SageAdapter

Options

version

Version of the tool that generated this parameters file.

decoy_prefix

Prefix on protein accession used to distinguish decoy from target proteins. Decoy proteins in the FASTA file should have this prefix in their accession. NOTE: Decoy suffix is currently not supported by Sage.

batch_size

Number of files to load and search in parallel. Setting this to 0 (default) uses an automatic value (typically number of CPUs/2). Default: 0

precursor_tol_left

Start (left side) of the precursor tolerance window w.r.t. precursor location. This value is relative to the experimental precursor mass and used to define the lower bound of the search window. Must be negative (e.g., -6 ppm means 6 ppm below the observed mass).

precursor_tol_right

End (right side) of the precursor tolerance window w.r.t. precursor location. This value is added to the experimental precursor mass to define the upper bound of the search window. Must be positive (e.g., 6 ppm means 6 ppm above the observed mass).

precursor_tol_unit

Unit of precursor tolerance (ppm or Da)

fragment_tol_left

Start (left side) of the fragment tolerance window w.r.t. fragment location. This value reduces the experimental fragment mass to define the lower bound of the search window. Must be negative (e.g., -20 ppm means 20 ppm below the observed mass).

fragment_tol_right

End (right side) of the fragment tolerance window w.r.t. fragment location. This value is added to the experimental fragment mass to define the upper bound of the search window. Must be positive (e.g., 20 ppm means 20 ppm above the observed mass).

fragment_tol_unit

Unit of fragment tolerance (ppm or Da)

min_matched_peaks

Minimum number of b+y ions required to match for PSM to be reported. Default: 6

min_peaks

Minimum number of peaks required for a spectrum to be considered. Spectra with fewer peaks will be ignored. Default: 15

max_peaks

Take the top N most intense MS2 peaks to search. Default: 150

report_psms

Number of peptide-spectrum matches (PSMs) to report for each spectrum. The top N scoring PSMs will be reported. Values higher than 1 can be useful for chimeric spectra but may affect downstream statistical analysis. Default: 1

bucket_size

How many fragments are in each internal mass bucket. Default: 8192 (optimal for high-resolution data). Try increasing it to 32768 or 65536 for low-resolution data. See also: fragment_tol_*

min_len

Minimum peptide length (in amino acids). Default: 5

max_len

Maximum peptide length (in amino acids). Default: 50

missed_cleavages

Maximum number of missed enzymatic cleavages to allow in peptide generation. Default: 2

fragment_min_mz

Minimum fragment m/z to consider. Fragment ions below this m/z will be ignored. Default: 200.0

fragment_max_mz

Maximum fragment m/z to consider. Fragment ions above this m/z will be ignored. Default: 2000.0

peptide_min_mass

Minimum monoisotopic peptide mass to consider for in silico digestion. Peptides below this mass will be excluded from the search database. Default: 500.0

peptide_max_mass

Maximum monoisotopic peptide mass to consider for in silico digestion. Peptides above this mass will be excluded from the search database. Default: 5000.0

min_ion_index

Minimum ion index to consider for preliminary scoring. This parameter controls which fragment ions are used in preliminary scoring. Default: 2 (skips b1/b2/y1/y2 ions, which are often missing or unreliable). Setting this to 1 would only skip b1/y1 ions. Does not affect the final scoring of PSMs.

max_variable_mods

Maximum number of variable modifications allowed per peptide. Default: 2

isotope_error_range

Range of C13 isotope errors to consider for precursor matching, specified as 'start,end' (e.g., '-1,3'). For a range of '-1,3', Sage will consider all isotope errors from -1 to +3 (i.e., -1, 0, 1, 2, 3). This is useful when the monoisotopic peak may not be selected. Can include negative values. Default: '-1,3'. Note: Searching with isotope errors is slower than using a wider precursor tolerance.

charges

Range of precursor charge states to consider if not annotated in the file, specified as 'start,end' (e.g., '2,5'). For a range of '2,5', Sage will consider charge states 2, 3, 4, and 5. This is only used when charge state information is missing from the input file. Default: '2,5'

enzyme

The enzyme used for peptide digestion.

fixed_modifications

Fixed modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

variable_modifications

Variable modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

q_value_threshold

The FDR (False Discovery Rate) threshold for filtering peptides. PSMs with q-values above this threshold will be excluded. Default: 1 (no filtering)

annotate_matches

Whether fragment ion matches should be annotated in the output. This provides additional information about which theoretical ions matched experimental peaks. Default: true

deisotope

Perform deisotoping and charge state deconvolution on MS2 spectra. Recommended for high-resolution MS2 data. May interfere with TMT-MS2 quantification. Default: false

chimera

Enable chimeric spectra search mode. When enabled, multiple peptide identifications can be reported for each MS2 scan, useful for co-fragmenting peptides. Default: false

predict_rt

Use retention time prediction model as a feature for machine learning scoring. Note: This is incompatible with label-free quantification (LFQ). Default: false

wide_window

Enable wide-window/DIA search mode. When enabled, the precursor_tol parameter is ignored and a dynamic precursor tolerance is used. Default: false

smoothing

Whether to smooth the PTM (post-translational modification) mass histogram and pick local maxima. If false, uses raw histogram data. Default: true

threads

Sets the number of threads allowed to be used by the TOPP tool

reindex

Recalculate peptide to protein association using OpenMS. Annotates target-decoy information.

log

Name of log file (created only when specified)

debug

Sets the debug level

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

decoy_string

String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins. If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix).

decoy_string_position

Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession? (ignored if decoy_string is empty)

missing_decoy_action

Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)

write_protein_sequence

If set, the protein sequences are stored as well.

write_protein_description

If set, the protein description is stored as well.

keep_unreferenced_proteins

If set, protein hits which are not referenced by any peptide are kept.

unmatched_action

If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit.

aaa_max

Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs. AAAs are 'B', 'J', 'Z' and 'X'.

mismatches_max

Maximal number of mismatched (mm) amino acids allowed when matching to a protein database. The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's.

IL_equivalent

Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable). Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching.

allow_nterm_protein_cleavage

Allow the protein N-terminus amino acid to clip.

name

Enzyme which determines valid cleavage sites - e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input

specificity

Specificity of the enzyme. Default: deduce from input. 'full': both internal cleavage sites must match. 'semi': one of two internal cleavage sites must match. 'none': allow all peptide hits no matter their context (enzyme is irrelevant).

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SageAdapter Std Output

The text sent to standard out during the execution of SageAdapter.

SageAdapter Error Output

The text sent to standard error during the execution of SageAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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