Command line tools

SageDDA Command line how-to

sagepro --help for more info

Basic SageDDA search run

1. sagepro config.json *.mzparquet --annotate-matches
2. Alternatively the input spectral files can be specified in the config file.

Example config file for SageDDA search with TMT quantification

Example config file for SageDDA search with LFQ (Label Free quantification)

SageDDA Parameters

1. DATABASE SETTINGS

bucket_size

• Hash bucket size for database.
• null = auto; integer allowed.

enzyme

• missed_cleavages — allowed cleavage misses (0–5 typical).
• min_len / max_len — peptide length (default ~6–50).
• restrict — enforce specific rule (e.g., "KR" for trypsin).
• semi_enzymatic — allow N- or C-terminal cleavage: true / false.

fragment_min_mz / fragment_max_mz

• Remove fragments outside this range (e.g., 150–1500).

peptide_min_mass / peptide_max_mass

• Mass filtering; null = no filtering.

ion_kinds Valid entries (any list):

• Standard: "b", "y", "a"
• ETD: "c", "z"
• Neutral losses: "b-H2O", "y-H2O", "b-NH3", etc.
• Default = "b","y".

min_ion_index

• Start scoring at ion index number (e.g., 1).

max_variable_mods

• Max variable mods per peptide (0–5 typical).

decoy_tag

• Prefix for decoys ("rev_", "decoy_", "DECOY").

generate_decoys Options:

• true / false
• "reverse"
• "shuffle"
• "pseudo" (depends on build)

fasta

• Absolute or relative FASTA path.

2. MASS TOLERANCES

precursor_tol.ppm

fragment_tol.ppm

• Format: [low, high]
• Example: [-100, 100].

3. SEARCH BEHAVIOR

report_psms

chimera

• Enable multi-precursor scoring: true / false.

wide_window

• DIA-specific large-window matching: true / false.

min_peaks / max_peaks

• Peak count filtering before scoring.

max_fragment_charge

• Highest fragment charge considered (1–3 typical).

min_matched_peaks

• Minimum fragment matches to accept PSM.

isotope_errors

• Allowed isotope offsets, e.g. [-1,3].

deisotope

• Enable deisotoping: true / false.

4. QUANTIFICATION

TMT / iTRAQ

• "TMT6"
• "TMT10"
• "TMT11"
• "TMT16"
• "TMT18"
• "iTRAQ4"
• OR explicit channel list (if supported)

quant.tmt_settings

• level — 2 or 3
• sn — signal/noise filtering (true / false)
• Additional supported fields (varies by build):
  • isolation_ppm — purity window
  • purity — min isolation purity
  • exclude_contaminants — skip reporter contaminants

Label-Free Quant (LFQ)

quant.lfq

• true / false

quant.lfq_settings

5. MACHINE LEARNING / FDR

FDR — ML score model

• "xgboost 10" — ML with N iterations
• "mixmax" — mixture model (if available)