Can the fragpipe analyze the dimethylation-peptides?
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Hi fcyu,
I know the DIANN can analyze the multiplexed DIA raw data (plexDIA). Can the Fragpipe do it?
If it can, how do I configure the parameters in the Linux workflow (attachment)?
Now I want to analyze the dimethyl labeling peptides from plexDIA (light:Δ0=28.0313,intermediate:Δ4=32.0564,heavy:Δ8=36.0757) using the Fragpipe in Linux. But I don't know how to set up the parameters.
Can you help me?
Hi Fengchao,
Thanks your reply. The attachment is the log file.
log_2024-06-14_12-11-09.txt
Best
You only enabled DIA-NN but it is the last step just for quantification. You need to run all steps starting from MSFragger. Here is a brief tutorial for the label-free DIA: https://fragpipe.nesvilab.org/docs/tutorial_DIA.html. The diaTOP_ABPP
workflow is the one you should take a look at.
Best,
Fengchao
Hi fucy,
I have built a spectral library, I think I just need to provide the library and DIA data file. In addition, I want to analyze the dimethyl-labeled DIA.
Best
How did you build the library? Could you upload the log file?
It seems that there is Dimethyl
string that is not recognized by DIA-NN, which makes sense since you didn't define it using the command line options. If you want the DIA-NN quant module to recognize Dimethyl
, you need to type the additional command in the opt cmds
box. Or, you could use our workflow to run from scratch.
Best,
Fengchao
Hi fucy,
I used the DIANN in window to analyze the dimethyl-based DIA, it is ok by setting up modification in the command line options. but it doesn't work using the Fragpipe in linux.
The attachment is the log file to build the library using the AlphapeptDeep.
logfile.zip
Best
I believe when you raw DIA-NN in Windows, you added additional command line options to let DIA-NN recognize your custom modifications in the spectral library. You should do the similar when running FragPipe in Linux.
Best,
Fengchao
Yes, you should copy the DIA-NN's command to the cmd line opts
box in the Quant (DIA)
tab. And you should also uncheck plex DIA
box, and remove all entries in the light
, medium
, and heavy
boxes since you build the spectral library by your own.
Best,
Fengchao
Thanks for your reply.
If I use your FragPipe workflow to run dimethyl-based DIA data from scratch, how I set up the parameters in Linux?
Now I want to built the library based on DDA fractions by FragPipe in Linux and analyze the DIA data.
Best
- Load the
DIA_SpecLib_Quant.workflow
in theworkflow
tab (remember to click "load"). - Load both of your DDA and DIA data in the
input LC-MS Files
panel of theworkflow
tab. - Set your DDA files to the
DDA
data type, and your DIA files to theDIA
data by using theset DDA
andset DIA
buttons. - Specify your fasta file in the
database
tab. - Add the dimethyl modifications to the variable modification panel in the
MSFragger
tab. - Enable the
plex DIA
checkbox, and configure thelight
andheavy
labels in theplex DIA
panel of theQuant (DIA)
tab. - Go to the
result
tab, specify the path of the result folder, and click run.
Best,
Fengchao
I think the settings look good. If you are not sure, could send me the log file to take a look after FragPipe finishes.
Best,
Fengchao
The library was bulit based on the dimethyl-peptides DDA rawdata using the FragPipe and all labels(light, intermedian, heavy) were configured as variable modification.
Thank you for your patient and detailed explanation. I understand now.
Best
UniMod:1
is another modification, Acetylation, which means that the peptide you were looking at did not have dimethyl. Could you check the psm.tsv and library.tsv to troubleshoot?
Thanks,
Fengchao
I apologize for the miscommunication. I meant you could check the same peptide ADQLTEEQIAEFK
against the psm.tsv
and library.tsv
to see if it indeed have acetylation on N-term. What you showed is a different peptide.
Could it be that the N-terminus is acetylated, making it less reactive with dimethyl labeling?
Yes. That was why in the MSFragger settings, both N-term acetylation and dimethyl labeling were variable modifications (one or the other or none).
Best,
Fengchao
The figure was not uploaded successfully.
Best,
Fengchao
Thanks, so there are no issues in FragPipe. Good to know.
Best,
Fengchao
Thank you very much for your patient and detailed explanation.
Hi fcyu,
I now want to build a large DDA spectral library based on dimethylation for methylated DIA analysis. Should I only use dimethylation as the light label for building the spectral library in DDA, and then use Fragpipe for analysis where DIANN extracts ion chromatograms based on light, medium, and heavy label mass differences? Or do I need to label with light, medium, and heavy labels separately, collect DDA data for each, and then build the spectral library?
Should I only use dimethylation as the light label for building the spectral library in DDA, and then use Fragpipe for analysis where DIANN extracts ion chromatograms based on light, medium, and heavy label mass differences?
Do you mean only generate light dimethyl labeled DDA data? Yes, it should work. But in the MSFragger search, since you load both DDA and DIA, you still need to specify light, medium, and heavy as variable modifications.
Or do I need to label with light, medium, and heavy labels separately, collect DDA data for each, and then build the spectral library?
Generate the DDA data with light, medium, and heavy labeling also works.
Best,
Fengchao
I understand that I should use only the light labeling sample, then collect DDA fractions. When building spectra library using Fragpipe, MSFraggers should be set to use only the modifications corresponding to the light label (n28.0313 as variable modification, K28.0313 as fixed modification), and then generate a spectral library containing only the light label. In the plexDIA tab, set light, medium, and heavy labeling. Finally, DIANN generates corresponding spectral libraries for medium and heavy labels based on the mass differences between light and medium, and heavy labels. This way, I can simplify the experiment by using only the light label for labeling and acquiring DDA data.
I understand that I should use only the light labeling sample, then collect DDA fractions.
If you want, you could use light, medium, and heavy samples to collect DDA fractions, respectively.
When building spectra library using Fragpipe, MSFraggers should be set to use only the modifications corresponding to the light label (n28.0313 as variable modification, K28.0313 as fixed modification), and then generate a spectral library containing only the light label.
No, you should still set all of light, medium, and heavy if you have loaded both DDA and DIA data, because there are three labels in DIA.
DIANN generates corresponding spectral libraries for medium and heavy labels based on the mass differences between light and medium, and heavy labels
It is not exactly how DIA-NN plexDIA works. DIA-NN only accept light-only spectral library. It did a "match-within-run" to detect the medium and heavy peptides.
I can simplify the experiment by using only the light label for labeling and acquiring DDA data.
You can only generate light DDA data. But remember to set all of light, medium, and heavy in the MSFragger search if you have loaded the DIA data.
Best,
Fengchao
Thank you for your detailed reply!
I just tested the Fragpipe workflow by constructing spectra library using only the light label and only analyzing DIA data containing only the light label. However, strangely, although I only labeled with the light tag in DIA data, the results still contain information about medium and heavy labels
Which file is the screenshot from? Do those medium and heavy peptides have non-zero intensity?
Thanks,
Fengchao
The screenshot from the 'diann-output.tsv ' file.
Those medium and heavy peptides have intensity.
Could you upload the file?
Thanks,
Fengchao
Hi fcyu,
I have identified the issue: when I set the cmd-opts in the workflow file to --fixed-mod Dimethyl,28.0313,nK --channels Dimethyl,0,nK,0:0; Dimethyl,4,nK,4.0251:4.0251; Dimethyl,8,nK,8.0444:8.0444, even with only one label in the DIA data, the results show three labels. However, when I set only --fixed-mod Dimethyl,28.0313,nK --channels Dimethyl,4,nK,4.0251:4.0251, the corresponding labels are only Dimethyl-n-4 or Dimethyl-K-4 modifications.
Best
The first command seems to be correct and the second one seems to be wrong, that was why you didn't see the light labels.
But, you should not add any command to DIA-NN's cmd opts
if you enabled plex DIA
, because FragPipe have taken care of that.
Check the DIA-NN commands in the log file and you will understand what I said.
Best,
Fengchao
This analysis is based on the spectral library I built using DDA components, analyzing another set of DIA data. Therefore, this analysis is equivalent to having an existing spectral library. So I disabled plex DIA and configured the parameter in DIA-NN's cmd opts. Now, the result is ok.