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ElucidataInc / ElMaven

LC-MS data processing tool for large-scale metabolomics experiments.
https://resources.elucidata.io/elmaven/
GNU General Public License v2.0
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Bookmark Peaks not showing up when loading mzroll #599

Open raaisakuk opened 6 years ago

raaisakuk commented 6 years ago

Have shared the data on drive with @sahil21 Filenames don't have special characters in them Using El Maven_v0.2.4

raaisakuk commented 6 years ago

  1. Somehow in the SamplesUsed tag all the samples got duplicated. I found it while trying to read mzroll using python. I am attaching the mzroll that I got after removing those samples. The bookmarks came back. You can compare the old mzroll with new and you will find in each SamplesUsed tag, after the column 3849, samples are repeated.

  2. Though I got the bookmarks back, I lost compound ids. I noticed the compoundId tag to be missing in some components. Adding it manually didn't give any ids in Peak Detailed format but it gave the ids in isotopeLabel column in Groups format.

  3. None of my mzrolls from this dataset are giving CompoundIds now in Peak Detailed Format. I am not sure if it is something related to new version or my dataset.

  4. In the database tag "Precursor Mz" and "Product Mz" have spaces and hence they are not read as tags. Because of this, loading the mzroll doesn't load the database. I tried removing the spaces. The database got loaded but names in SRM widget became weird so I changed this behaviour back to original.

  5. In El Maven 0.2.4 if I have bookmarked certain peaks and I try to upload a new mzroll, El Maven adds the peaks from mzroll to the bookmarked peaks. Is that a desired behavior? I expected it to replace the current session.

raaisakuk commented 6 years ago

Just adding a detail. I think I deleted a sample from the Sample Widget while processing this dataset. That is the only thing that I remember doing differently from my usual workflow.

raaisakuk commented 6 years ago

@sahil21 Is it possible to move the compoundids issue to high priority. I have faced it twice and Tiago faced it today too.

sahil21 commented 6 years ago

@raaisakuk Yes. We'll be releasing the patch soon.