Hi Zhijun,

We do have some work to do with RT alignment for small molecules. In the meantime, it would be interesting to see if we can work with your XCMS-aligned data - can you provide an example?

Thanks

Brian Pratt

Yes, Brian is working on #1 similar to our iRT support for peptides.

On #2, I assume you are referring to this method:
https://www.ncbi.nlm.nih.gov/pubmed/16448051

What file format do you end up with after this alignment? Is it aligning the actual spectra in time and producing a new file, like mzML?

The paper is new to us, and you are the first to ask. Yes, supplying example data files will help us determine how much work, if any, would be required to support XCMS.

Thanks for posting to the Skyline support board.

--Brendan

Hi Brendan,
          Yes, your assumption is right. I will send you a example after I get it ready. I used XCMS (R package: http://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html) to process the raw data. After aligned, it produces a new object (XCMSnExp object which includes chromatographic peaks or correspondence). and the package provides one function to save it as mzDATA format. However, all m/z and RT information are available in XCMSnExp object, and I think it is possible to extract the information from XCMSnExp object and save them as skyline readable format.
           Thanks,
zhijun

Hi Brian,
        Would you please send me instructions to do RT alignment for small molecules? is spectral library required? (my skyline version is 4.1.0.11796)
         Thank you,
zhijun

Hi Zhijun,

As I said before, this is an area we're still working on for small molecules. We hadn't made it a top priority as our first small molecule users indicated that their chromatography was pretty solid compared to peptide work. This obviously won't always be true, so it is an area of concern but we aren't ready with it yet. The fundamentals are there but some care has to be taken to back out any assumptions that the molecule of interest is always a peptide.

Brian