[proteowizard-support] Question: General library usage

[Magnus A. <mag...@bi...>]

Hi,

I just downloaded version 2_1_2599 of pwiz and started looking at it to 
see if I could utilize it in my projects.

Browsing through the source code I must say it's beautifully designed 
and a well organized library!

I've compiled it using vendor support from Thermo (MSFileReader) and the 
msvc2008 toolchain, and I am applying it to a makefile-based project.


However, I have a few questions about general usage:

1.
My first idea is to use it for reading Thermo raw files (Orbitrap) and I 
managed to do that via the MSDataFile and Reader_Thermo objects. I got 
access to all the spectral data including scan information. But I wonder 
if it would be better for me to use the approach described in 
pwiz_aux/sfcap/old/rawdump/rawdump.cpp or is all this information 
retained and accessible via the MSData object?

2.
Using the MSData approach I am having a hard time figuring out the use 
of cvParam(). For example:

Precursor p;
std::cout << p.activation.cvParam(MS_collision_energy).value;

Although this will print the collision energy, it is not always clear to 
me which CVID I should use in the different ParamContainer objects.
It seems to me that I really have to know which CVIDs to use for every 
object; maybe some convenience-functions like this could be an idea?

p.activation.getCollisionEnergy();

Is there a list somewhere that states which CVIDs to use in the 
different containers?

3.
How can I access the tune-information, like e.g. 'FTMS Full Max Ion Time'?

4.
According to the MaxQuant-guys, their software cannot support 64-bits 
since XRawfile2.dll from Thermo is only 32-bits. Does this apply to your 
library as well?


Thanks a lot for any input you have to these questions!

Regards,
Magnus Arntzen
The Biotechnology Center of Oslo
Norway