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Topic: How to combine picked peaks into isotopic clusters (Read 3576 times) previous topic - next topic

How to combine picked peaks into isotopic clusters

I am new to this list, although not new to MS data analysis.
I may be missing something obvious, but I cannot find any xcms function that corrals the peaks identified by findPeaks into isotopic clusters (features). I am trying to develop R code that will find the most likely monoisotopic peak in glycopeptide MS1 features. I have the locations of my MS2 scans for glycopeptides (identified de novo from mgfs) in m/z and RT. I want to find MS1 features at those locations and use them to correct the (often incorrect) monoisotopic m/z taken from the mgf files.  Are there any xcms functions that help with this, or do I need to sift through the findPeaks results and try to form the clusters by RT and by m/z values separated by 1/charge?
I'd appreciate any help you can provide.
Thanks,
Peter Warren
Boston Children's Hospital Urologic Dept.


Re: How to combine picked peaks into isotopic clusters

Reply #2
Hi, Jan,

Thank you for the CAMERA suggestion. I tried it out, but it is specifically geared toward metabolites. As I mentioned, I am working with peptides, which have a very different isotopic pattern (more peaks) per molecule.

Any other suggestions specific to peptide/protein research?

Thanks,
- Peter