Open search of timsTOFpro data errs with could not find mzData message #463
Assignees
Labels
Comments
|
It looks like an error from PTM-Shepherd. Danny @danielgeiszler , can you take a look when you have time? Thanks, Fengchao |
|
Hi animesh, Unfortunately, PTM-Shepherd can't process files that have spaces in their pathnames. It's something we're working on currently, but the only way around this currently is to rename your files and the folder name. PTM-Shepherd will just provide summarizations of the mass shifts in your dataset. Depending on your intentions, it may not be necessary. Can you elaborate on what it is your goal with the open search is? |
|
Removing the space in the file name seems to have worked @danielgeiszler 👍🏽 although i did not get much out of the open-search workflow (full run appended below), wondering if it is not optimized for timsTOFpro DDA data? Does it work for DIA BTW? We are looking for a modification in the sample which we don't know from beforehand but we have some idea that it is some sort of glycosylation. Do you thing glyco-workflow will have a better change is finding it? |
|
The search does not find many PSMs from your data. The reasons could be incorrect settings (enzyme, chemical labelling, database....) or your data. Please double check. There is no issue for your tools open search ddaPASEF data. Open search does not support DIA. Best, Fengchao |
|
I have loaded the analysis folder at https://drive.google.com/drive/folders/1g7Ofd_GWBO5l-zzwYivJP1dPmwtr8yZ_?usp=sharing , can you see if there is some issue with setup @fcyu 👍🏽 |
|
Sure. I am quite busy recently, will take a look when I have time. Best, Fengchao |
|
Is this some sort of enriched data? Why do you have so few scans in general? |
|
in a way, yes @danielgeiszler as it is a protein extracted from a gel-band so we are not expecting a lot (cf. MaxQuant reports about 100 ProteinIDs) |
|
So you're looking for a single modification on a single protein and you're not sure about the modification's mass? Do you know where on the protein it is? I think this is a difficult problem, and doing open searches and searching entire databases on your enriched data is pulling in a bunch of noise. Even when doing the PeptideProphet modeling, the models were only able to converge for peptides at a 3+ charge state. |
|
Hi Danny, I think this is what open search for. As long as the modification is abundant enough and not exists multiple times in one peptide, open search can find it. Best, Fengchao |
|
Can you describe more what you expect your data and modification to look like? Should this dataset be extremely enriched for your modification, or just the protein it's on? Are you sure that your modification weighs <500 Da, which is the mass range you used? |
|
To be honest, we are really shooting here in the dark @danielgeiszler . What we know for sure is that one file has a protein roughly 500Da+ than other but this could be anywhere from ~100Da-1000Da and we expect it to be some sort of glycosylation? It should be in one file almost 100% and missing in the other file, so almost 0%... so far we have tried to proteases, GluC and Try/P, and as far as MaxQuant can see, it see both proteins in both files... so i guess the discriminatory peptide is not being caught by it. I was expecting the dependent-peptide to work but alas it fails https://groups.google.com/g/maxquant-list/c/g7ipwuMnUgI/m/Ve3KXm-vAAAJ ... |
|
Hi @animesh Sorry for the late reply, I missed the notification. Try increasing your mass range to 1500 Da or so in the MSFragger tab for the open search. You're only looking up to 500 Da, so you might be missing it if it's heavy. |
|
looks like nothing much happened with 1500 @danielgeiszler , could crystal-C being not supported for this type of data be an issue? also is there a plan for making DIA work for open search too? |
|
Crystal-C shouldn't affect this, it only cleans up your search results. We don't have any plans to make DIA work for open search, but that wouldn't help in your case. If your modification is supposed to be there at high levels but it isn't showing up at all, there isn't much we can do to help you at this point. It could be a sample prep issue, which we have no control over. I'd suggest taking a look at your protein sequence and making sure that it produces peptides that can be found with your current settings, but there's nothing else we can do. Good luck. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
I am trying to run open-workflow on a timsTOFpro data but it is failing with "could not find mzData" message? I have loaded the output folder at https://drive.google.com/drive/folders/1U_n-hxpWwUq7EDjEC40sD-SC_ykMXeqt , let me know if more information is needed? I must mention that fragpipe did complain about crystal-c ...
The text was updated successfully, but these errors were encountered: