I have done spectral count using Orbitrap data with the free software Scaffold. You can have the number of spectrum identified per protein.

Cheers

I. Ortea

First off, Scaffold is not free. You can use the Viewer for free and you get a 14-day evaluation, but you'll need to pay for it after that time. Secondly, it doesn't take output from ProteinPilot. That is going to be your major headache, PP plays with very few other pieces of software.

If you can use Mascot (you can export an MGF using the AB software) then that uses emPAI to quantitate. It's a slightly more sophisticated method of spectral counting that takes into account sequence coverage. It is included by default in any Mascot search. See here; http://www.matrixscience.com/help/quant_empai_help.html

As long as your data files don't exceed the limit (10, 000 spectra I think), then you can use the public site for searching.

Another alternative is Skyline (https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view). This works with PP output and will use the area under the curve rather than spectral counting. AUC is arguably superior to spectral counting anyway. See here for more info; https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

Skyline is brilliant software and their support is excellent.

If you're set on spectral counting, then ABACUS is worth a look. You'll need to work with the TPP. Details; http://abacustpp.sourceforge.net/ or just check out here for other options from the same lab; http://www.nesvilab.org/software.html

Census is another one, but I've had issues with the stability of this software. See here; http://fields.scripps.edu/census/index.php

There are many others, here's a selection;

http://pappso.inra.fr/bioinfo/masschroq/

https://trac.nbic.nl/mscompare/

http://sourceforge.net/projects/qspec/

Peter, I fully agree - Skyline is an excellent piece of software and I highly recommend trying this.

I also fully support your recommendation towards using AUC based quantification, which is far more reliable than spectral counting approaches.

Thx guys, that's really a great help!