Cycloquest

Cycloquest

(Download Cycloquest)

Linux Installation

run 'cmake .' and then run 'make'
Windows users should try our webserver at cyclo.ucsd.edu.

Run

cycloquest_html : database search for linear/cyclic peptides

The only required parameters of cycloquest are address of mgf/mzxml file, and fasta file. the parameters are described below:

Required arguments:
-------------------
<path to input mzxml/mgf file>
<path to input fasta file>

Optional cycloquest_html arguments:
-----------------------------
-out <path to output html file> (default : out.html)
-linear search only for linear peptides
-cyclic search only for cyclic peptides
-num_top X number of top search hits returned (default: 20)
-num_peaks X number of top peaks kept in spectra
-parent_mass X Parent Mass in Da (Default : from mzxml/mgf file)
-charge (Default : from mzxml/mgf file)
-add_decoy search decoy DB
-precursor_ion_tolerance Default : 0.5 Da
-product_ion_tolerance Default : 0.5 Da
-scan_num X Default : analyze all scans
-filter_parent_mass X Y only analyze the species with
parent mass between X and Y
-num_cys X only accept peptides with X cysteines
-reduced
-IAM_reduced
-MAL_reduced
-PFA_reduced
-NaBH4_reduced
-CMet_reduced
-NIPIA_reduced

Cycloquest output

Cycloquest outputs an html file, containing top hits to each spectrum in the spectral dataset.

Publication

This workflow is described at www.ncbi.nlm.nih.gov/pubmed/21851130

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