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Comprehensive understanding of the spec-kit methodology. Constitution-driven feature development with specify, plan, tasks, and implement phases.
Adversarial requirements engineering skill that compiles ambiguous feature requests into a validated JSON spec, then instructs the LLM to generate context-appropriate artifacts in…
Use when turning an approved SpecRail product and technical spec into the numbered `tasks.md` plan. Creates stable task IDs, owners, done-when conditions, verification commands,…
Organize spec files. Use when creating specs. For EARS syntax, use the ears skill.
Извлечение характеристик товара из текста карточки или structured specs WB. Возвращает словарь key→value без нормализации.
Use quando o usuário pede para promover uma entrada ou backlog já refinado, criar, iniciar ou consolidar uma especificação nova ou ainda em Draft em `spec.md`.
Construir a documentação técnica em docs/ e o inventário npm/Composer em .specsfy/PACKAGES.md. Use ao documentar sistemas ou após implementações.
Ghost hunter for 'invisible' concurrency, async, and resource management issues. Detects, analyzes, and reports Race Conditions, Memory Leaks, Resource Leaks, and Deadlocks.
Spectra orchestrator — auto-detect which spectra sub-skill to invoke based on project state and user intent
Spec Kit 五層深度規格展開 + OpenSpec/Spectra 變更管理框架的融合方法論。 適用情境：用戶提到「寫 spec」「寫規格」「展開需求」「需求規格」「proposal」 「openspec」「spectra」「spec kit」「五層展開」「深度規格」「變更管理」 「delta spec」「changes…
Use when when loading MS/MS spectra from MGF files for FIDDLE model training or evaluation, or when preparing spectrum–annotation pairs for rescore model data augmentation (TCN…
Use when when you need to extract m/z and intensity peak values from a Spectra object backed by MsBackendMzR or similar on-disk backends; when analyzing subsets of spectra without…
SPECTRA v4 — vendor-agnostic specification and planning methodology for AI agents.
Use when you have mass spectrometry spectral data (m/z and intensity pairs, precursor m/z, MS level, and metadata) in R memory or in a file format (mzML, mzXML, CDF, MGF, MSP),…
Use when when you have extracted and concatenated MS/MS spectra from multiple replicates for a set of metabolomic features (stored in a preprocessed list), and need to apply…
Use when when implementing a custom MsBackend and the spectraData() method needs to return all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of…
Use when when processing raw or aggregated mass spectra datasets (from .mgf, .msp, .json, or .
Use when you have loaded raw MSI spectral data (imzML format) in profile or centroid mode and need to remove background noise and baseline artifacts before intensity normalization…
Use when after running spectral networking on tandem MS data and obtaining a network graph, when you need to assess which spectra cluster together, determine cluster…
Use when you have computed a sparse pairwise distance matrix from MS/MS spectra (via nearest neighbor indexing) and need to partition spectra into homogeneous clusters—typically…
Use when you have a collection of tandem mass spectrometry spectra in mzML or similar format and need to prepare them for LDA-based motif discovery.
Use when you have preprocessed 1H NMR spectral data (e.g., from plasma or biological samples acquired on a 600 MHz instrument) and need to identify the chemical composition of a…
Use when you have completed a ViMMS simulation run or processed real LC-MS/MS data and need to quantitatively assess whether one DDA controller (e.g., WeightedDEWController with…
Use when you have raw IM-MS data in Agilent MassHunter (.d) or UIMF format from drift tube (DT) or SLIM instruments, and you need to reduce data volume while preserving s — from…
Use when you have completed msFeaST pipeline preprocessing and generated a JSON output file (dashboard_data.
Use when when you have downloaded raw spectral datasets from multiple spectroscopic modalities (NMR, HSQC, COSY, IR) in their native or proprietary formats and need to convert…
Use when after converting existing mass spectrometry formats (mzML, vendor formats) into mzPeak using command-line tools or when receiving mzPeak files from external sources.
Use when after converting mass-spectrometry data from an existing format (mzML, mzXML, or vendor-specific formats) into mzPeak using command-line tools or API calls.
Use when apply TIC normalization when you have raw, unprocessed mass spectrometry data (Cardinal objects or imaging matrices with 10,000+ m/z features and 1,000+ spectra) where…
Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct-injection MS (DI-MS), ASAP-MS, or other ambient ionization instruments (AI-MS, LDI-MS — from…
Use when importing raw or public mass spectrometry spectral data in formats such as MGF, MSP, or mzML that may contain incomplete metadata (e.g., missing instrument type,…
Use when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/...
Use when you have generated predicted fragment spectra for a set of compounds using CFM-ID or similar in-silico prediction tools and need to organize these results into a…
Use when you need to generate synthetic LC/GC-MS feature tables or raw mzML files with realistic peak complexity, ion multiplicities, and natural spectral variation—not just…
Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON…
Use when when you have an unknown mass spectrum (query spectrum) and need to search it against a reference database of billions of spectra to find matching or structurally related…
Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected)
Use when you have untargeted MS2 spectra from environmental or clinical samples that will be used for natural product identification (e.g., linking to BGCs via IOKR or other…
Use when you have high-resolution tandem MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or searched at scale (millions of spectra).
Use when after generating a tile matrix or feature count matrix from single-cell ATAC-seq, RNA-seq, Hi-C, or methylation data, before clustering or UMAP visualization, when you…
Use when you have a set of preprocessed MS/MS spectra (binned to 10,000 m/z bins with intensities square-root transformed) and a trained MS2DeepScore Siamese neural network model,…
Use when you have a collection of pre-processed MS/MS spectra (binned, intensity-normalized) and a trained MS2DeepScore base network, and you need to compute structural similarity…
Use when after training a transformer-encoder-based mass spectrometry embedding model (e.
Use when you have a large single-cell count matrix (≥10 million cells) in CSR format and need to verify whether the matrix-free spectral embedding in SnapATAC2 achieves its…
Use when when you have preprocessed MS/MS spectral peak data (m/z and intensity pairs) and need to compute a complexity metric for individual spectra prior to similarity…
Use when after feature detection and alignment in untargeted MS data processing, when you need to filter or rank candidate metabolite annotations by spectral quality before…
Use when you have MS2 fragmentation spectra from multiple metabolomics samples and need to compare them in a retention time-agnostic manner, especially when samples are chemically…
Use when when generating augmented variants of single-channel or multi-channel ion images for contrastive learning in mass spectrometry imaging analysis.
Use when processing raw MS/MS spectra (in MGF, mzML, mzXML, JSON, or MSP format) prior to MS2Query library matching or MS2Deepscore embedding calculation.
Use when you have a Thermo Fisher Orbitrap .raw file and need to recover the intensity profile of a specific m/z value or peptide across the LC separation dimension…
Use when after submitting an LC-MS/MS fragmentation spectrum to the MSNovelist web service and receiving a JSON response containing ranked de-novo structure candidates.
Use when you have received chemical annotations from GNPS spectral library matching and need to (1) assess annotation confidence and validity for downstream analysis, (2)…
Use when after MS2Deepscore has selected the top 2000 candidate spectra from a library based on spectral similarity, and you need to re-rank these candidates to surface the single…
Use when when migrating an existing file-based spectral library (stored as JSON, CSV, or binary formats) into a production system that requires frequent subset queries by metadata…
Use when after theoretical spectra have been generated for lipid–adduct combinations with enumerated fragment masses and intensities, and you need to deploy them for downstream…
Use when you have one or more MS/MS spectra in .mgf format (or USI identifiers) and need to: (1) identify unknowns by searching against domain-curated reference data; (2) assign…
Use when you have raw GC-MS output in CSV format (with Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, and File.Name columns) and need to systematically…
Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a…
Use when when you have MS/MS fragment spectra (in .mgf format) acquired from unknown metabolite features and need to annotate them against known compounds.