Claude Skills by HolobiomicsLab

Use when when loading and processing raw or recalibrated FT-ICR mass

Use when after feature extraction from mzML/mzXML breath analysis data

Use when you have mass spectrometry data in .raw, .d, or mzXML format

Use when converting raw MS/MS spectra from library files (e.g., .msp

Use when after scipy.signal.find_peaks has identified candidate peaks

Use when traditional peak extraction algorithms have produced a feature

Use when you have preprocessed (smoothed and baseline-corrected) 2D-GCxGC-MS

Use when you have raw LC-MS/MS spectra from vendor instruments (mzML,

Use when after peak picking and alignment have been performed on MSImagingArrays

Use when you have raw MS/MS spectra (in formats like mzML, json, mgf,

Use when when you have tandem mass spectra (mz/intensity pairs with precursor

Use when you have raw metabolomic LC-MS data processed through XCMS CentWave

Use when when applying iterative peak detection (local-maximum or Gaussian-fit

Use when after peak detection and clustering have been completed on aligned

Use when you have a metabolomic feature table (rows=features, columns=samples)

Use when you have a filtered MS-DIAL peak list (post-generic filtering)

Use when after executing feature detection and quantification on raw

Use when after peak filtering (by m/z, isotopic presence, formula assignment

Use when when training Word2Vec embeddings on mass spectra represented

Use when you have raw MS/MS spectral peak lists with absolute intensity

Use when when you have imported raw mass spectrometry spectral data (in

Use when you have loaded raw mass spectrometry spectral data (in MGF,

Use when you have a peak intensity matrix from LC/GC-MS analysis with

Use when immediately after automatic peak detection on a raw or processed

Use when when uploading a new peak list or complex sample data file with

Use when you have acquired MS/MS spectra containing suspect noise ions—either

Use when you have extracted a raw peak list (chemical shifts in a TXT

Use when after successfully resolving a USI string to a specific mass

Use when when importing raw mass spectrometry data from vendor or open

Use when you need to validate batch correction or normalization algorithms,

Use when when you have LC-MS-MS metabolomics data in MGF format and need

Use when after peak detection when you have a table of detected peaks

Use when when you have loaded mass spectrometry data (from mzML or Bruker

Use when you have raw mass spectra (e.g., from NIST 2017 or MassBank)

Use when when you have raw MS2 spectra (m/z and intensity pairs) and

Use when when you have raw mzML files and a corresponding feature table

Use when you have picked peaks (coordinates and intensities) from INADEQUATE

Use when after peak clustering has produced peak network groups (ideally

Use when you have aligned MS2 spectra from multiple samples and need

Use when after molecular formula assignment and peak filtering are complete,

Use when you have centroided high-resolution Orbitrap or GC-CI-MS mzML

Use when you have claims in a paper or tool documentation that one peak

'Use when at the entry point of SLAW processing when you have centroided

Use when analyzing raw 2D MS data (m/z vs. retention time maps) where

Use when when reconstructing a metabolite fragment library entry from

Use when when you have completed non-targeted peak picking and alignment

Use when you have raw or baseline-corrected mass spectra from MSImagingArrays

Use when when processing LC-MS mass tracks (EICs) and you need to identify

Use when when you have identified the set of analytes (peptides, nucleosides,

Use when you have a CSV file containing nucleoside or peptide molecular