Claude Skills by HolobiomicsLab

Use when after converting a CSV file of molecule definitions into a peak

Use when after elution peaks have been detected on composite mass tracks

Use when after calculating 12 peak-quality metrics on a development set

Use when when you have manually labeled LC-MS peaks as 'High quality'

Use when you have completed XCMS preprocessing (getEIC() and fillPeaks())

Use when when you have loaded aligned peak-alignment data from a molecular

Use when after composite-map peak detection (scipy.signal.find_peaks)

Use when after applying cluster-based filtering with quasi-molecular

Use when after applying cluster-based filtering with quasi-molecular

Use when when validating a metabolomics pathway analysis method (particularly

Use when when identifying landmark peaks for retention time alignment

Use when after peak detection in a nontargeted LC-MS workflow when you

Use when when extracting benchmark peaks from mzML files for multiple

Use when you have a set of picked peaks from INADEQUATE NMR spectra and

Use when after peak detection has been applied to untargeted or targeted

Use when your peak table contains ions with similar retention time and

Use when you have raw or converted spectral data (jcamp, RAW, or mzML

Use when you have a table of detected chromatographic peaks (e.g., from

Use when after generating a peak table from XCMS peakTable() output in

Use when when receiving a peak or feature table output from an unknown

Use when when you have extracted peak tables from multiple independent

Use when after peak clustering in a GCIMS preprocessing pipeline, when

Use when you need to validate the reference-semantics behavior of mpactr

Use when when using mpactr filter functions (e.g., filter_mispicked_ions,

Use when after converting peak-picker output (from MZmine, XCMS, MS-DIAL,

Use when when you have a fragment peak list (m/z values and intensities)

Use when you have a raw peak-intensity matrix from untargeted LC-MS data

Use when after running a 1D peak detection function (e.g., mzapy.peaks.find_peaks_1d_localmax

Use when you have raw or semi-processed m/z peak detection output from

Use when you have extracted m/z and retention time (m/z-RT) information

Use when when you have mass spectrometry data organized in a Pandas DataFrame

Use when you have mass spectrometry data loaded into a Pandas DataFrame

Use when after annotating mass-difference pairs with candidate adduct

Use when when you have two co-registered LA-ICP-MS element images and

Use when when performing reverse spectral search on MS/MS data suspected

Use when preparing code for contribution to a Python project that mandates

Use when when you have a peptide sequence and need to predict which fragment

Use when you have raw mass spectrometry data in MS1 format and need to

Use when you have a peptide sequence, precursor charge state, and observed

Use when after embedding MS/MS spectra into a 32-dimensional vector space

Use when you have a list of polypeptide sequences (one per line or CSV

'Use when when you have an observed MS/MS spectrum and need to annotate

'Use when you have PSM files from a proteomics search engine (e.g., MaxQuant,

Use when you have peptide or protein sequences (as FASTA strings or text

Use when when you have a pre-trained Casanovo model, annotated MS/MS

Use when when you have a peptide sequence and need to predict its fragmentation

Use when when you have a peptide sequence, observed MS2 spectrum peaks

'Use when when you have a tandem mass spectrum (MSMS) with known peptide

Use when when you have high-resolution tandem mass spectrometry data

Use when you have a collection of MS/MS spectra (in mzML or MGF format)