Exporting Glycopeptide Search Results¶

glycresoft stores its search results in a SQLite3 database like the one it writes hypotheses into. This lets it search for results quickly, but the format is not as easy to read through as a text file, and adds extra layers of complexity to find information requiring complex SQL queries. It’s possible to export search results in several other formats which can be read by other tools.

glycresoft export glycopeptide-identification¶

Write each distinct identified glycopeptide in CSV format

glycresoft export glycopeptide-identification [OPTIONS] DATABASE_CONNECTION
                                              ANALYSIS_IDENTIFIER

Options

-o, --output-path <path>¶: Path to write to instead of stdout

-r, --report¶: Export an HTML report instead of a CSV [default: False]

-m, --mzml-path <path>¶: Path to read processed spectra from instead of the path embedded in the analysis metadata

-t, --threshold <float>¶: The minimum MS2 score threshold (larger is better) [default: 0]

-f, --fdr-threshold <float>¶: The maximum FDR threshold (smaller is better) [default: 1]

Arguments

DATABASE_CONNECTION¶: Required argument <databaseconnectionparam> A connection URI for a database, or a path on the file system

ANALYSIS_IDENTIFIER¶: Required argument <string> The ID number or name of the glycopeptide analysis to use

glycresoft export glycopeptide-spectrum-matches¶

Write each matched glycopeptide spectrum in CSV format

glycresoft export glycopeptide-spectrum-matches [OPTIONS] DATABASE_CONNECTION
                                                ANALYSIS_IDENTIFIER

Options

-o, --output-path <path>¶: Path to write to instead of stdout

-t, --threshold <float>¶: The minimum MS2 score threshold (larger is better) [default: 0]

-f, --fdr-threshold <float>¶: The maximum FDR threshold (smaller is better) [default: 1]

Arguments

DATABASE_CONNECTION¶: Required argument <databaseconnectionparam> A connection URI for a database, or a path on the file system

ANALYSIS_IDENTIFIER¶: Required argument <string> The ID number or name of the glycopeptide analysis to use

glycresoft export mzid¶

Write identified glycopeptides as mzIdentML file, and associated MSn spectra to a paired mzML file if the matched data are available. If an mzML file is written it will also contain the extracted ion chromatograms for each glycopeptide with an extracted elution profile.

glycresoft export mzid [OPTIONS] DATABASE_CONNECTION ANALYSIS_IDENTIFIER
                       OUTPUT_PATH

Options

--embed-protein-sequences, --exclude-protein-sequences¶: Include protein sequences in the output file [default: True]

-m, --mzml-path <path>¶: Alternative path to find the source mzML file

Arguments

DATABASE_CONNECTION¶: Required argument <databaseconnectionparam> A connection URI for a database, or a path on the file system

ANALYSIS_IDENTIFIER¶: Required argument <string> The ID number or name of the glycopeptide analysis to use

OUTPUT_PATH¶: Required argument <string>