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Matched ions #106
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Hi Kevin, |
BTW, if you want to know which peaks could be matched, you can use PDV to plot the annotated spectra. Best, Fengchao |
Thanks, Fengchao and Daniel. I know Comet will export matched ions, but perhaps their
format is not standard pepXML? It has been a while since I looked at it.
Anyway, I will either get the ions out myself or use Comet to do it.
Thanks for pointing me to PDV. It isn't useful for this particular case
because I am pulling out the matched ions from hundreds of runs, but it
looks like a very nice tool and I was unaware of it.
Best wishes,
Kevin
…On Thu, Oct 15, 2020, 5:30 PM Fengchao, ***@***.***> wrote:
BTW, if you want to know which peaks could be matched, you can use PDV
<https://github.com/wenbostar/PDV> to plot the annotated spectra.
Best,
Fengchao
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Hi Kevin, Yes, Comet can output matched ions only for .out files. As far as I know, pepxml doesn't have any field for this information. Best, Fengchao |
Hello, Are there any plans to implement this feature in the future? Thanks, |
Yes. Best, Fengchao |
We are also highly interested in this and more features !! It would also be very nice to get the matched m/z error for each fragment ion too. We are switching from MQ atm, and this is one of the very useful columns in MQ. It's a helpful qc / optimisation metric for the mass analyser and for creating all sorts of spectral visualisations. Is there also a way to add percolator score and q value for each psm? At the moment it's not possible from the xml alone to get to the final outcome because the percolator information is missing. Thanks & Best |
Which xml file were you referring to? As to the q-value, the results are not/should not be filtered with a single PSM-level q-value. FragPipe applied sequential or 2-D filtering combining PSM- and protein-level FDR. I guess you'd probably better to use the psm.tsv file. Best, Fengchao |
Thanks for the fast reply...
Thanks for pointing to the other xml file. I only checked the *.pepXML but not the interact-*.pep.xml.
I totally agree for standard usage. But, we were playing a bit around (e.g. Plot target decoy distribution of scores, mass errors, etc...) while optimising a new MS + search engines atm. And we couldn't find all the values we were interested in the psm.tsv, that's why I started to look at other places too. Yes, one can put things again together from the Percolator output file (if not deleted) but for the not so programming experienced colleagues its not that straight forward. Thus would be cool if the PSM_Ranks, Percolator Score, Percolator PEP that was actually used would appear in the psm.tsv file eventually. |
Here is the tutorial (https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#psmtsv), but it is a little outdated. I will update it in the following weeks.
That's correct,
Best, Fengchao |
Hello,
I am interested in getting lists of of matched ions for each PSM as part of the search results. For example, something like:
I do not see anything in the parameters that looks like this. Is there a switch for this that I am not seeing?
Thanks!
Kevin
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