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. NOTE: Decoy suffix is currently not supported by sage.

batch_size

Number of files to load and search in parallel (default = # of CPUs/2)

precursor_tol_left

Start (left side) of the precursor tolerance window w.r.t. precursor location. Usually used with negative values smaller or equal to the 'right' counterpart.

precursor_tol_right

End (right side) of the precursor tolerance window w.r.t. precursor location. Usually used with positive values larger or equal to the 'left' counterpart.

precursor_tol_unit

Unit of precursor tolerance (ppm or Da)

fragment_tol_left

Start (left side) of the fragment tolerance window w.r.t. precursor location. Usually used with negative values smaller or equal to the 'right' counterpart.

fragment_tol_right

End (right side) of the fragment tolerance window w.r.t. precursor location. Usually used with positive values larger or equal to the 'left' counterpart.

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

min_peaks

Minimum number of peaks required for a spectrum to be considered

max_peaks

Take the top N most intense MS2 peaks only for matching

report_psms

Number of hits (PSMs) to report for each spectrum

bucket_size

How many fragments are in each internal mass bucket (default: 8192 for hi-res data). Try increasing it to 32k or 64k for low-res. See also: fragment_tol_*

min_len

Minimum peptide length

max_len

Maximum peptide length

missed_cleavages

Number of missed cleavages

fragment_min_mz

Minimum fragment m/z

fragment_max_mz

Maximum fragment m/z

peptide_min_mass

Minimum monoisotopic peptide mass to consider a peptide from the DB

peptide_max_mass

Maximum monoisotopic peptide mass to consider a peptide from the DB

min_ion_index

Minimum ion index to consider for preliminary scoring. Default = 2 to skip b1/y1 AND (sic) b2/y2 ions that are often missing.

max_variable_mods

Maximum number of variable modifications

isotope_error_range

Range of (C13) isotope errors to consider for precursor.Can be negative. E.g. '-1,3' for considering '-1/0/1/2/3'

charges

Range of precursor charges to consider if not annotated in the file.

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)'

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

threads

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

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).

Views

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.)

Workflows

• No workflows found

Links

• No links available

Developers