How I can get all the information of proteins?

Question

[yueli7]

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

[GenoMax]

yueli7 : You have asked this question a third time with a different title. Please don't do this.

Is this file is a result of some kind of mass spec/proteomic analysis? If that is the case perhaps there is an option in the instrument software to export the contained data into format you can use.

You should provide specific information about where/how you got this file (which appears to be a SQLite DB file) since people have already tried to help you in last two threads:

software or R package to change protein *.msf file to any readable file
change *.msf file into excel file

[yueli7]

Hello genomax,

Thank you so much for your comments!

I try to improve my question.

Thank you again!

Best,

Yue

[Matteo Schiavinato]

I would suggest you to edit the question adding more details.

1. Which package?
2. What type of information?
3. On what environment? (I guess R)

Otherwise the question is way too vague and no one will be able to help you.

[yueli7]

Hello Macspide,

Thank you for your suggestion!

Best,

Yue

Answer 1

[yueli7]

setwd("~/HASM_SILAC")
library(RSQLite)
con <- dbConnect(RSQLite::SQLite(), "AC2_enriched01.msf")
con
dbListTables(con)
AminoAcidModifications<-dbReadTable(con, "AminoAcidModifications")

[Ram]

If you wish to export all tables to flat files, you can use this script: https://coderwall.com/p/byoycg/export-all-tables-in-a-sqlite3-db-to-csv-files

The trick you need to learn is how to search the web for what you want. In your case, you needed to search "export all tables sqlite" - and you'd have gotten this script yourself.

[yueli7]

Hello _r_am,

Thank you so much for your great help!

Thank you again!

Best,

Yue

   p0xxx:~$ sh sqlite2csv.sh OstromR_Set7_Enriched.msf