crux pipeline [options] <mass spectra> <peptide source>
Given one or more sets of tandem mass spectra as well as a protein database, this command runs a series of Crux tools and reports all of the results in a single output directory. There are three steps in the pipeline:
All of the command line options associated with the individual tools in the pipeline can be used with the pipeline command.
Given one or more sets of tandem mass spectra as well as a protein database, this command runs a series of Crux tools and reports all of the results in a single output directory. There are four steps in the pipeline:
All of the command line options associated with the individual tools in the pipeline can be used with the pipeline command.
mass spectra – The name of the file(s) from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alteratively, with Tide-search, these files may be binary spectrum files produced by a previous run of crux tide-search using the store-spectra parameter. Multiple files can be included on the command line (space delimited), prior to the name of the database.assign-confidence.target.txt – a tab-delimited text file that contains the targets, sorted by score. The file will contain one new column, named "<method> q-value", where <method> is either "tdc" or "mix-max".assign-confidence.log.txt – a log file containing a copy of all messages that were printed to stderr.assign-confidence.params.txt – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.spectral-counts.target.txt – a tab-delimited text file containing the protein IDs and their corresponding scores, in sorted order.spectral-counts.params.txt – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.spectral-counts.log.txt – All messages written to standard error.--bullseye T|F – Run the Bullseye algorithm on the given MS data, using it to assign high-resolution precursor values to the MS/MS data. If a spectrum file ends with .ms2 or .cms2, matching .ms1/.cms1 files will be used as the MS1 file. Otherwise, it is assumed that the spectrum file contains both MS1 and MS2 scans. Default = false.--search-engine comet|tide-search – Specify which search engine to use. Default = tide-search.--post-processor percolator|assign-confidence|none – Specify which post-processor to apply to the search results. Default = percolator.--post-processor percolator|assign-confidence – Specify which post-processor to apply to the search results. Default = percolator.--memory-limit <integer> – The maximum amount of memory (i.e., RAM), in GB, to be used by tide-index. Default = 4.--auto-modifications-spectra <string> – Specify the spectra file to be used for modification inference when the auto-modifications option is enabled. Multiple files may be separated by commas. Default = <empty>.--use-tailor-calibration T|F – Fast, but heuristic PSM score calibration as described in this article. Default = false.--top-match-in <integer> – Specify the maximum rank to allow when parsing results files. Matches with ranks higher than this value will be ignored (a value of zero allows matches with any rank). Default = 0.--combine-charge-states T|F – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = false.--combine-modified-peptides T|F – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = false.--parsimony none|simple|greedy – Perform a parsimony analysis on the proteins, and report a "parsimony rank" column in the output file. This column contains integers indicating the protein's rank in a list sorted by spectral counts. If the parsimony analysis results in two proteins being merged, then their parsimony rank is the same. In such a case, the rank is assigned based on the largest spectral count of any protein in the merged meta-protein. The "simple" parsimony algorithm only merges two proteins A and B if the peptides identified in protein A are the same as or a subset of the peptides identified in protein B. The "greedy" parsimony algorithm does additional merging, by identifying the longest protein (i.e., the protein with the most peptides) that contains one or more shared peptides. The shared peptides are assigned to the identified protein and removed from any other proteins that contain them, and the process is then repeated. Note that, with this option, some proteins end up being assigned no peptides at all; these orphan proteins are not reported in the output. Default = none.--threshold <float> – Only consider PSMs with a threshold value. By default, q-values are thresholded using a specified threshold value. This behavior can be changed using the --custom-threshold and --threshold-min parameters. Default = 0.01.--threshold-type none|qvalue|custom – Determines what type of threshold to use when filtering matches. none : read all matches, qvalue : use calculated q-value from percolator, custom : use --custom-threshold-name and --custom-threshold-min parameters. Default = qvalue.--input-ms2 <string> – MS2 file corresponding to the psm file. Required to measure the SIN. Ignored for NSAF, dNSAF and EMPAI. Default = <empty>.--unique-mapping T|F – Ignore peptides that map to multiple proteins. Default = false.--quant-level protein|peptide – Quantification at protein or peptide level. Default = protein.--measure RAW|NSAF|dNSAF|SIN|EMPAI – Type of analysis to make on the match results: (RAW|NSAF|dNSAF|SIN|EMPAI). With exception of the RAW metric, the database of sequences need to be provided using --protein-database. Default = NSAF.--custom-threshold-name <string> – Specify which field to apply the threshold to. The direction of the threshold (<= or >=) is governed by --custom-threshold-min. By default, the threshold applies to the percolator q-value, specified by "percolator q-value". Default = <empty>.--custom-threshold-min T|F – When selecting matches with a custom threshold, custom-threshold-min determines whether to filter matches with custom-threshold-name values that are greater-than or equal (F) or less-than or equal (T) than the threshold. Default = true.--mzid-use-pass-threshold T|F – Use mzid's passThreshold attribute to filter matches. Default = false.--protein-database <string> – The name of the file in FASTA format. Default = <empty>.