Want to do some top-down data processing on the cheap? Are you willing to write a command line here and there and jump through a data conversion hoop or two? Then there are a couple of tools that will work for you or the bioinformatics guy who is doing your processing.
The first is the MS-Deconv from the CCMS. Simple deconvolution of MS and MS/MS spectra. It is available for download as a command line driven algorithm, or with a simple graphical user interface. In order to run with this program, you will first have to convert your data to mzXML. Unfortunately, unlike in some programs, it doesn't seem like you can get away with uploading mzml. That X is essential here. (For Thermo Elite, QE, or Fusion, first convert your RAW file to mzml with the PD full version or viewer software, then use ProteoWizard to convert mzml to mzXml, instructions here.) For most instruments, you can directly convert your RAW files with this tool directly to mzXmL, but I haven't tested this tool for the newer Thermo instruments in quite a while and it didn't seem to like the RAW data for these when I last did.
The next tool is MS-Align. Which can directly take the output for MS-Deconv and process it for LC driven intact analysis.
I'm doing some intact analysis with a QE today, we'll see how these two tools compare to other ones out there. Yes, there are some hoops to jump through (and you'll notice a lack of control settings in the MS-Deconv algorithm that you may want), but these could be a nice complementary resource for your top-down studies.
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