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Topic: RT correction (Read 5746 times) previous topic - next topic

RT correction

Has anyone used RT correction successfully? I can see that it works to align the shifted peaks from my two batches of analysis (see RT_correction screenshot) but the peaks are distorted. See other pics for examples. Won't this affect quantification?
I'm running v4.9.221218
Thanks,
 Chris

Re: RT correction

Reply #1
Yeah, I don't like this. Instead I've worked out that converting your data to mzML means you can just add an RT shift to the time value of each scan. I've just done a fixed shift but if I spend a couple more hours sampling different shifts between my batches I could use a function to correct it instead. 

Re: RT correction

Reply #2
Yeah, I don't like this. Instead I've worked out that converting your data to mzML means you can just add an RT shift to the time value of each scan. I've just done a fixed shift but if I spend a couple more hours sampling different shifts between my batches I could use a function to correct it instead. 

Please tell me more about this, is this done in ProteoWizard? I follow your blog and have benefitted when converting .L to .msp and merging them, so thank you.

Re: RT correction

Reply #3
Hi, glad you found that post useful. It took me a year or so to work it out for myself so I'm glad other people are benefitting. Is it too late to give it a DOI?  :))

To manually shift the RT of mzML files you need to write a script that creates a copy of the file line-by-line and edits the RT with a fixed shift. It's simple brute force but it works. I thought about using a polynomial instead but that will corrupt the quantitative information in the data as this depends on a uniform scan interval.

 

Re: RT correction

Reply #4
Yeah, I don't like this. Instead I've worked out that converting your data to mzML means you can just add an RT shift to the time value of each scan. I've just done a fixed shift but if I spend a couple more hours sampling different shifts between my batches I could use a function to correct it instead. 

Please tell me more about this, is this done in ProteoWizard? I follow your blog and have benefitted when converting .L to .msp and merging them, so thank you.

Hi, I found the script I wrote to do this and have put it up on GitHub and Zenodo.
https://zenodo.org/doi/10.5281/zenodo.11095185