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kevinkovalchik / RawQuant

RawQuant is a Python package for extracting scan meta data and quantification values from Thermo .raw files.
MIT License
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Error extracting MS2 using RawQuant on PRM RAW files #16

Open FloHaaa opened 6 years ago

FloHaaa commented 6 years ago

grafik

Hello together, I was trying to use your nice parsing tool on targeted PRM RAW-Files. While it did work without problems on DDA-files, i cannot extract information for the MS2-Infos on my PRM-scans. I am not sure this tool is intended for this kind of data and wanted to ask you about the nature of the error in the software (see picture). Is there something i can do to circumvent this? Best wishes, Florian

kevinkovalchik commented 6 years ago

Hello! Thanks for checking out the tool. We did develop RawQuant with DDA in mind, but we would be interesting in expanding its applications. A couple questions regarding this:

  1. Do you have a PRM file you would be willing to share with us? This would help address the specific error you are running into, as well as develop the tool further for PRM use.

  2. What data would be most useful to you? I would think to include fill times, median and/or summed intensity, isolation windows. What else might be useful?

Please note that we are actively working on a replacement for RawQuant which will be a standalone program (which will also be open-source and freely available). Any PRM or DIA functionality we add will probably go into this new program, but we can certainly continue to discuss it here since the new one isn't available yet.

FloHaaa commented 6 years ago

Hello and thanks for the quick response! Regarding your questions:

  1. I actually found a file on PRIDE, measured on a similar instrument, which resulted in the exact same error. It is downloadable under the following link: https://www.ebi.ac.uk/pride/data/archive/2018/06/PXD008211/20161221_LG_Ecoli_Trypsin_Phospho_pooled_Sample2_PRM_01.raw

  2. That sounds exactly right. To me, most interesting would be the actual fill time corresponding to a specific scan number to start with.

Thanks for looking into this.

kevinkovalchik commented 6 years ago

Thanks. I'll check out the file when I get a chance. Working on a deadline right now, so it might be a week or two...