Question: How I can get all the information of proteins?
0
gravatar for yueli7
8 weeks ago by
yueli7190
China
yueli7190 wrote:

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
software error • 162 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by yueli7190
1

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by GenoMax95k

Hello genomax,

Thank you so much for your comments!

I try to improve my question.

Thank you again!

Best,

Yue

ADD REPLYlink written 8 weeks ago by yueli7190

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.

ADD REPLYlink written 8 weeks ago by Macspider3.3k

Hello Macspide,

Thank you for your suggestion!

Best,

Yue

ADD REPLYlink written 8 weeks ago by yueli7190
0
gravatar for yueli7
8 weeks ago by
yueli7190
China
yueli7190 wrote:
setwd("~/HASM_SILAC")
library(RSQLite)
con <- dbConnect(RSQLite::SQLite(), "AC2_enriched01.msf")
con
dbListTables(con)
AminoAcidModifications<-dbReadTable(con, "AminoAcidModifications")
ADD COMMENTlink written 8 weeks ago by yueli7190
1

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.

ADD REPLYlink written 8 weeks ago by _r_am32k

Hello _r_am,

Thank you so much for your great help!

Thank you again!

Best,

Yue

   p0xxx:~$ sh sqlite2csv.sh OstromR_Set7_Enriched.msf
ADD REPLYlink written 7 weeks ago by yueli7190
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