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RobertsLab / project-oyster-oa

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Fail at step 2d in SRM analysis instructions #8

Closed sr320 closed 6 years ago

sr320 commented 6 years ago

When trying to paste proteome in get the follow error.

image

yaaminiv commented 6 years ago

Huh. I can investigate later today. I'm assuming it doesn't resolve itself when you press "OK"?

grace-ac commented 6 years ago

Correct @yaaminiv . I'm testing it out and that is the step that got us stuck.

sr320 commented 6 years ago

Pretty sure it is related to step 2b. There is no fasta file provided. image

thus error for 2d. no fasta.

yaaminiv commented 6 years ago

http://owl.fish.washington.edu/spartina/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt is the file that I used in my DIA analyses as well (nb here)

I'm wondering if just changing the file extension may work....?

sr320 commented 6 years ago

@emmats What are your thoughts on this? Maybe this is cause of issue with replicates. A tab-delimited text file is being used instead of fasta? Is this possible?

@yaaminiv maybe.. but regardless your protocol fails at step 2b as currently written. So make sure you can demonstrate it works (follow your own protocol). I would suggest maybe you did not use this file for SRM as we cannot seem to reproduce (ie get errors)?

yaaminiv commented 6 years ago

I'm going to troubleshoot this more today and adjust the protocol so it can be reproduced.

emmats commented 6 years ago

Skyline wants fastas, I'm pretty sure.

I don't think this is the problem with the replicates, though.

yaaminiv commented 6 years ago

There was a FASTA file on the Windows machine I forgot to upload to OWL. It can now be found here.

Additionally, in Step 2d, sometimes copying and pasting the sequences in the lefthand window doesn't work. I've updated the instructions so you can import a FASTA file and populate the analyte tree. I've also updated the DIA protocols in RobertsLab/resources with this information (SRM one cites DIA protocol so it doesn't need to be updated).

Your issues should be resolved! I updated my workflow accordingly.