Export Glycopeptide Search Results

Export 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 glycopeptide-training-mgf¶

Export identified glycopeptide spectrum matches for model training as an annotated MGF file.

glycresoft export glycopeptide-training-mgf [OPTIONS] DATABASE_CONNECTION
                                            ANALYSIS_IDENTIFIER

Options

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

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

-t, --threshold <float>¶: Minimum MS2 score to export

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 identified-glycans-from-glycopeptides¶

Export the glycans attached to any identified glycopeptides.

The files are written in an importable format to be used to create a new glycan hypothesis.

glycresoft export identified-glycans-from-glycopeptides [OPTIONS]
                                                        DATABASE_CONNECTION
                                                        ANALYSIS_IDENTIFIER

Options

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

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 annotate-matched-spectra¶

Export graphical renderings of individual MS/MS assignments of glycopeptides to PDF.

The output file will contain one spectrum per PDF page.

glycresoft export annotate-matched-spectra [OPTIONS] DATABASE_CONNECTION
                                           ANALYSIS_IDENTIFIER

Options

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

-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

glycresoft export write-csv-spectrum-library¶

Export individual MS/MS assignments of glycopeptides to CSV.

Each row corresponds to a single product ion match, partitioned by scan ID. Unmatched peaks are ignored.

glycresoft export write-csv-spectrum-library [OPTIONS] DATABASE_CONNECTION
                                             ANALYSIS_IDENTIFIER

Options

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

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

-t, --fdr-threshold <float>¶: [default: 0.05]

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

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