Key Data Identifiers
The following key data fields are essential for organizing data in
MiDAR. These data key fields are used in organizing the
data within the MidarExperiment object and some functions
in the MiDAR package employ these fields.
| Table | Field | Description |
|---|---|---|
| Analyses | analysis_id |
Unique identifier of each analysis. |
qc_type |
QC/Sample type, see next section. | |
batch_id |
Unique identifier of each batch level. | |
| sample_id | Unique identifier pf the (physical) sample that was tested | |
| Features | feature_id |
Unique identifier for each feature. |
istd_feature_id |
The feature_id of the internal standard used to
normalize raw intensities (each internal standard must be defined as a
feature). |
|
| analyte_id | Unique identifier of the analyte |
Certain field names differ from conventional terminology
(e.g., analysis_id instead of sample_id) to
allow more flexible workflows and to reduce confusion with other
identifiers. A sample may be measured multiple times across different
methods or processing replicates, necessitating distinct identifiers.
Similarly, analytes can be quantified through multiple transitions or
adducts, which is why feature_id is designated as the
primary identifier.
QC types (Sample Types)
QC types categorize samples based on their analytical purpose and are utilized throughout various functions in the MiDAR package. This classification system combines nomenclature from multiple sources: several standardized terms (SPL, BQC, TQC, LTR, RQC) were introduced by Broadhurst et al. (2018) in “Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays,” while others (LQC, MQC, HQC, CAL, NIST, SST, and various blank types) derive from traditional terminology in analytical and clinical chemistry. The integration of these nomenclature systems provides a comprehensive framework for quality control in analytical workflows.
| QC type | Group | Description |
|---|---|---|
| SPL | Unknowns | Study sample (‘unknowns’) |
| BQC | QC | Batch/Process QC |
| TQC | QC | Technical QC |
| LQC | QC | Low QC |
| MQC | QC | Mid QC |
| HQC | QC | High QC |
| CAL | Calibration | Calibration sample |
| RQC | QC | Response QC |
| LTR | Reference Material | Long-Term Reference |
| NIST | Reference Material | NIST Standard Reference Material |
| SST | QA | System Suitability Test Sample |
| PBLK | Process Blank | No matrix, processed with ISTD as all other samples |
| UBLK | Blank | Unextrated Blank. No matrix, with ISTD without undergoing sample processing |
| SBLK | Blank | Solvent Blank/double Blank, no matrix, no ISTD, just solvents |
| IBLK | Blank | Instrument Blank with/without injection |
| MBLK | Blank | Matrix Blank. Matrix processed as samples without ISTDs |
QC type is represented with a consistent color scheme (both fill and line colors) and specific point shapes in all plots generated by the MiDAR package. This visual coding allows consistent identification and comparison of different QC types across various visualizations.