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

Hello

I have some protein *.msf file. I can not open it.

Which software or R package that can change this kind of *.msf to any readable file?

Thanks in advance for great help!

Best,

Yue

software error
• 2,401 views • link
updated by realpopeofchillitown • realpopeofchillitown • written by yueli7 yueli7

How was this file generated? What does the command file <filename>.msf return? Have you tried head, more and less on the file?

Also, how is the software error tag relevant here?

• 0 views • link
written by Ram Ram

Hello RamRS,

Thank you so much for your great help!

I think it is a SQLite database.

Thank you again!

Best,

Yue

-p0xxx:~$ file OstromR_Set7_Enriched.msf 
OstromR_Set7_Enriched.msf: SQLite 3.x database, last written using SQLite version 3007011
• 0 views • link
written by yueli7 yueli7

From this, it is apparent that the msf file is a database that can be opened in SQLite. OP should be looking for R packages that can read in SQLite DBs, such as RSQLite: https://db.rstudio.com/databases/sqlite/

• 0 views • link
written by Ram Ram

Hello RamRS,

Thank you so much for your great help!

Best,
Yue

• 0 views • link
updated by Ram Ram • written by yueli7 yueli7

Hi @yueli7,

Did you happen to figure out the database schema for these msf files to be used via sqllite?

I'm trying to look at the tables but there are way too many times to manually figure out the schema.

Any pointers are highly appreciated.

Thanks!

• 0 views • link
written by realpopeofchillitown • realpopeofchillitown

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