC sample (not strictly defined)
`CAL`	Calibration	Calibration sample
`RQC`	QC	Response QC (dilution series)
`LTR`	Reference material	Long-Term Reference
`NIST`	Reference material	NIST Standard Reference Material
`EQA`	QC	External Quality Assessment sample, e.g. from proficiency-testing (PT) schemes
`SST`	QA	System Suitability Test sample
`PBLK`	Process blank	No matrix, processed with ISTD as all other samples
`UBLK`	Blank	Unextracted Blank: no matrix, with ISTD, without undergoing sample processing
`SBLK`	Blank	Solvent / double blank: no matrix, no ISTD, just solvents
`TBLK`	Blank	Technical blank (instrument blank)
`MBLK`	Blank	Matrix Blank: matrix processed as samples but without ISTDs
`BLK`	Blank	Generic blank, when the specific blank type is unknown or unspecified

Which samples are used where

The reference QC types for drift and batch correction are user-selected (ref_qc_types), typically the QC pool (BQC). The table below summarises the usual roles.

Processing step	Uses	Typical sample types
Drift correction (QC-based models)	Signal anchors	`BQC` (or the selected `ref_qc_types`)
Batch correction (centering)	Cross-batch alignment	`BQC` (or the selected `ref_qc_types`)
QC metrics (CV, bias)	Precision monitoring	`BQC`, `TQC`, `PBLK`
Calibration curves	Quantification	`CAL`
Excluded from study results	Not reported	all blanks, `CAL`, `RQC`, `SST`

Setting the sample type in the annotation

The analysis annotation must have a column called sample_type or qc_type. Labels are matched case-insensitively against the types listed above (so CAL, Cal, and cal are equivalent), and a small set of vendor labels is recognised as aliases: Sample → SPL, Blank → BLK, DoubleBlank → SBLK, MatrixBlank → MBLK, and ResponseCheck → RQC. Unrecognised labels are retained but dropped from QC metrics and plots that expect a standard type. Every analysis must carry a label, and QC samples used as drift/batch anchors should be evenly distributed across the run (at least five per batch for reliable drift correction).

analysis_id,sample_type,batch_id,analysis_order
Inj_001,SBLK,Batch_1,1
Inj_002,BQC,Batch_1,2
Inj_003,SPL,Batch_1,3
Inj_004,SPL,Batch_1,4
...
Inj_010,BQC,Batch_1,10
Inj_080,BQC,Batch_1,80
Inj_081,SBLK,Batch_1,81

Typical batch layout

Colour coding

Each qc_type is drawn with a consistent line colour and point shape in every plot MRMhub produces. The swatches below are the exact line colours defined in the package (qc_type_col).

Type	Colour
`SPL`	grey
`SST`	yellow-green
`BQC`	red
`TQC`	blue
`PQC`	orange
`QC` / `HQC` / `MQC` / `LQC`	dark orange
`RQC`	periwinkle
`CAL`	blue
`NIST`	navy
`LTR` / `EQA`	purple
`EQC`	brown
`SBLK`	blue
`TBLK`	red
`UBLK`	magenta
`PBLK`	green
`MBLK`	black
`BLK`	grey

Next steps

MRMhub overview: broader terminology
Importing metadata: preparing the annotation files
Drift and batch correction: where the QC types are used

References

Broadhurst, David, Royston Goodacre, Stacey N. Reinke, et al. 2018. “Guidelines and Considerations for the Use of System Suitability and Quality Control Samples in Mass Spectrometry Assays Applied in Untargeted Clinical Metabolomic Studies.” Metabolomics 14 (6): 72. https://doi.org/10.1007/s11306-018-1367-3.