chemodiversity-descriptor-calculation
Summary
Compute molecular chemodiversity descriptors (mass-based statistics, elemental stoichiometry diversity indices, and molecular complexity metrics) from formula-assigned FT-ICR MS datasets to characterize the molecular diversity and transformation patterns of environmental organic complex mixtures.
When to use
Apply this skill when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify the molecular chemodiversity, elemental composition diversity, or complexity of environmental organic samples for cross-sample comparison or transformation analysis.
When NOT to use
- Input is not formula-assigned: MoleTrans requires parsed molecular formulas; raw m/z values without formula assignment cannot be processed.
- Data source is not FT-ICR MS or supported mass spectrometry: while MoleTrans can partially support compound-annotated results from other MS approaches, it is optimized for FT-ICR formula assignments.
- Sample lacks sufficient molecular diversity: descriptor computation assumes a heterogeneous molecular population; homogeneous or single-compound samples may not benefit from chemodiversity metrics.
Inputs
- formula-assigned FT-ICR MS dataset (CSV or tab-delimited table)
- columns: molecular formulas, mass values, sample identifiers
Outputs
- structured descriptor table with sample identifiers and chemodiversity metrics
- mass-based statistics per sample
- elemental stoichiometry diversity indices per sample
- molecular complexity metrics per sample
How to apply
Load the formula-assigned FT-ICR MS dataset into MoleTrans post-analysis module. Parse the molecular formula assignments to extract elemental composition (C, H, O, N, S, P counts) for each formula. Compute a suite of chemodiversity descriptors including mass-based statistics (e.g., mean, median, standard deviation of molecular masses), elemental stoichiometry diversity indices (ratios and proportional distributions of elements), and molecular complexity metrics across the sample. Export a structured output table or report mapping sample identifiers to descriptor values. Validate that computed indices capture expected trends in molecular complexity and that elemental counts match the input formulas.
Related tools
- MoleTrans (post-analysis and data-mining platform for computing chemodiversity descriptors from formula-assigned FT-ICR MS datasets) — github.com/JibaoLiu/MoleTrans
Evaluation signals
- Output descriptor table contains one row per sample with all expected chemodiversity metrics (mass statistics, elemental diversity indices, complexity scores) populated and non-null.
- Elemental composition counts (C, H, O, N, S, P) in parsed formulas match the elemental tallies reflected in stoichiometry diversity indices.
- Molecular complexity metrics show expected correlation with formula mass and elemental richness (e.g., higher complexity for larger, more heteroatom-rich molecules).
- Sample identifiers in output table map one-to-one to input dataset rows; no duplicates or drops.
- Descriptor values fall within chemically plausible ranges (e.g., mass > 0, diversity indices 0–1 or within documented scale).
Limitations
- MoleTrans can only partially support combined analysis on compound-annotated results from non-FT-ICR MS approaches; full optimization is for FT-ICR formula-assigned data.
- Requires user registration (or demo account) to access the live webtool; source code from the repository provides only the main calculation functions and algorithms, not the complete web interface.
- Descriptor computation assumes adequate sample size and molecular diversity; very small or homogeneous datasets may yield uninformative or unreliable indices.
- Post-analysis is limited to elemental composition (C, H, O, N, S, P); other elements present in formulas may not be represented in standard diversity metrics.
Evidence
- [other] formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values): "Load the formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) into the MoleTrans post-analysis module"
- [other] chemodiversity descriptors including mass-based statistics, elemental stoichiometry diversity indices, and molecular complexity metrics: "Compute molecular chemodiversity descriptors including mass-based statistics, elemental stoichiometry diversity indices, and molecular complexity metrics across the sample."
- [readme] MoleTrans is a webtool for post analysis and data mining on the formula assigned datasets from FT-ICR MS: "MoleTrans is a webtool for post analysis and data mining on the formula assigned datasets from FT-ICR MS."
- [readme] it can partialy support the combined analysis on the compound annotated results based on other mass spectrometry: "Alternatively, it can partialy support the combined analysis on the compound annotated results based on other mass spectrometry."
- [other] Extract elemental composition (C, H, O, N, S, P counts): "Parse the molecular formula assignments and extract elemental composition (C, H, O, N, S, P counts)."
1---2name: chemodiversity-descriptor-calculation3description: Use when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify the molecular chemodiversity, elemental composition diversity, or complexity of environmental organic samples for cross-sample comparison or.4license: CC-BY-4.05---67# chemodiversity-descriptor-calculation89## Summary1011Compute molecular chemodiversity descriptors (mass-based statistics, elemental stoichiometry diversity indices, and molecular complexity metrics) from formula-assigned FT-ICR MS datasets to characterize the molecular diversity and transformation patterns of environmental organic complex mixtures.1213## When to use1415Apply this skill when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify the molecular chemodiversity, elemental composition diversity, or complexity of environmental organic samples for cross-sample comparison or transformation analysis.1617## When NOT to use1819- Input is not formula-assigned: MoleTrans requires parsed molecular formulas; raw m/z values without formula assignment cannot be processed.20- Data source is not FT-ICR MS or supported mass spectrometry: while MoleTrans can partially support compound-annotated results from other MS approaches, it is optimized for FT-ICR formula assignments.21- Sample lacks sufficient molecular diversity: descriptor computation assumes a heterogeneous molecular population; homogeneous or single-compound samples may not benefit from chemodiversity metrics.2223## Inputs2425- formula-assigned FT-ICR MS dataset (CSV or tab-delimited table)26- columns: molecular formulas, mass values, sample identifiers2728## Outputs2930- structured descriptor table with sample identifiers and chemodiversity metrics31- mass-based statistics per sample32- elemental stoichiometry diversity indices per sample33- molecular complexity metrics per sample3435## How to apply3637Load the formula-assigned FT-ICR MS dataset into MoleTrans post-analysis module. Parse the molecular formula assignments to extract elemental composition (C, H, O, N, S, P counts) for each formula. Compute a suite of chemodiversity descriptors including mass-based statistics (e.g., mean, median, standard deviation of molecular masses), elemental stoichiometry diversity indices (ratios and proportional distributions of elements), and molecular complexity metrics across the sample. Export a structured output table or report mapping sample identifiers to descriptor values. Validate that computed indices capture expected trends in molecular complexity and that elemental counts match the input formulas.3839## Related tools4041- **MoleTrans** (post-analysis and data-mining platform for computing chemodiversity descriptors from formula-assigned FT-ICR MS datasets) — github.com/JibaoLiu/MoleTrans4243## Evaluation signals4445- Output descriptor table contains one row per sample with all expected chemodiversity metrics (mass statistics, elemental diversity indices, complexity scores) populated and non-null.46- Elemental composition counts (C, H, O, N, S, P) in parsed formulas match the elemental tallies reflected in stoichiometry diversity indices.47- Molecular complexity metrics show expected correlation with formula mass and elemental richness (e.g., higher complexity for larger, more heteroatom-rich molecules).48- Sample identifiers in output table map one-to-one to input dataset rows; no duplicates or drops.49- Descriptor values fall within chemically plausible ranges (e.g., mass > 0, diversity indices 0–1 or within documented scale).5051## Limitations5253- MoleTrans can only partially support combined analysis on compound-annotated results from non-FT-ICR MS approaches; full optimization is for FT-ICR formula-assigned data.54- Requires user registration (or demo account) to access the live webtool; source code from the repository provides only the main calculation functions and algorithms, not the complete web interface.55- Descriptor computation assumes adequate sample size and molecular diversity; very small or homogeneous datasets may yield uninformative or unreliable indices.56- Post-analysis is limited to elemental composition (C, H, O, N, S, P); other elements present in formulas may not be represented in standard diversity metrics.5758## Evidence5960- [other] formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values): "Load the formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) into the MoleTrans post-analysis module"61- [other] chemodiversity descriptors including mass-based statistics, elemental stoichiometry diversity indices, and molecular complexity metrics: "Compute molecular chemodiversity descriptors including mass-based statistics, elemental stoichiometry diversity indices, and molecular complexity metrics across the sample."62- [readme] MoleTrans is a webtool for post analysis and data mining on the formula assigned datasets from FT-ICR MS: "MoleTrans is a webtool for post analysis and data mining on the formula assigned datasets from FT-ICR MS."63- [readme] it can partialy support the combined analysis on the compound annotated results based on other mass spectrometry: "Alternatively, it can partialy support the combined analysis on the compound annotated results based on other mass spectrometry."64- [other] Extract elemental composition (C, H, O, N, S, P counts): "Parse the molecular formula assignments and extract elemental composition (C, H, O, N, S, P counts)."
HolobiomicsLab