Multiplex Denovo Sequencing

Multiplex Denovo Sequencing

(Download Multiplex Denovo Sequencing)

Linux Installation

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

Run

Denovo_LCMSMS_html : denovo sequencing of linear/cyclic peptides from LC-MS/MS datasets

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

Optional Denovo_LCMSMS_html arguments:
-----------------------------
-scan_num X                                                   Default : analyze all scans
-filter_parent_mass X Y         only analyze the species with parent mass between X and Y
-length X                                                                  peptide length
-out <path to output html file>                                      (default : out.html)
-lin                                                                 do linear sequencing
-cyc                                                                       cyclic peptide
-branch lin_first pos                       branch-cyclic peptide (default offset : -H2O)
-num_top X                               number of top search hits returned (default: 10)
-num_peaks X                            number of top peaks kept in spectra (default: 50)
-parent_mass X                                                        Parent Mass (in Da)
-standard                                                        use standard amino acids
-tag X                                                        consider a tag of mass X Da
-num_rand                                                       number of random peptides
-correct_mass n m1 ... mn                                        correct peptide sequence
-print_score n m1 ... mn                                                     print score
-pval_est                                                                 estimate pvalue
-print_spectrum_detail                                                                   
-verbose                                                                                 
-print_spectrum                                                            print spectrum
-spec_net_prefix                                                                         
-spec_net_num_rep                                                                        
-score_type                                                                 (default : 1)
-score_type_mod                                                             (default : 1)
-use_charge                                                       use charge from dataset
-max_charge X                                                              use max charge
-fix_charge X                                                                            
-fix_cluster_charge X                                                                    
-scan_index                                                                              
-glob_scan_index                                                                         
-num_rep                                                                    (default : 2)
-int_pm X                                                                                
-int_pm_flag                                                                             
-specnet_cosine                                                                          
-msgf_prm_generate                                                                       
-msgf_prm msgf_prm_file                                                                  
-chem_score                                                                              
-hcd                                                                                     
-num_rep_msgf                                                                         

Publication

This workflow is described at http://www.ncbi.nlm.nih.gov/pubmed/22035290

Enter labels to add to this page:
Please wait 
Looking for a label? Just start typing.