crux tide-search
Usage:
crux tide-search [options] <mass spectra> <peptide index>
Description:
Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST® algorithm, which assigns peptides to spectra by comparing the observed spectra to a catalog of theoretical spectra derived from a database of known proteins. Tide's primary advantage is its speed. Our published paper provides more detail on how Tide works. If you use Tide in your research, please cite:
Benjamin J. Diament and William Stafford Noble. “Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra.” Journal of Proteome Research. 10(9):3871-9, 2011.To use
crux tide-search
, you must first create a database index using thecrux tide-index
command.When
tide-search
runs, it performs several intermediate steps, as follows:By default, the intermediate binary files are stored in the output directory and deleted when Tide finishes execution. If you plan to search a given set of spectra more than once, then you can direct Tide to save the binary spectrum files. Subsequent runs of the program will go faster if provided with inputs in binary format.
- Convert the given fragmentation spectra to a binary format.
- Search the spectra against the database and store the results in binary format.
- Convert the results to one or more requested output formats.
Input:
- <spectra> – The name of the file from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alternatively, the argument may be a binary spectrum file produced by a previous run of
crux tide-search
using thestore-spectra
parameter.- <peptide index> – An index created by a previous run of
crux tide-index
.Output:
The program writes files to the folder
crux-output
by default. The name of the output folder can be set by the user using the--output-dir
option. The following files will be created:- tide-search.target.txt: a tab-delimited text file containing the target PSMs. See txt file format for a list of the fields.
- tide-search.decoy.txt: a tab-delimited text file containing the decoy PSMs. This file will only be created if the index was created with decoys.
- tide-search.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.- tide-search.log.txt: a log file containing a copy of all messages that were printed to the screen during execution.
Options:
Search parameters
--exact-p-value T|F
– Enable the calculation of exact p-values for the XCorr score, as described in this article. Calculation of p-values increases the running time but increases the number of correct identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value," and the "xcorr score" column will be replaced with a "refactored xcorr" column. Note that, currently, p-values can only be computed when themz-bin-width
parameter is set to its default value. Variable and static mods are allowed on non-terminal residues in conjunction with p-value computation, but currently only static mods are allowed on the N-terminus, and no mods on the C-terminus. Default = F.--precursor-window <float>
– Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window
' of the spectrum value. The precursor window units depend uponprecursor-window-type
. Default = 3.0.--precursor-window-type mass|mz|ppm
– Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by theprecursor-window
option, and candidate peptides must fall within this window. For themass
window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass ±precursor-window
. If the m+h value is not available, then the mass is calculated from the precursor m/z and provided charge. The peptide mass is computed as the sum of the average amino acid masses plus 18 Da for the terminal OH group. Themz
window-type calculates the window as spectrum precursor m/z ±precursor-window
and then converts the resulting m/z range to the peptide mass range using the precursor charge. For the parts-per-million (ppm
) window-type, the spectrum mass is calculated as in themass
type. The lower bound of the mass window is then defined as the spectrum mass / (1.0 + (precursor-window
/ 1000000)) and the upper bound is defined as spectrum mass / (1.0 - (precursor-window
/ 1000000)). Default = mass.--compute-sp T|F
– Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed bypercolator
orBarista
. Ifsqt-output
is enabled, thencompute-sp
is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spectrum, so turning on this switch involves significant computational overhead. Default = F.--spectrum-min-mz <float>
– The lowest spectrum m/z to search in the ms2 file. Default = 0.0--spectrum-max-mz <float>
– The highest spectrum m/z to search in the ms2 file. Default = no maximum.--min-peaks <int>
– The minimum number of peaks a spectrum must have in order to be searched. Default = 20.--spectrum-charge 1|2|3|all
– The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge will be searched. Default = all.--scan-number <int>|<int>-<int>
– A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = search all spectra.--remove-precursor-peak T|F
– If true, all peaks around the precursor m/z will be removed, within a range specified by the--remove-precursor-tolerance
option. Default = F.--remove-precursor-tolerance <float>
– This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the--remove-precursor-peak
option is invoked. Default=1.5.--print-search-progress <int>
– Show search progress by printing every n spectra searched. Set to 0 to show no search progress. Default = 1000.--use-flanking-peaks T|F
– When set to T,tide-search
includes flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default=F.--use-neutral-loss-peaks T|F
– Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. Default=F.--mz-bin-width <float>
– Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. By default, the mz-bin-width is 1.0005079 Da.--mz-bin-offset <float>
– In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). The parameter must lie in the range 0 ≤ mz-bin-offset ≤ 1. Default=0.40.Input and output
--spectrum-parser pwiz|mstoolkit
– Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser should be able to read the MS/MS file formats listed here. The alternative is MSToolkit parser. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = pwiz.--top-match <integer>
– Specify the number of matches to report for each spectrum. Default=5.--concat T|F – When set to T, target and decoy search results are reported in a single file named "tide-search.txt," and only the top-scoring N matches (as specified via
--top-match
) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = F.--fileroot <string>
– Thefileroot
string will be added as a prefix to all output file names. Default = none.--store-spectra <filename>
– Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs ofcrux tide-search
will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by--output-dir
).--output-dir <filename>
– The name of the directory where output files will be created. Default = crux-output.--overwrite T|F
– Replace existing files if true (T) or fail when trying to overwrite a file if false (F). Default = F.--txt-output T|F
– Output a tab-delimited results file to the output directory. Note that printing only tab-delimited output will give the fastest performance. Enabling other output formats (SQT, PepXML, mzIdentML, or PIN) requires a conversion step that takes additional time. Default = T.--sqt-output T|F
– Output an SQT results file to the output directory. Note that ifsqt-output
is enabled, thencompute-sp
is automatically enabled and cannot be overridden. Default = F.--pepxml-output T|F
– Output a pepXML results file to the output directory. Default = F.--mzid-output T|F
– Output an mzIdentML results file to the output directory. Default = F.--pin-output T|F
– Output a Percolator input (PIN) file to the output directory. Default = F.--parameter-file <filename>
– A file containing command-line or additional parameters. See the parameter documentation page for details. Default = no parameter file.--verbosity <0-100>
– Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.