Question: How Do I Transform A Binary Mass Spec File To Ascii Text Format
2
gravatar for Shigeta
8.6 years ago by
Shigeta460
Berkeley, CA
Shigeta460 wrote:

I'm looking for a utility to take a binary "dmp" file and turn it into an ascii format like DTA, PKL or MGF.

[edit; sorry for the typo - its a dmp file...]

Can anyone point me in the right direction? I'm not entirely sure what machine this came from so I'm a little lost.

format conversion mass-spec • 4.8k views
ADD COMMENTlink modified 8.4 years ago by Laurent1.6k • written 8.6 years ago by Shigeta460
1

I've never seen that format for machine-generated raw mass-spec data. Are you sure it's from a mass spec machine? This is a long shot, but perhaps the first few bytes of the file might be an ASCII representation of the generating instrument?

ADD REPLYlink written 8.5 years ago by Bio_X2Y3.7k
1

Unsurprising that you're lost if you don't know where the file originated. There's not much you can do without that information, unless you get lucky with a Google search.

ADD REPLYlink written 8.5 years ago by Neilfws48k

You will need to be more specific. Raw files from different machines are not compatible. Perhaps if you post some of the filenames, somebody here will recognise the machine (e.g. Agilent raw data is stored in ".d" directories). Also, I strongly suggest you contact the people who provided you with the files and request more details about the experiment - it will be difficult to perform meaningful analysis without knowing what kind of data you have, e.g. different software is optimised for different machines.

ADD REPLYlink written 8.6 years ago by Bio_X2Y3.7k

Same here, have never seen that format...

ADD REPLYlink written 8.5 years ago by Laurent1.6k

Thanks guys - i think i figured it out - looks like an oracle binary dump file. the above tends to substantiate this. will have to confirm this week...

ADD REPLYlink written 8.5 years ago by Shigeta460
2
gravatar for Bio_X2Y
8.6 years ago by
Bio_X2Y3.7k
Ireland
Bio_X2Y3.7k wrote:

Different machines generate raw data in different formats. A typical first step is to convert your specific raw data into a commonly used generic format like mzXML or mzML.

You might then want to convert this into other formats for downstream analysis. E.g. you might convert into MGF to allow the software Mascot to identify peptides in your data.

So your first step should be to identify the machine your data comes from. I strongly suggest you go back to the person who gave you the data and request more details about the experiment - without knowing exactly what you're looking it, it will be very difficult to perform a meaningful analysis (e.g. different software is optimised for different machines). Also, you should know things like whether labeling like SILAC was used.

If for some reason you can't do this, perhaps you can post some examples of the filenames/directory names you have, and somebody here might be able to recognise the machine. For example, Agilent raw data is stored in ".d" directories.

The following website provides a large list of mass spectrometry software, including format conversion utilities:

See especially msconvert, which converts "from RAW / WIFF / T2D / Agilent / Bruker / Waters / mzML / mzXML / MGF / MS2 to mzML / mzXML / MGF / MS2".

ADD COMMENTlink modified 12 weeks ago by RamRS25k • written 8.6 years ago by Bio_X2Y3.7k
1
gravatar for Laurent
8.6 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

Vendor software generally has options to export data in one or several open formats. You could ask the original provider to send the converted file, as the vendor specific binaries are pretty much useless without their software.

The state-of-the-art converter is msconvert, part of proteowizard. It is also distributed with the ISB's Trans-Proteomic Pipeline (TPP), that will provide you with additional software to do whatever analysis you are looking for. Note that you will need to perform the conversion from binary to text/xml format on a Windows machine, as the vendor libraries that provide access to binary data only run on the Microsoft OS.

The ms-utils.org link provided by Bio_X2Y is a very helpful resource. To visualise your data, once converted in mzML for instance, I would also suggest EBI's PRIDE Inspector, which will also provide some QC plots for free.

Hope this helps.

ADD COMMENTlink modified 12 weeks ago by RamRS25k • written 8.6 years ago by Laurent1.6k
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