iProphet mistakenly parses FPKM values when using a NextProt peff database (TPP v. 5.0)

[Jason Winget]

I've done several searches using the nextprot_all peff database from ftp://ftp.nextprot.org/pub/current_release/peff/

At the iProphet step I see the message that the FPKM model is being activated:

FPKM values are available, to disable rerun with option NOFPKM ... 

This is probably due to the overloading of the ID line in the PEFF format to include mods & sNPs triggering whatever parse rules are used to find FPKMs.

It's not a big deal to include the NOFPKM flag for now, but it may be useful in the future to refine the automatic parsing of FPKM values.

[David Shteynberg]

Hello Jason,

In an earlier version of iProphet FPKM message was being printed erroneously.   Does the peff database actually contain "FPKM=" in the description? If the FPKM model was actually used you would have an FPKM model reported in the pepXML file and the models viewer should display it. 

Cheers,

-David

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[Jason]

I can't find the string "FPKM=" anywhere in the database, so perhaps it's an erroneous message.

My version is TPP v5.0.0a5 downloaded on 3/10/2016

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[David Shteynberg]

Ah yes...it was a bug I meant to fix ;)  Thanks for testing!