Re: [Open-ms-general] MSGF+ and replicates

[Christopher H. <chr...@em...>]

Hi all,

I have a couple of questions.

1. We are very interested in getting MSGF data into OpenMS.  Converting the mzid output to pepXML, then back to idXML is cumbersome.  I have tried compiling the OpenMS source version that contains the MSGF adapter (https://github.com/mwalzer/OpenMS/tree/MSGF+-Adapter).  However, this doesn’t seem to work.  It compiles fine, but then the MSGF Adapter isn’t part of the output in the /bin directory.  I can see the compile target in the /src/topp/MSGFplusAdapter.C location…however, in the /src/topp/CMakeFiles/ there is no MSGFAdapter .dir target.  Any ideas why it isn’t being included in the compilation of cmake targets?

2. When working from the command line, what is the best way to handle multiple files? For example, lets say I have 10 fractions from a single sample. My analysis steps would be: 1. search fraction, 2. quant fraction, 3. combine search and quant for all fractions.  In the windows pipeline I would just put all 10 fractions in the Input File node for the database search and the quantification.  Where is the best point to combine fractions when you are doing identification and quantification?

Thanks for any input!

Cheers,
Chris