Has anyone successfully used CAMERA for peptide MS data? Peptides have different isotopic distributions from metabolizes, due mostly (I believe) to their generally larger masses and higher charge states. I tried CAMERA with default settings on xcms centWave-picked peaks, hoping to get isotopic clusters annotated. But the annotations were mostly 1+, with a smaller number of 2+ Isotopes (perhaps a few 3+). Whereas my peptides run up to 5+, with the majority of them 2+ and 3+.
First, can this be done? And if so, is it done by modifying the isotopeMatrix? From earlier postings, it appears this only handles one charge state. Do I construct multiple matrices, one per charge state?
Thank you, - Peter
P.S. This is related to my recent question on the xcms forum, where Jan suggested using CAMERA.
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.