ms-index¶

Data Conversion¶

mzML Conversion¶

ms-index mzml¶

Convert source into mzML format written to output, applying a collection of optional data transformations along the way.

ms-index mzml [OPTIONS] SOURCE OUTPUT

Options

-r, --ms1-filter <func>¶

-rn, --msn-filter <func>¶

-p, --pick-peaks¶: Enable peak picking, centroiding profile data

-f, --reprofile¶: Enable reprofiling, converting all MS1 spectra into smoothed profile data

-z, --compress¶: Compress the output file using gzip

-c, --correct-precursor-mz¶: Adjust the precursor m/z of each MSn scan to the nearest peak m/z in the precursor

--update-metadata, --no-update-metadata¶: Whether or not to add the conversion program’s metadata to the mzML file.

-X, --option <tuple>¶: Pass an arbitrary key-value pair through to configure the writer (May specify more than once)

Arguments

SOURCE¶: Required argument <string>

OUTPUT¶: Required argument <path>

MGF Conversion¶

ms-index mgf¶

Convert a mass spectrometry data file to MGF. MGF can only represent centroid spectra and generally does not contain any MS1 information.

ms-index mgf [OPTIONS] SOURCE OUTPUT

Options

-z, --compress¶: Compress the output file using gzip

-rn, --msn-filter <func>¶

Arguments

SOURCE¶: Required argument <string>

OUTPUT¶: Required argument <path>

mzMLb Conversion¶

This feature requires h5py to be installed, and hdf5plugin for the faster non-zlib based compressors to be available.

ms-index mzmlb¶

Convert source into mzML format written to output, applying a collection of optional data transformations along the way.

ms-index mzmlb [OPTIONS] SOURCE [OUTPUT]

Options

-r, --ms1-filter <func>¶

-rn, --msn-filter <func>¶

-p, --pick-peaks¶: Enable peak picking, centroiding profile data

-f, --reprofile¶: Enable reprofiling, converting all MS1 spectra into smoothed profile data

-c, --correct-precursor-mz¶: Adjust the precursor m/z of each MSn scan to the nearest peak m/z in the precursor

--update-metadata, --no-update-metadata¶: Whether or not to add the conversion program’s metadata to the mzML file.

-z, --compression <choice>¶: The compressor to use

Choices: [

gzip; blosc; blosc:lz4;

blosc:lz4hc; blosc:zlib; blosc:zstd;

zlib]

-X, --option <tuple>¶: Pass an arbitrary key-value pair through to configure the writer (May specify more than once)

Arguments

SOURCE¶: Required argument <string>

OUTPUT¶: Optional argument <path>

Indexing¶

ms-index byte-index¶

Build an external byte offset index for a MS data file, saving time when opening the file with indexing enabled.

Supported Formats: mzML, mzXML, MGF

ms-index byte-index [OPTIONS] [PATHS]...

Arguments

PATHS¶: Optional argument(s) <path>

ms-index metadata-index¶

Build an external scan metadata index for a mass spectrometry data file.

This extended index is saved in a separate JSON file that can be loaded with ExtendedScanIndex. It includes the scan time of all scans, the precursor mass of MSn scans, as well as the relationships between precursor and product ion scans, as well as other details. See ExtendedScanIndex for more information

ms-index metadata-index [OPTIONS] [PATHS]...

Options

-D, --deconvoluted¶: Whether or not to assume this file has been processed specifically by ms_deisotope’s deconvolution algorithm

-p, --processes <int>¶: Number of worker processes to use. Defaults to 4 or the number of CPUs, whichever is lower

Arguments

PATHS¶: Optional argument(s) <path>

ms-index msms-intervals¶

Construct an interval tree spanning time and m/z domains where MSn spectra were acquired in the LC-MS map.

The interval tree is serialized to JSON.

ms-index msms-intervals [OPTIONS] [PATHS]...

Options

-o, --output <path>¶

-p, --processes <int>¶: Number of worker processes to use. Defaults to 4 or the number of CPUs, whichever is lower

Arguments

PATHS¶: Optional argument(s) <path>

Analytical Utilities¶

ms-index describe¶

Produces a minimal textual description of a mass spectrometry data file.

ms-index describe [OPTIONS] PATH

Options

-d, --diagnostics¶: Run more diagnostics, greatly increasing runtime but producing additional informatoin

Arguments

PATH¶: Required argument <path>

ms-index charge-states¶

Count the different precursor charge states in a mass spectrometry data file.

This command will construct a metadata index if it is not found.

ms-index charge-states [OPTIONS] PATH

Arguments

PATH¶: Required argument <path>

ms-index precursor-clustering¶

Cluster precursor masses in a mass spectrometry data file.

This command will construct a metadata index if it is not found.

ms-index precursor-clustering [OPTIONS] PATH

Arguments

PATH¶: Required argument <path>

ms-index spectrum-clustering¶

Cluster spectra by precursor mass and cosine similarity.

Spectrum clusters are written out to a text file recording cluster precursor mass, within-cluster similarity, and the source file and scan ID for each cluster member.

ms-index spectrum-clustering [OPTIONS] [PATHS]...

Options

-m, --precursor-error-tolerance <float>¶

-t, --similarity-threshold <float>¶

-o, --output <path>¶

-c, --cache-size <int>¶: The number of scans to cache in memory when not using –in-memory. If you are clustering multiple files, this number will be apply to each file separately.

-M, --in-memory¶: Whether to load the entire dataset into memory for better performance

-D, --deconvoluted¶: Whether to assume the spectra are deconvoluted or not

Arguments

PATHS¶: Optional argument(s) <path>