RT correction March 27, 2023, 03:47:06 AM 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 v4.9.221218Thanks, Chris Quote Selected Last Edit: March 27, 2023, 03:51:18 AM by drchrispook
Re: RT correction Reply #1 – March 28, 2023, 12:47:07 AM 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. Quote Selected
Re: RT correction Reply #2 – April 12, 2023, 07:04:27 AM Quote from: drchrispook – on March 28, 2023, 12:47:07 AMYeah, 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. Quote Selected
Re: RT correction Reply #3 – June 18, 2023, 04:46:54 AM 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. Quote Selected
Re: RT correction Reply #4 – April 30, 2024, 10:11:53 PM Quote from: agentfourty7 – on April 12, 2023, 07:04:27 AMQuote from: drchrispook – on March 28, 2023, 12:47:07 AMYeah, 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 Quote Selected