Comments (7)
Here one example - all three peaks have MS2 spectra that correspond to the sample glycopeptide.
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Rob will comment on this I'm sure. We have some nice updates on the way for metamorpheus that will improve coverage and quantification of glycopeptides. Some of these updates are in a pull request. So, hopefully within a month you'll see something. I'll try to remember to send you an email so you'll have a chance to see it in action.
from flashlfq.
Great, thanks!
from flashlfq.
Hi D,
Do you mean the same glycopeptide has more than one MS1 features? Can you show me an example?
Thanks,
Lei
from flashlfq.
Some peaks are combined together into one peak in FlashLFQ to avoid noisy, near-baseline peaks from being double-counted, which throws off the intensity measurement for a particular peptide, since FlashLFQ uses peak height instead of area for quantification. The tolerance for combining peaks is 5 min, so every peak with the same modified sequence within 5 min of each other is combined into one. I can make this into a user-editable setting. You can also make a workaround with the current code by making the full sequence of each ID different. For example you could do:
Base Sequence: REEQFNTTFR
Full Sequence REEQFN(Glyco)TTFR_1
Base Sequence: REEQFNTTFR
Full Sequence REEQFN(Glyco)TTFR_2
Then each of those would be reported separately in the Peaks file (and in the Quantified Peptides file). I know it's a little annoying, but it'll work.
from flashlfq.
thanks!
from flashlfq.
FYI, I've changed this in the upcoming FlashLFQ version. I've decided to not merge peaks together unless they have the same apex. Should help make this kind of thing easier to interpret, but it will probably report several peaks for peptides that bounce in and out of the limit of detection.
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Related Issues (20)
- Duplicated column names in BayesianFoldChangeAnalysis.tsv
- Support for Percolator output files HOT 77
- Advice on parameter setting HOT 10
- RT alignment? HOT 2
- Support for more conditions
- FlashLFQ normalization issue HOT 8
- setting up license on linux HOT 2
- FlashLFQ crashed HOT 1
- extra trailing tab in output HOT 1
- will/does it support timsTOF data? HOT 1
- Question about quantification
- crashed - invalid parametrization for the distribution HOT 6
- Enquiry on where the actual namespace for FlashLFQ exists HOT 2
- Question about using with PeptideShaker HOT 3
- No Posterior Error Probability in Bayesian Protein Fold Change Analysis in Command Line tool
- Problem with file name excluding format extension HOT 5
- Shared peptide quantification
- Fail in the command-line mode HOT 2
- Questions about the generic input format HOT 3
- Commandline version dependent on Microsoft.WindowsDesktop.App Framework HOT 13
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