(Deprecated) Retention Time Modeling for Glycopeptide Identifications

(Deprecated) Retention Time Modeling for Glycopeptide Identifications¶

Note

This topic covers the stand-alone RT model described in Klein, J., & Zaia, J. (2020). Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC–MS/MS. Journal of Proteome Research, 19(5), 2113–2121. https://doi.org/10.1021/acs.jproteome.0c00051.

Another retention time modeling strategy was added to the glycopeptide search tools that is more robust and has more features. This is retained purely for reference to that publication.

GlycReSoft can use chromatographic retention time to refine glycan composition assignments to glycopeptides using related glycoforms as points of reference.

Preparing Input Data¶

The model fitting process uses a simplified representation of glycopeptide chromatograms which can be exported as a CSV file from a result database.

glycresoft export glycopeptide-chromatogram-records¶

Export a simplified table of glycopeptide chromatographic features, formatted for retention time modeling.

glycresoft export glycopeptide-chromatogram-records [OPTIONS]
                                                    DATABASE_CONNECTION
                                                    ANALYSIS_IDENTIFIER

Options

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

-r, --apex-time-range <tuple>¶: The range of apex times to include [default: 0, inf]

-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

Fitting The Model¶

glycresoft analyze retention-time fit-glycopeptide-retention-time¶

Fit a retention time model to glycopeptide chromatogram observations, and evaluate the chromatographic apex: retention of each glycopeptide based upon the model fit. For large enough groups, try to fit a model to just that group.

glycresoft analyze retention-time fit-glycopeptide-retention-time 
    [OPTIONS] CHROMATOGRAM_CSV_PATH OUTPUT_PATH

Options

-t, --test-chromatogram-csv-path <path>¶: Path to glycopeptide CSV chromatograms to evaluate with the model, but not fit on

-p, --prefer-joint-model¶: Prefer the joint model over the peptide-specific ones [default: False]

-m, --minimum-observations-for-specific-model <int>¶: The minimum number of observations required to fit a peptide sequence-specific model [default: 20]

-r, --use-retention-time-normalization¶: [default: False]

Arguments

CHROMATOGRAM_CSV_PATH¶: Required argument <path>

OUTPUT_PATH¶: Required argument <path>

Re-using A Fitted Model¶

glycresoft analyze retention-time evaluate-glycopeptide-retention-time¶

Predict and evaluate the retention time of glycopeptides using an existing model.

The model file should have the extension .pkl and have been produced by the same version of GlycReSoft.

glycresoft analyze retention-time evaluate-glycopeptide-retention-time 
    [OPTIONS] MODEL_PATH CHROMATOGRAM_CSV_PATH OUTPUT_PATH

Arguments

MODEL_PATH¶: Required argument <path>

CHROMATOGRAM_CSV_PATH¶: Required argument <path>

OUTPUT_PATH¶: Required argument <path>

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