toppic 1.5 error with combined search

Mowei Zhou

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Dec 9, 2021, 7:28:44 PM12/9/21

to TopPIC

Hi Xiaowen,

I was trying the new function of keeping decoy hits in v1.5. But it had an error during "finding PrSM clusters" step.

I ran the same files with v1.4.13 (combined mode) and had no problem. I don't know if v1.5 topFD had some changes and I will need to rerun topFD with v1.5?

Thanks,

Mowei

In Kwon Choi

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Dec 10, 2021, 9:06:45 AM12/10/21

to Mowei Zhou, TopPIC

Hi Dr. Zhou,

We will look into the issue. Would it be possible for you to share your input data with us?

Thank you,

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In Kwon Choi

James Fulcher

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Dec 10, 2021, 10:49:22 AM12/10/21

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Hello all,

I don't believe this issue is related to the "keep decoy" option. I have encountered the same error on a different analysis using the GUI:

Looks like it stopped at a different point in the run too.

Bests,

James

In Kwon Choi

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Dec 10, 2021, 11:04:52 AM12/10/21

to James Fulcher, TopPIC

Hi all,

From our testing result as well, "from decoy" option does not seem to be the cause of the problem. When we processed the data using v1.5 TopFD and v1.5 TopPIC along with the "keep decoy" option, we did not have the issue. However, we could exactly reproduce Dr. Zhou's issue when we ran v1.4 TopFD with v1.5 TopPIC. There has been a change to the output file format in v1.5 TopFD from v1.4 TopFD, so it could have caused the issue.

For Dr. Zhou, could you try running the v1.5 version of TopFD and TopPIC to process the data?

For James, which version of TopFD did you use before running TopPIC? If it was v1.5, could you share the data and the commands with us so that we can look into the issue?

Thank you,

To view this discussion on the web visit https://groups.google.com/d/msgid/top-down-toppic/fb2274a4-05dd-471b-9880-d0e6be0f66f0n%40googlegroups.com.

liuxia...@gmail.com

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Dec 10, 2021, 10:40:35 PM12/10/21

to TopPIC

Hi, Mowei,

- I don't know if v1.5 topFD had some changes and I will need to rerun topFD with v1.5?

We changed the output format of TopFD v1.5, so if you would like to use TopPIC v1.5 to do database search, you need to use TopFD v1.5 to rerun spectral deconvolution.