Hello,
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!
Best,
Yue
Following is my code:
>setwd("~/HASM_SILAC")
> library(RSQLite)
> con <- dbConnect(RSQLite::SQLite(), "AC2_enriched01.msf")
> con
<SQLiteConnection>
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