How I can get all the information of *msf file?
(1) By yueli (yueli7) on 2020-11-27 00:54:43 [link] [source]
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
(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 [source]
Hello Kmedcalf,
Thank you for your great help!
Thank you again!
Best,
YUe
setwd("~/HASM_SILAC")
library(RSQLite)
con <- dbConnect(RSQLite::SQLite(), "AC2_enriched01.msf")
con
dbListTables(con)
AminoAcidModifications<-dbReadTable(con, "AminoAcidModifications")
(5) By anonymous on 2020-11-27 07:57:13 in reply to 1 [link] [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.