Index

Symbols

--adduct glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --analysis-name glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --analysis-path glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --annotation-path glycresoft-build-hypothesis-glycopeptide-fa command line option --apex-time-range glycresoft-export-glycopeptide-chromatogram-records command line option --averagine glycresoft-mzml-preprocess command line option --background-reduction glycresoft-mzml-preprocess command line option --constant-modification glycresoft-build-hypothesis-glycopeptide-fa command line option --decoy-database-connection glycresoft-analyze-search-glycopeptide command line option --decoy-hypothesis-identifier glycresoft-analyze-search-glycopeptide-multipart command line option --default-precursor-ion-selection-window glycresoft-mzml-preprocess command line option --delta-rt glycresoft-analyze-search-glycan command line option --derivatization glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-text command line option --detatch-substituent glycresoft-build-hypothesis-glycan-glyspace command line option --edge-strategy glycresoft-build-hypothesis-glycan-network-build-network command line option --end-time glycresoft-mzml-preprocess command line option --enzyme glycresoft-build-hypothesis-glycopeptide-fa command line option --export glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --expression-rule glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option --extract-only-tandem-envelopes glycresoft-mzml-preprocess command line option --fdr-estimation-strategy glycresoft-analyze-search-glycopeptide-multipart command line option --fdr-threshold glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-export-glycopeptide-chromatogram-records command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option glycresoft-export-write-csv-spectrum-library command line option --glycan-hypothesis glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --glycan-score-threshold glycresoft-analyze-search-glycopeptide-multipart command line option --glycan-source glycresoft-build-hypothesis-glycopeptide-fa command line option --glycan-source-identifier glycresoft-build-hypothesis-glycopeptide-fa command line option --glycan-source-type glycresoft-build-hypothesis-glycopeptide-fa command line option --glycan-type glycresoft-build-hypothesis-glycan-combinatorial command line option --glycopeptide-hypothesis glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --glycoproteome-smoothing-model glycresoft-analyze-search-glycopeptide-multipart command line option --grouping-error-tolerance glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --ignore-msn glycresoft-mzml-preprocess command line option --importable glycresoft-export-glycan-hypothesis command line option --include-children glycresoft-build-hypothesis-glycan-glyspace command line option --include-n-x-c-glycosylation glycresoft-build-hypothesis-glycopeptide-fa command line option --input-path glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-network-add-prebuilt-neighborhoods command line option --isotope-probing-range glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --isotopic-strictness glycresoft-mzml-preprocess command line option --mass-error-tolerance glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --mass-offset glycresoft-mzml-preprocess command line option --mass_shift glycresoft-analyze-search-glycan command line option --mass_shift-combination-limit glycresoft-analyze-search-glycan command line option --max-variable-modifications glycresoft-build-hypothesis-glycopeptide-fa command line option --maximum-charge glycresoft-mzml-preprocess command line option --maximum-mass glycresoft-analyze-search-glycopeptide command line option --memory-database-index glycresoft-analyze-search-glycopeptide-multipart command line option --minimum-mass glycresoft-analyze-search-glycan command line option --minimum-observations-for-specific-model glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option --missed-cleavages glycresoft-build-hypothesis-glycopeptide-fa command line option --missed-peaks glycresoft-mzml-preprocess command line option --motif-class glycresoft-build-hypothesis-glycan-glyspace command line option --ms1-averaging glycresoft-mzml-preprocess command line option --ms1-scoring-feature glycresoft-analyze-search-glycan command line option --msn-averagine glycresoft-mzml-preprocess command line option --msn-background-reduction glycresoft-mzml-preprocess command line option --msn-isotopic-strictness glycresoft-mzml-preprocess command line option --msn-mass-error-tolerance glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --msn-missed-peaks glycresoft-mzml-preprocess command line option --msn-score-threshold glycresoft-mzml-preprocess command line option --msn-transform glycresoft-mzml-preprocess command line option --mzml-path glycresoft-export-annotate-matched-spectra command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-training-mgf command line option glycresoft-export-write-csv-spectrum-library command line option --name glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-network-add-prebuilt-neighborhoods command line option glycresoft-build-hypothesis-glycan-text command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option --network-path glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycan command line option --no-require-multiple-observations glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --no-retention-time-modeling glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --not-full-crossproduct glycresoft-build-hypothesis-glycopeptide-fa command line option --occupied-glycosites glycresoft-build-hypothesis-glycopeptide-fa command line option --output-path glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-network-add-prebuilt-neighborhoods command line option glycresoft-build-hypothesis-glycan-network-build-network command line option glycresoft-export-annotate-matched-spectra command line option glycresoft-export-glycan-hypothesis command line option glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-chromatogram-records command line option glycresoft-export-glycopeptide-hypothesis command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option glycresoft-export-glycopeptide-training-mgf command line option glycresoft-export-identified-glycans-from-glycopeptides command line option glycresoft-export-write-csv-spectrum-library command line option --oxonium-threshold glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --peptide-length-range glycresoft-build-hypothesis-glycopeptide-fa command line option --peptide-masses-per-scan glycresoft-analyze-search-glycopeptide-multipart command line option --permute-decoy-glycan-fragments glycresoft-analyze-search-glycopeptide command line option --prefer-joint-model glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option --processes glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option --psm-fdr-threshold glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --range-rule glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option --rare-signatures glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --ratio-rule glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option --reduction glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-text command line option --regularization-model-path glycresoft-analyze-search-glycan command line option --regularize glycresoft-analyze-search-glycan command line option --report glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-identification command line option --require-msms-signature glycresoft-analyze-search-glycan command line option --require-multiple-observations glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --retain-all-peptides glycresoft-build-hypothesis-glycopeptide-fa command line option --retention-time-modeling glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --reverse glycresoft-build-hypothesis-glycopeptide-fa command line option --save-intermediate-results glycresoft-analyze-search-glycopeptide command line option

--score-threshold glycresoft-mzml-preprocess command line option --semispecific-digest glycresoft-build-hypothesis-glycopeptide-fa command line option --signal-to-noise-threshold glycresoft-mzml-preprocess command line option --smoothing-limit glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --start-time glycresoft-mzml-preprocess command line option --tandem-scoring-model glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option --target-hypothesis-identifier glycresoft-analyze-search-glycopeptide-multipart command line option --target-taxon glycresoft-build-hypothesis-glycan-glyspace command line option --test-chromatogram-csv-path glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option --threshold glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option glycresoft-export-glycopeptide-training-mgf command line option --transform glycresoft-mzml-preprocess command line option --unobserved-penalty-scale glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --use-peptide-mass-filter glycresoft-analyze-search-glycopeptide command line option --use-retention-time-normalization glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option --variable-modification glycresoft-build-hypothesis-glycopeptide-fa command line option --verbose glycresoft-mzml-preprocess command line option --workload-size glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option -a glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -an glycresoft-mzml-preprocess command line option -b glycresoft-mzml-preprocess command line option -bn glycresoft-mzml-preprocess command line option -C glycresoft-build-hypothesis-glycopeptide-fa command line option -c glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -D glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-mzml-preprocess command line option -d glycresoft-analyze-search-glycan command line option glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-text command line option -e glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-network-build-network command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -F glycresoft-build-hypothesis-glycopeptide-fa command line option -f glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option -G glycresoft-analyze-search-glycopeptide command line option glycresoft-build-hypothesis-glycopeptide-fa command line option -g glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -i glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-network-add-prebuilt-neighborhoods command line option glycresoft-export-glycan-hypothesis command line option glycresoft-mzml-preprocess command line option -in glycresoft-mzml-preprocess command line option -k glycresoft-analyze-search-glycan command line option -M glycresoft-analyze-search-glycopeptide-multipart command line option -m glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-export-annotate-matched-spectra command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-training-mgf command line option glycresoft-export-write-csv-spectrum-library command line option glycresoft-mzml-preprocess command line option -mn glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-mzml-preprocess command line option -mo glycresoft-mzml-preprocess command line option -n glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-network-add-prebuilt-neighborhoods command line option glycresoft-build-hypothesis-glycan-text command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -o glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-network-add-prebuilt-neighborhoods command line option glycresoft-build-hypothesis-glycan-network-build-network command line option glycresoft-export-annotate-matched-spectra command line option glycresoft-export-glycan-hypothesis command line option glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-chromatogram-records command line option glycresoft-export-glycopeptide-hypothesis command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option glycresoft-export-glycopeptide-training-mgf command line option glycresoft-export-identified-glycans-from-glycopeptides command line option glycresoft-export-write-csv-spectrum-library command line option -P glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycopeptide-multipart command line option -p glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -q glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option -R glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycopeptide-fa command line option -r glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option glycresoft-analyze-search-glycan command line option glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option glycresoft-build-hypothesis-glycan-text command line option glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-chromatogram-records command line option glycresoft-export-glycopeptide-identification command line option glycresoft-mzml-preprocess command line option -rn glycresoft-mzml-preprocess command line option -S glycresoft-analyze-search-glycopeptide-multipart command line option -s glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -snr glycresoft-mzml-preprocess command line option -T glycresoft-analyze-search-glycopeptide-multipart command line option -t glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option glycresoft-analyze-search-glycan command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-chromatogram-records command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option glycresoft-export-glycopeptide-training-mgf command line option glycresoft-export-write-csv-spectrum-library command line option glycresoft-mzml-preprocess command line option -tn glycresoft-mzml-preprocess command line option -u glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-build-hypothesis-glycopeptide-fa command line option -V glycresoft-build-hypothesis-glycopeptide-fa command line option -v glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-mzml-preprocess command line option -w glycresoft-analyze-fit-glycoproteome-smoothing-model command line option glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option -x glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option -y glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycopeptide-fa command line option -z glycresoft-build-hypothesis-glycopeptide-fa command line option

A

ANALYSIS_IDENTIFIER glycresoft-export-annotate-matched-spectra command line option glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-chromatogram-records command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option glycresoft-export-glycopeptide-training-mgf command line option glycresoft-export-identified-glycans-from-glycopeptides command line option glycresoft-export-write-csv-spectrum-library command line option

C

CHROMATOGRAM_CSV_PATH glycresoft-analyze-retention-time-evaluate-glycopeptide-retention-time command line option glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option

D

DATABASE_CONNECTION glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option glycresoft-build-hypothesis-glycan-combinatorial command line option glycresoft-build-hypothesis-glycan-glyspace command line option glycresoft-build-hypothesis-glycan-network-build-network command line option glycresoft-build-hypothesis-glycan-text command line option glycresoft-build-hypothesis-glycopeptide-fa command line option glycresoft-export-annotate-matched-spectra command line option glycresoft-export-glycan-hypothesis command line option glycresoft-export-glycan-identification command line option glycresoft-export-glycopeptide-chromatogram-records command line option glycresoft-export-glycopeptide-hypothesis command line option glycresoft-export-glycopeptide-identification command line option glycresoft-export-glycopeptide-spectrum-matches command line option glycresoft-export-glycopeptide-training-mgf command line option glycresoft-export-identified-glycans-from-glycopeptides command line option glycresoft-export-write-csv-spectrum-library command line option

DECOY_DATABASE_CONNECTION glycresoft-analyze-search-glycopeptide-multipart command line option

F

FASTA_FILE glycresoft-build-hypothesis-glycopeptide-fa command line option

G

glycresoft-analyze-fit-glycoproteome-smoothing-model command line option --analysis-path --fdr-threshold --glycan-hypothesis --glycopeptide-hypothesis --network-path --no-require-multiple-observations --output-path --processes --require-multiple-observations --smoothing-limit --unobserved-penalty-scale -a -g -i -o -p -P -q -r -u -w glycresoft-analyze-retention-time-evaluate-glycopeptide-retention-time command line option CHROMATOGRAM_CSV_PATH MODEL_PATH OUTPUT_PATH glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option --minimum-observations-for-specific-model --prefer-joint-model --test-chromatogram-csv-path --use-retention-time-normalization -m -p -r -t CHROMATOGRAM_CSV_PATH OUTPUT_PATH glycresoft-analyze-search-glycan command line option --analysis-name --delta-rt --export --grouping-error-tolerance --mass-error-tolerance --mass_shift --mass_shift-combination-limit --minimum-mass --ms1-scoring-feature --msn-mass-error-tolerance --network-path --output-path --processes --regularization-model-path --regularize --require-msms-signature -a -d -f -g -k -m -mn -n -o -p -r -s -t -w DATABASE_CONNECTION HYPOTHESIS_IDENTIFIER SAMPLE_PATH glycresoft-analyze-search-glycopeptide command line option --adduct --analysis-name --decoy-database-connection --export --grouping-error-tolerance --isotope-probing-range --mass-error-tolerance --maximum-mass --msn-mass-error-tolerance --no-retention-time-modeling --output-path --oxonium-threshold --permute-decoy-glycan-fragments --processes --psm-fdr-threshold --rare-signatures --retention-time-modeling --save-intermediate-results --tandem-scoring-model --use-peptide-mass-filter --workload-size -a -D -f -g -G -m -mn -n -o -p -q -R -s -w -x DATABASE_CONNECTION HYPOTHESIS_IDENTIFIER SAMPLE_PATH glycresoft-analyze-search-glycopeptide-multipart command line option --adduct --analysis-name --decoy-hypothesis-identifier --export --fdr-estimation-strategy --glycan-score-threshold --glycoproteome-smoothing-model --grouping-error-tolerance --isotope-probing-range --mass-error-tolerance --memory-database-index --msn-mass-error-tolerance --no-retention-time-modeling --output-path --oxonium-threshold --peptide-masses-per-scan --processes --psm-fdr-threshold --rare-signatures --retention-time-modeling --tandem-scoring-model --target-hypothesis-identifier --workload-size -a -D -f -g -M -m -mn -n -o -p -P -q -R -s -S -T -w -x -y DATABASE_CONNECTION DECOY_DATABASE_CONNECTION SAMPLE_PATH glycresoft-build-hypothesis-glycan-combinatorial command line option --derivatization --glycan-type --name --reduction -c -d -n -r DATABASE_CONNECTION RULE_FILE glycresoft-build-hypothesis-glycan-glyspace command line option --derivatization --detatch-substituent --include-children --motif-class --name --reduction --target-taxon -d -i -m -n -r -s -t DATABASE_CONNECTION glycresoft-build-hypothesis-glycan-network-add-neighborhood command line option --expression-rule --input-path --name --output-path --range-rule --ratio-rule -a -e -i -n -o -r

glycresoft-build-hypothesis-glycan-network-add-prebuilt-neighborhoods command line option --input-path --name --output-path -i -n -o glycresoft-build-hypothesis-glycan-network-build-network command line option --edge-strategy --output-path -e -o DATABASE_CONNECTION HYPOTHESIS_IDENTIFIER glycresoft-build-hypothesis-glycan-text command line option --derivatization --name --reduction -d -n -r DATABASE_CONNECTION TEXT_FILE glycresoft-build-hypothesis-glycopeptide-fa command line option --annotation-path --constant-modification --enzyme --glycan-source --glycan-source-identifier --glycan-source-type --include-n-x-c-glycosylation --max-variable-modifications --missed-cleavages --name --not-full-crossproduct --occupied-glycosites --peptide-length-range --processes --retain-all-peptides --reverse --semispecific-digest --variable-modification -a -c -C -e -F -g -G -m -n -p -R -s -u -v -V -y -z DATABASE_CONNECTION FASTA_FILE glycresoft-export-annotate-matched-spectra command line option --mzml-path --output-path -m -o ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-export-glycan-hypothesis command line option --importable --output-path -i -o DATABASE_CONNECTION HYPOTHESIS_IDENTIFIER glycresoft-export-glycan-identification command line option --output-path --report --threshold -o -r -t ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-export-glycopeptide-chromatogram-records command line option --apex-time-range --fdr-threshold --output-path -o -r -t ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-export-glycopeptide-hypothesis command line option --output-path -o DATABASE_CONNECTION HYPOTHESIS_IDENTIFIER glycresoft-export-glycopeptide-identification command line option --fdr-threshold --mzml-path --output-path --report --threshold -f -m -o -r -t ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-export-glycopeptide-spectrum-matches command line option --fdr-threshold --output-path --threshold -f -o -t ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-export-glycopeptide-training-mgf command line option --mzml-path --output-path --threshold -m -o -t ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-export-identified-glycans-from-glycopeptides command line option --output-path -o ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-export-write-csv-spectrum-library command line option --fdr-threshold --mzml-path --output-path -m -o -t ANALYSIS_IDENTIFIER DATABASE_CONNECTION glycresoft-mzml-preprocess command line option --averagine --background-reduction --default-precursor-ion-selection-window --end-time --extract-only-tandem-envelopes --ignore-msn --isotopic-strictness --mass-offset --maximum-charge --missed-peaks --ms1-averaging --msn-averagine --msn-background-reduction --msn-isotopic-strictness --msn-missed-peaks --msn-score-threshold --msn-transform --name --processes --score-threshold --signal-to-noise-threshold --start-time --transform --verbose -a -an -b -bn -c -D -e -g -i -in -m -mn -mo -n -p -r -rn -s -snr -t -tn -v MS_FILE OUTFILE_PATH

H

HYPOTHESIS_IDENTIFIER glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-build-hypothesis-glycan-network-build-network command line option glycresoft-export-glycan-hypothesis command line option glycresoft-export-glycopeptide-hypothesis command line option

M

MODEL_PATH glycresoft-analyze-retention-time-evaluate-glycopeptide-retention-time command line option

MS_FILE glycresoft-mzml-preprocess command line option

O

OUTFILE_PATH glycresoft-mzml-preprocess command line option

OUTPUT_PATH glycresoft-analyze-retention-time-evaluate-glycopeptide-retention-time command line option glycresoft-analyze-retention-time-fit-glycopeptide-retention-time command line option

R

RULE_FILE glycresoft-build-hypothesis-glycan-combinatorial command line option

S

SAMPLE_PATH glycresoft-analyze-search-glycan command line option glycresoft-analyze-search-glycopeptide command line option glycresoft-analyze-search-glycopeptide-multipart command line option

T

TEXT_FILE glycresoft-build-hypothesis-glycan-text command line option