MSGFPlusAdapter

Options

version

Version of the tool that generated this parameters file.

precursor_mass_tolerance

Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')

precursor_error_units

Unit of precursor mass tolerance (MS-GF+ parameter '-t')

isotope_error_range

Range of allowed isotope peak errors (MS-GF+ parameter '-ti'). Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2.

fragment_method

Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')

instrument

Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')

enzyme

Enzyme used for digestion, or type of cleavage. Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')

protocol

Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')

tryptic

Level of cleavage specificity required (MS-GF+ parameter '-ntt')

min_precursor_charge

Minimum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-minCharge')

max_precursor_charge

Maximum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-maxCharge')

min_peptide_length

Minimum peptide length to consider (MS-GF+ parameter '-minLength')

max_peptide_length

Maximum peptide length to consider (MS-GF+ parameter '-maxLength')

matches_per_spec

Number of matches per spectrum to be reported (MS-GF+ parameter '-n')

add_features

Output additional features (MS-GF+ parameter '-addFeatures'). This is required by Percolator and hence by default enabled.

max_mods

Maximum number of modifications per peptide. If this value is large, the search may take very long.

max_missed_cleavages

Maximum number of missed cleavages allowed for a peptide to be considered for scoring. (default: -1 meaning unlimited)

tasks

(Override the number of tasks to use on the threads; Default: (internally calculated based on inputs)) More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs). 1 <= tasks <= numThreads: will create one task per thread, which is the original behavior. tasks = 0: use default calculation - minimum of: (threads*3) and (numSpectra/250). tasks < 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means "2 * numThreads" tasks). One task per thread will use the most memory, but will usually finish the fastest. 2-3 tasks per thread will use comparably less memory, but may cause the search to take 1.5 to 2 times as long.

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)'

legacy_conversion

Use the indirect conversion of MS-GF+ results to idXML via export to TSV. Try this only if the default conversion takes too long or uses too much memory.

java_memory

Maximum Java heap size (in MB)

java_permgen

Maximum Java permanent generation space (in MB); only for Java 7 and below

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

MSGFPlusAdapter Std Output

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

MSGFPlusAdapter Error Output

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

Workflows

• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTOpenMS
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTKNIME Hub
• Phosphoproteomics_IDKNIME Hub
• Phosphoproteomics_IDOpenMS

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