How to combine picked peaks into isotopic clusters October 10, 2014, 06:23:48 AM 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 WarrenBoston Children's Hospital Urologic Dept. Quote Selected
Re: How to combine picked peaks into isotopic clusters Reply #1 – October 10, 2014, 06:57:49 AM Sounds like you are looking for the CAMERA package?http://pubs.acs.org/doi/abs/10.1021/ac202450g Quote Selected
Re: How to combine picked peaks into isotopic clusters Reply #2 – October 10, 2014, 10:00:38 AM 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 Quote Selected