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Messages - pgwarren

1
CAMERA / Re: CAMERA for peptide isotopic distributions?
Hi, Steffen,

Thanks for your reply. Is the intensity model something I can fiddle with? Or is that deep in the code? In my particular case, I'm dealing with glycopeptides, so I would probably need a somewhat different intensity model than straight peptides... a blend of peptide and glycan intensity models, with knowledge of the contributions of each (which in my case I can derive from my de novo glycan identification software, but which others may not have access to).

In the meantime I've started in on my own isotope grouping approach, which is showing some promise. Unless I can tweak CAMERA's intensity model myself (which also needs to be mass-dependent), I will probably not be able to use the tool.

Thanks,
- Peter
2
CAMERA / CAMERA for peptide isotopic distributions?
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.
3
XCMS / Re: How to combine picked peaks into isotopic clusters
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
4
XCMS / 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.