qc-sample-type-classification

name	qc-sample-type-classification
description	Use when when constructing a sample list from an Excel template for LC/GC-MS analysis, you must classify each QC sample by type before proceeding to plate layout and randomization steps.
license	CC-BY-4.0
metadata	{"edam_operation":"http://edamontology.org/operation_3763","edam_topics":["http://edamontology.org/topic_0091","http://edamontology.org/topic_3370"],"tools":["InjectionDesign","pandas or openpyxl"],"techniques":["GC-MS"]}
derived_from	[{"doi":"10.1101/2023.02.26.530140v1.article-info","title":"InjectionDesign"}]
evidence_spans	["LC/GC-MS-based Multi-Omics Injection-Plate Design Web Service"]
claims	[]
provenance	{"collection":"https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2","assembled_by":"scripts/collect_metabolomics_collection.py","sources":[{"build":"coll_injectiondesign_cq","doi":"10.1101/2023.02.26.530140v1.article-info","title":"InjectionDesign"}],"dedup_kept_from":"coll_injectiondesign_cq"}
schema_version	0.2.0
attribution	{"generator":"AgenticScienceBuilder","original_doi":"10.1101/2023.02.26.530140v1.article-info","all_source_dois":["10.1101/2023.02.26.530140v1.article-info"],"zenodo_doi":"10.5281/zenodo.20794027","curators":[],"promoter":"Louis-Félix Nothias","sponsor":"CNRS & Université Côte d'Azur"}

QC Sample Type Classification

Summary

Classify and designate quality control samples into predefined types (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, or custom QC) within a sample list prior to injection-plate design. This classification enables systematic QC positioning and visual differentiation across LC/GC-MS injection sequences.

When to use

When constructing a sample list from an Excel template for LC/GC-MS analysis, you must classify each QC sample by type before proceeding to plate layout and randomization steps. Use this skill when you have a structured sample list with sample identifiers and metadata but QC samples lack explicit type assignments that the injection design algorithm requires.

When NOT to use

• Input sample list has already been processed through injection-plate design and finalized; re-classification would require re-running the entire design pipeline.
• All samples in the list are biological/study samples with no QC samples; classification is unnecessary if no QC samples exist.
• QC type information is not required by the downstream injection-design algorithm (e.g., if using a different plate-design tool with different QC requirements).

Inputs

• Parsed sample list (JSON or CSV) with sample identifiers, classification dimensions, and sample-type flags from Excel template ingestion
• Sample metadata rows including indicator columns or fields marking which samples are QC samples

Outputs

• Classified sample list with QC type designation (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, or custom QC) added to each QC sample record
• Color-coded sample list visualization showing QC sample types

How to apply

After parsing the uploaded sample Excel template into a structured sample list (task_id=task_001), examine each sample row and assign a QC type designation from the five predefined categories: Blank QC (solvent or matrix blank), Solvent QC (solvent control), Pooled QC (pooled biological sample), Long-Term Reference QC (stability reference), or custom QC (user-defined). Mark each QC sample with its type in the sample metadata record. The system uses these type assignments to color-code QC samples in the visualization and to apply QC-specific positioning rules during inter-batch balancing in Step 3. Classification must occur before the Design Parameters step, as it determines how the algorithm reserves plate positions and applies balancing constraints.

Related tools

• InjectionDesign (Web service that accepts classified sample lists and uses QC type designations to guide inter-batch balancing, QC positioning, and visualization of injection-plate layout) — https://github.com/CSi-Studio/InjectionDesign
• pandas or openpyxl (Spreadsheet parser used in Step 1 to load and validate the Excel template structure before QC type assignment)

Evaluation signals

• Every QC sample record in the output list has a QC type field populated with one of the five allowed values (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, or custom QC); no QC sample has a null or unrecognized type.
• Non-QC (biological study) samples have null or distinct non-QC type values; they are not mistakenly labeled as QC types.
• QC type assignments are consistently applied: identical QC samples (e.g., multiple blank controls) receive the same type designation across the list.
• Visualization in InjectionDesign Step 2 displays QC samples in distinct colors corresponding to their assigned types, confirming type information was correctly parsed downstream.
• The final injection worksheet generated after Steps 2–4 shows QC samples positioned according to their type-specific rules (e.g., Long-Term Reference QC samples appear at defined intervals for stability monitoring).

Limitations

• InjectionDesign supports only five predefined QC types plus one custom type; if a workflow requires more than six distinct QC categories, custom types must be mapped to one of the five standard types, potentially losing granularity.
• Classification is manual or rule-based on sample metadata; no automated QC-type inference from sample name patterns or historical data is described in the article.
• Classification occurs before inter-batch balancing (Step 3); if balancing constraints later require reallocation of QC positions, QC type assignments are not retroactively refined—only plate positions adjust.

Evidence

• [readme] InjectionDesign predefined four QC type: Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC. and one custom QC.: "InjectionDesign predefined four QC type: Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC. and one custom QC."
• [intro] Extract sample metadata rows and map each row to a sample record with sample identifier, classification dimensions (up to three), and QC type designation (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, or custom QC).: "map each row to a sample record with sample identifier, classification dimensions (up to three), and QC type designation (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, or custom QC)."
• [readme] Different QC type has be marked as different color.: "Different QC type has be marked as different color."
• [readme] After upload samples. Users can modify the sample list for future operation.: "After upload samples. Users can modify the sample list for future operation."