Sample Study Size Stratified Algorithm Selection

sample-study-size-stratified-algorithm-selection

Summary

A performance-conscious strategy for selecting between pairwise and nearest-neighbor mass alignment algorithms based on study sample count. This skill enables asari to scale across small (≤10 samples) and large studies by choosing algorithmically matched approaches that balance CPU and memory use.

When to use

When beginning mass alignment in a multi-sample LC-MS metabolomics study, before constructing the MassGrid. The decision depends on the total sample count in your project: small studies benefit from pairwise anchor-track prioritization, while large studies require binning-based nearest-neighbor clustering to avoid quadratic scaling.

When NOT to use

• Study has already been aligned into a feature table or composite map—the algorithm selection applies only at the mass track alignment stage, before composite peak detection.
• Sample count or mass track data are unavailable or incomplete—study size determination requires exact sample enumeration.
• Samples have been preprocessed with external alignment tools (e.g., XCMS, MZmine) that have already produced a unified m/z grid—this skill targets the initial asari-native alignment decision.

Inputs

• sample count (integer)
• mass track list per sample (m/z, intensity, retention time tuples)
• anchor mass track identifiers (13C/12C isotopes or Na/H adducts)
• mz_tolerance parameter (ppm)

Outputs

• MassGrid (aligned consensus m/z across samples)
• _mass_grid_mapping.csv (mapping of aligned mass track identifiers to consensus m/z and sample membership)
• recalibrated m/z values (if pairwise path, when systematic difference >1 ppm)

How to apply

First, count the number of LC-MS samples in your study. If ≤10 samples, use pairwise sample-wise alignment: identify the reference sample by counting anchor mass tracks (13C/12C isotopes or Na/H adducts) and select the one with the highest count; then align anchor tracks between each sample and the reference list, recalibrating all m/z values if systematic difference exceeds 1 ppm, before aligning remaining mass tracks. For studies with >10 samples, use nearest-neighbor clustering by m/z: bin all sample mass tracks using histogram-based m/z seed detection (ensuring 2 peaks separated by at least mz_tolerance), then construct consensus m/z for each bin as the mean of median m/z and m/z at highest intensity. In both paths, generate _mass_grid_mapping.csv documenting aligned mass track identifiers, consensus m/z values, and sample membership.

Related tools

• asari mass_functions module (nn_cluster_by_mz_seeds) (Implements nearest-neighbor clustering by m/z seeds for large-study alignment path) — https://github.com/shuzhao-li/asari
• asari MassGrid class (build_grid_sample_wise, add_sample, build_grid_by_centroiding, bin_track_mzs) (Constructs and populates the aligned MassGrid; dispatches between pairwise and binning-based strategies) — https://github.com/shuzhao-li/asari
• Python (Language for implementing study-size check and invoking asari mass functions)

Examples

python3 -m asari.main process -i mydir/projectx_dir --mode pos

Evaluation signals

• Sample count threshold (≤10 vs. >10) is correctly identified and logged at workflow start; verify in asari project.json or console output.
• _mass_grid_mapping.csv is generated with consistent m/z consensus values (mean of median m/z and highest-intensity m/z) across all aligned bins or pairwise pairs.
• For pairwise path: reference sample is the one with the highest count of anchor mass tracks; verify by counting 13C/12C or Na/H adducts in asari output.
• For pairwise path: systematic m/z drift >1 ppm triggers recalibration; confirm by comparing pre- and post-calibration m/z values in output.
• Nearest-neighbor bins show 2+ peaks separated by ≥mz_tolerance in large studies; verify histogram-based seed detection in intermediate pickle files or audit logs.

Limitations

• Threshold of ≤10 samples is empirically motivated but may require tuning for specific instrument types, ionization modes, or sample complexity; no adaptive optimization is reported.
• Anchor mass track identification relies on prior knowledge of isotope (13C/12C) and adduct (Na/H) m/z differences; isotopically labeled or non-standard adducts may not be recognized.
• The 1 ppm recalibration threshold is fixed and may not account for mass calibration drift over long run sequences or across different instrument platforms.
• Nearest-neighbor clustering seed detection requires 2+ peaks separated by mz_tolerance; sparse or low-intensity mass tracks may not form reliable seeds in large studies.
• GC-MS workflow and MS/MS-specific alignment strategies are handled separately (GC-MS workflow added in version 1.16.6); this skill applies primarily to LC-MS data.

Evidence

• [other] if ≤10 samples, use pairwise alignment with anchor mass track prioritization; else use nearest-neighbor clustering method: "if ≤10 samples, use pairwise alignment with anchor mass track prioritization; else use nearest-neighbor clustering method."
• [other] Asari is designed as a scalable program that uses performance-conscious approaches, operating with disciplined memory and CPU use, enabling it to handle studies of varying sizes through conditional algorithm selection.: "Asari is designed as a scalable program that uses performance-conscious approaches, operating with disciplined memory and CPU use, enabling it to handle studies of varying sizes through conditional"
• [other] For small studies, perform pairwise sample-wise alignment: align anchor mass tracks first between each sample and reference list, recalibrate all sample m/z values if systematic difference exceeds 1 ppm, then align remaining mass tracks.: "For small studies, perform pairwise sample-wise alignment: align anchor mass tracks first between each sample and reference list, recalibrate all sample m/z values if systematic difference exceeds 1"
• [other] For large studies, bin all sample mass tracks by m/z using nearest-neighbor clustering with histogram-based m/z seed detection, ensuring 2 peaks separated by at least mz_tolerance.: "For large studies, bin all sample mass tracks by m/z using nearest-neighbor clustering with histogram-based m/z seed detection, ensuring 2 peaks separated by at least mz_tolerance."
• [other] Construct consensus m/z for each aligned bin as mean of median m/z and m/z at highest intensity.: "Construct consensus m/z for each aligned bin as mean of median m/z and m/z at highest intensity."
• [readme] Scalable, performance conscious, disciplined use of memory and CPU: "Scalable, performance conscious, disciplined use of memory and CPU"