Updated msconvert and Skyline to handle Agilent neutral loss/gain scan data

[bspratt]

Reported by user Cristina

[bspratt]

Agilent reader test failure on TC isn't seen on my local build, trying again with the settings used on TC.

[chambm]

If you didn't see that failure I have to expect you didn't actually run that test. The failure looks correct: it's a neutral loss test file (judging from NL in the filename) which we previously didn't support, so it was empty, and now we support it, so now it's not empty. :)

Adding support for NL/NG isn't as simple as this though. I think we need to do something extra with the precursor or product element, I'm trying to remember/research now.

[chambm]

OK, it's like this in Thermo:
scan.set(MS_analyzer_scan_offset, scanInfo->analyzerScanOffset(), MS_m_z);

Did you see a way to get that offset in the Agilent API?

[bspratt]

Yes, the test simply didn't run locally for some reason. I'll have to dive into my standard build batch file.

And yes, I missed the analyzer_scan_offset business, I'll see what I can find in the API.

[bspratt]

OK, it's like this in Thermo: scan.set(MS_analyzer_scan_offset, scanInfo->analyzerScanOffset(), MS_m_z);

Did you see a way to get that offset in the Agilent API?

I don't see anything quite that convenient, but it should be knowable as the difference in either lower or upper bounds of Q1 and Q3 windows.