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How I can get all the information of *msf file?

How I can get all the information of *msf file?

(1) By yueli (yueli7) on 2020-11-27 00:54:43 [link] [source]


I have a protein file of "AC2_enrich01.msf" (1.6GB) which in R environment of RSQLite package.

It is a SILAC mass spectrometry protein data which comes out of the Thermo Fisher machine. It is a SQLite DB file.

I can not open the whole file and only got the title of this file.

How I can get all the information of the proteins?

Thank you in advance for great help!



Following is my code:

   > library(RSQLite)
   > con <- dbConnect(RSQLite::SQLite(), "AC2_enriched01.msf")
   > con
   Path: /home/li/HASM_SILAC/AC2_enriched01.msf
Extensions: TRUE
   > dbListTables(con)
 [1] "AminoAcidModifications"               "AminoAcidModificationsAminoAcids"     "AminoAcidModificationsAminoAcidsNL"   "AminoAcidModificationsNeutralLosses"  "AminoAcids"                          
[6] "AnnotationDataVersion"                "AnnotationDataset"                    "AnnotationGroups"                     "AnnotationTypes"                      "Annotations"                         
[11] "AnnotationsAnnotationGroups"          "AnnotationsProtein"                   "Chromatograms"                        "CustomDataFields"                     "CustomDataPeptides"                  
[16] "CustomDataPeptides_decoy"             "CustomDataProcessingNodes"            "CustomDataProteins"                   "CustomDataProteins_decoy"             "CustomDataSpectra"                   
[21] "Enzymes"                              "EnzymesCleavageSpecificities"         "EventAnnotations"                     "EventAreaAnnotations"                 "Events"                              
[26] "FastaFiles"                           "FastaFilesProteinAnnotations"         "FileInfos"                            "MassPeakRelations"                    "MassPeaks"                           
[31] "PeptideScores"                        "PeptideScores_decoy"                  "Peptides"                             "PeptidesAminoAcidModifications"       "PeptidesAminoAcidModifications_decoy"
[36] "PeptidesProteins"                     "PeptidesProteins_decoy"               "PeptidesReferenceSpectra"             "PeptidesTerminalModifications"        "PeptidesTerminalModifications_decoy" 
[41] "Peptides_decoy"                       "PrecursorIonAreaSearchSpectra"        "PrecursorIonQuanResults"              "PrecursorIonQuanResultsSearchSpectra" "ProcessingNodeConnectionPoints"      
[46] "ProcessingNodeExtensions"             "ProcessingNodeFilterParameters"       "ProcessingNodeInterfaces"             "ProcessingNodeParameters"             "ProcessingNodeScores"                
[51] "ProcessingNodes"                      "ProcessingNodesSpectra"               "ProteinAnnotations"                   "ProteinIdentificationGroups"          "ProteinScores"                       
[56] "ProteinScores_decoy"                  "Proteins"                             "ProteinsProteinGroups"                "PtmAnnotationData"                    "ReferenceSpectra"                    
[61] "ReporterIonQuanResults"               "ReporterIonQuanResultsSearchSpectra"  "ScanEvents"                           "SchemaInfo"                           "Spectra"                             
[66] "SpectrumHeaders"                      "SpectrumScores"                       "TaxonomyNames"                        "TaxonomyNodes"                        "WorkflowInfo"                        
[71] "WorkflowMessages"                     "mtcars"                               "sqlite_sequence"

The error:

   > dbWriteTable(con, "AC2_enrich01", AC2_enriched01)
Error in dbWriteTable(con, "AC2_enrich01", AC2_enriched01) : 
object 'AC2_enriched01' not found

(2) By John Dennis (jdennis) on 2020-11-27 01:33:25 in reply to 1 [link] [source]

I have no experience of RSQLite, but it appears to me that AC2_enriched01.msf is the name of the database. There are 70+ tables in this database. You need to add or retrieve data from a table, not the whole database.

(3) By Keith Medcalf (kmedcalf) on 2020-11-27 02:07:08 in reply to 1 [link] [source]

Seems pretty clear to me. It is complaining that you are referring to some object called AC2_enriched01, but no such object exists.

Error messages are often (except when produced by Microsoft) descriptive of the error condition they describe.

(4) By yueli (yueli7) on 2020-11-27 05:49:44 in reply to 3 [link] [source]

Hello Kmedcalf,

Thank you for your great help!

Thank you again!



con <- dbConnect(RSQLite::SQLite(), "AC2_enriched01.msf")
AminoAcidModifications<-dbReadTable(con, "AminoAcidModifications")

(5) By anonymous on 2020-11-27 07:57:13 in reply to 1 [source]

Hello, is this the R programming mailing list? I've got this Pikchr problem...

Thanks for providing an understandable example, but this is an R problem, not an SQLite problem. dbWriteTable wants either a data.frame or a file name as a string as its third argument, but the variable you provided does not exist (yet?).

May I offer you R-help or one of the special interest groups instead? When you contact them, make sure to mention where you expect to get the AC2_enriched01 variable. People won't be able to help you otherwise.