change *.msf file into excel file

Question

[yueli7]

Hello

I have a *.msf file.

How I can change my protein *.msf file to the excel file?

Thanks in advance for great help!

Best,

Yue

$ sqlite3
SQLite version 3.22.0 2018-01-22 18:45:57
Enter ".help" for usage hints.
Connected to a transient in-memory database.
Use ".open FILENAME" to reopen on a persistent database.
sqlite> .open LD-CS-150113_OstromR_OR_AC2_enriched.msf
sqlite> .table
AminoAcidModifications                PeptidesProteins_decoy              
AminoAcidModificationsAminoAcids      PeptidesReferenceSpectra            
AminoAcidModificationsAminoAcidsNL    PeptidesTerminalModifications       
AminoAcidModificationsNeutralLosses   PeptidesTerminalModifications_decoy 
AminoAcids                            Peptides_decoy                      
AnnotationDataVersion                 PrecursorIonAreaSearchSpectra       
AnnotationDataset                     PrecursorIonQuanResults             
AnnotationGroups                      PrecursorIonQuanResultsSearchSpectra
AnnotationTypes                       ProcessingNodeConnectionPoints      
Annotations                           ProcessingNodeExtensions            
AnnotationsAnnotationGroups           ProcessingNodeFilterParameters      
AnnotationsProtein                    ProcessingNodeInterfaces            
Chromatograms                         ProcessingNodeParameters     
CustomDataPeptides_decoy              ProcessingNodesSpectra              
CustomDataProcessingNodes             ProteinAnnotations                  
CustomDataProteins                    ProteinIdentificationGroups         
CustomDataProteins_decoy              ProteinScores                       
CustomDataSpectra                     ProteinScores_decoy                 
Enzymes                               Proteins                            
EnzymesCleavageSpecificities          ProteinsProteinGroups               
EventAnnotations                      PtmAnnotationData                   
EventAreaAnnotations                  ReferenceSpectra                    
Events                                ReporterIonQuanResults              
FastaFiles                            ReporterIonQuanResultsSearchSpectra 
FastaFilesProteinAnnotations          ScanEvents                          
FileInfos                             SchemaInfo                          
MassPeakRelations                     Spectra                             
MassPeaks                             SpectrumHeaders                     
PeptideScores                         SpectrumScores                      
PeptideScores_decoy                   TaxonomyNames                       
Peptides                              TaxonomyNodes                       
PeptidesAminoAcidModifications        WorkflowInfo                        
PeptidesAminoAcidModifications_decoy  WorkflowMessages                    
PeptidesProteins

[GenoMax]

If @Pierre's answer did not address your question then please unmark it as accepted.

[GenoMax]

Answered by @yueli7 in a parallel thread: A: How I can get all the information of proteins?

Answer 1

[Pierre Lindenbaum]

echo ".tables" | sqlite3  db.sqlite  | tr -s " " | tr " " "\n" | while read T; do echo "select * from $T ;" | sqlite3 -header -separator $'\t' db.sqlite > ${T}.tsv ; done

and ... do not use excel.

[yueli7]

Hello Pierre,

Thank you so much for your great help.

It seems do not have any response. What can I do in next step?

Thank you again for your great help!

Best,

Yue

p0xxx:~$ sqlite3

SQLite version 3.22.0 2018-01-22 18:45:57

Enter ".help" for usage hints.

Connected to a transient in-memory database.

Use ".open FILENAME" to reopen on a persistent database.

sqlite> .open OstromR_Set7_Enriched.msf

sqlite> .table

AminoAcidModifications                PeptidesProteins_decoy              
AminoAcidModificationsAminoAcids      PeptidesReferenceSpectra            
AminoAcidModificationsAminoAcidsNL    PeptidesTerminalModifications       
AminoAcidModificationsNeutralLosses   PeptidesTerminalModifications_decoy 
AminoAcids                            Peptides_decoy                      
AnnotationDataVersion                 PrecursorIonAreaSearchSpectra       
AnnotationDataset                     PrecursorIonQuanResults             
AnnotationGroups                      PrecursorIonQuanResultsSearchSpectra
AnnotationTypes                       ProcessingNodeConnectionPoints      
Annotations                           ProcessingNodeExtensions            
AnnotationsAnnotationGroups           ProcessingNodeFilterParameters      
AnnotationsProtein                    ProcessingNodeInterfaces            
Chromatograms                         ProcessingNodeParameters            
CustomDataFields                      ProcessingNodeScores                
CustomDataPeptides                    ProcessingNodes                     
CustomDataPeptides_decoy              ProcessingNodesSpectra              
CustomDataProcessingNodes             ProteinAnnotations                  
CustomDataProteins                    ProteinIdentificationGroups         
CustomDataProteins_decoy              ProteinScores                       
CustomDataSpectra                     ProteinScores_decoy                 
Enzymes                               Proteins                            
EnzymesCleavageSpecificities          ProteinsProteinGroups               
EventAnnotations                      PtmAnnotationData                   
EventAreaAnnotations                  ReferenceSpectra                    
Events                                ReporterIonQuanResults              
FastaFiles                            ReporterIonQuanResultsSearchSpectra 
FastaFilesProteinAnnotations          ScanEvents                          
FileInfos                             SchemaInfo                          
MassPeakRelations                     Spectra                             
MassPeaks                             SpectrumHeaders                     
PeptideScores                         SpectrumScores                      
PeptideScores_decoy                   TaxonomyNames                       
Peptides                              TaxonomyNodes                       
PeptidesAminoAcidModifications        WorkflowInfo                        
PeptidesAminoAcidModifications_decoy  WorkflowMessages                    
PeptidesProteins 

sqlite> echo "1.tables" | sqlite3  db.sqlite  | tr -s " " | tr " " "\n" | while read T; do echo "select * from $T ;" | sqlite3 -header -separator $'\t' db.sqlite > ${T}.tsv ; done