I am using two software programs to analyze patient protomics: MaxQuant and FragPipe. While MaxQuant provides reliable results, FragPipe’s analysis seems less consistent. I am investigating whether the issue might be related to the conversion of RAW data to the mzML format.
Could the conversion process impact the quality of the data or its compatibility with FragPipe? If so, I plan to evaluate the method I use for the conversion and explore alternative approaches to improve the results.
Thank you
Hi Renan,
MaxQuant will take the raw file without the need to convert it to mzML.
Best,
Hediye
Hi Renan,
the conversion can definitely affect the outcome. You also need to consider the analysis parameters used with each tool. Make sure you understand what they do and set them accordingly. I strongly suggest you do not just click through the options.
Generally, with MSConvert the best bet is to use Vendor peak picking as you seem to have selected. The tools should provide guidance for data conversion.
Good luck,
Peter
- Badges
- Science method
- Similar topics
- Mathematics
- Statistics
- Statistical Techniques
- Structural Equation Modeling