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glycresoft-analyze-retention-time-evaluate-glycopeptide-retention-time command line option
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glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option
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glycresoft-analyze-search-glycan command line option
- --export <choice>
- --mass_shift-combination-limit <int>
- -a, --mass_shift <string>
- -d, --minimum-mass <float>
- -f, --ms1-scoring-feature <choice>
- -g, --grouping-error-tolerance <relative mass error>
- -k, --network-path <path>
- -m, --mass-error-tolerance <relative mass error>
- -mn, --msn-mass-error-tolerance <relative mass error>
- -n, --analysis-name <string>
- -o, --output-path <string>
- -p, --processes <int>
- -r, --regularize <regularization parameter>
- -s, --require-msms-signature <float>
- -t, --delta-rt <float>
- -w, --regularization-model-path <path>
- DATABASE_CONNECTION
- HYPOTHESIS_IDENTIFIER
- SAMPLE_PATH
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glycresoft-analyze-search-glycopeptide command line option
- --export <choice>
- --isotope-probing-range <int>
- --maximum-mass <float>
- --save-intermediate-results <path>
- -D, --decoy-database-connection <string>
- -G, --permute-decoy-glycan-fragments
- -R, --rare-signatures
- -a, --adduct <string>
- -f, --use-peptide-mass-filter
- -g, --grouping-error-tolerance <relative mass error>
- -m, --mass-error-tolerance <relative mass error>
- -mn, --msn-mass-error-tolerance <relative mass error>
- -n, --analysis-name <string>
- -o, --output-path <path>
- -p, --processes <int>
- -q, --psm-fdr-threshold <float>
- -s, --tandem-scoring-model <choice or>
- -w, --workload-size <int>
- -x, --oxonium-threshold <float>
- DATABASE_CONNECTION
- HYPOTHESIS_IDENTIFIER
- SAMPLE_PATH
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glycresoft-analyze-search-glycopeptide-multipart command line option
- --export <choice>
- --isotope-probing-range <int>
- -D, --decoy-hypothesis-identifier <int>
- -M, --memory-database-index
- -R, --rare-signatures
- -S, --glycoproteome-smoothing-model <path>
- -T, --target-hypothesis-identifier <int>
- -a, --adduct <string>
- -f, --fdr-estimation-strategy <choice>
- -g, --grouping-error-tolerance <relative mass error>
- -m, --mass-error-tolerance <relative mass error>
- -mn, --msn-mass-error-tolerance <relative mass error>
- -n, --analysis-name <string>
- -o, --output-path <path>
- -p, --processes <int>
- -q, --psm-fdr-threshold <float>
- -s, --tandem-scoring-model <choice or>
- -w, --workload-size <int>
- -y, --glycan-score-threshold <float>
- DATABASE_CONNECTION
- DECOY_DATABASE_CONNECTION
- SAMPLE_PATH
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glycresoft-build-hypothesis-glycan-combinatorial command line option
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glycresoft-build-hypothesis-glycan-glyspace command line option
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glycresoft-build-hypothesis-glycan-text command line option
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glycresoft-build-hypothesis-glycopeptide-fa command line option
- -F, --not-full-crossproduct
- -G, --glycan-source-identifier <string>
- -R, --reverse
- -V, --max-variable-modifications <int>
- -c, --constant-modification <string>
- -e, --enzyme <string>
- -g, --glycan-source <string>
- -m, --missed-cleavages <int>
- -n, --name <string>
- -p, --processes <int>
- -s, --glycan-source-type <choice>
- -u, --occupied-glycosites <int>
- -v, --variable-modification <string>
- -y, --semispecific-digest
- -z, --peptide-length-range <tuple>
- DATABASE_CONNECTION
- FASTA_FILE
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glycresoft-export-glycopeptide-chromatogram-records command line option
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glycresoft-export-glycopeptide-identification command line option
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glycresoft-export-glycopeptide-spectrum-matches command line option
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glycresoft-export-mzid command line option
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glycresoft-mzml-preprocess command line option
- --ignore-msn
- -a, --averagine <averagine>
- -an, --msn-averagine <averagine>
- -b, --background-reduction <float>
- -bn, --msn-background-reduction <float>
- -c, --maximum-charge <int>
- -e, --end-time <float>
- -g, --ms1-averaging <int>
- -m, --missed-peaks <int>
- -mn, --msn-missed-peaks <int>
- -mo, --mass-offset <float>
- -n, --name <string>
- -p, --processes <int>
- -r, --transform <choice>
- -rn, --msn-transform <choice>
- -s, --start-time <float>
- -snr, --signal-to-noise-threshold <float>
- -t, --score-threshold <float>
- -tn, --msn-score-threshold <float>
- -v, --extract-only-tandem-envelopes
- MS_FILE
- OUTFILE_PATH
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