No_Enzyme_Search_Failure using High Performance Desktop with Proteome Discover version 2.3

[BenSamy2020]

Greeting,

I am currently performing No_Enzyme_Search using Proteome Discover version 2.3. I am consistently experience search failure. Please refer to attachment for search failure error message, MSFragger parameters and High Performance Desktop Specs. Please do advise me on how to progress to achieve successful No_Enzyme_Search using MSFragger in Proteome Discover version 2.3. I am utilizing the No_Enzyme_Search parameters provided at: https://github.com/Nesvilab/MSFragger/tree/master/parameter_files

If you require more information please to notify me.

Lastly, I would like to thank you in advance for your assistance.

Regards, Samy

[huiyinc]

Hi Samy,

Sorry for the late reply. The error happens because PeptideProphet can't recognize 'No-enzyme-' as the enzyme name. We haven't fully test non-specific search using MSFragger-PD node because it requires lots of computer memory. It might take us some time to update and test the node for this issue. Is it possible that you try to run non-specific search using MSFragger+Percolator and see if it works? Thanks.

Huiyin

BenSamy2020 notifications@github.com 於 2020年8月24日 週一 下午6:23寫道：

Greeting,

I am currently performing No_Enzyme_Search using Proteome Discover version 2.3. I am consistently experience search failure. Please refer to attachment for search failure error message, MSFragger parameters and High Performance Desktop Specs. Please do advise me on how to progress to achieve successful No_Enzyme_Search using MSFragger in Proteome Discover version 2.3. I am utilizing the No_Enzyme_Search parameters provided at: https://github.com/Nesvilab/MSFragger/tree/master/parameter_files

If you require more information please to notify me.

Lastly, I would like to thank you in advance for your assistance.

Regards, Samy

[image: High Performace Desktop Specs] https://user-images.githubusercontent.com/69944967/91033383-a0e9d680-e646-11ea-97db-cd2c119511e7.JPG [image: MSFragger_NoEnzyme_Search_Failure] https://user-images.githubusercontent.com/69944967/91033389-a21b0380-e646-11ea-9010-34e11d69f944.JPG [image: MSFragger_NoEnzyme_Search_Setting_Part_A] https://user-images.githubusercontent.com/69944967/91033395-a47d5d80-e646-11ea-9d9f-2aef8bc91037.JPG [image: MSFragger_NoEnzyme_Search_Setting_Part_B] https://user-images.githubusercontent.com/69944967/91033397-a5ae8a80-e646-11ea-8060-50e280ec6352.JPG

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-- Hui-Yin Chang, 張彙音 Assistant Professor, 助理教授 Department of Biomedical Sciences and Engineering, 生醫科學與工程學系 National Central University (Taiwan), 國立中央大學 (台灣)

[BenSamy2020]

Greetings Huiyin,

You don't have to apologise. Your replies are prompt and I appreciate it.

I tried running MSFragger with percolator (to troubleshoot) using NoEnzyme setting. But the runs kept on failing due to insufficient decoy peptide or peptides (I cannot remember exactly what the error is). I believe percolator requires at least 200 peptides for performing its task. Using the exact same files, I was able to successfully performance close searches (MSFragger+ PeptideProphet or MSFragger+Percolator) with about 1100+ protein groups.

Based on the above issue I am facing, I guess FragPipe would be able to performance NoEnzyme search successfully compared to PD?

Also can you provide me with your email address, I am thinking of potential collaboration with the use of MSFragger.

Lastly, I would like to thank you for your amazing MSFragger support!

Regards, Samy

[huiyinc]

Hi Samy,

Thanks for your understanding. Yes, FragPipe is a better platform for NoEnzyme search. We didn't test fNon-specific enzyme search in PD before because we didn't expect users having enough memory for it. Well, you just show us that everything is possible. Here is my email address: dr.chuiyin@gmail.com. Please feel free to email me if you have any questions.

Thanks.

Huiyin

BenSamy2020 notifications@github.com 於 2020年8月25日 週二 下午8:31寫道：

Greetings Huiyin,

You don't have to apologise. Your replies are prompt and I appreciate it.

I tried running MSFragger with percolator (to troubleshoot) using NoEnzyme setting. But the runs kept on failing due to insufficient decoy peptide or peptides (I cannot remember exactly what the error is). I believe percolator requires at least 200 peptides for performing its task. Using the exact same files, I was able to successfully performance close searches (MSFragger+ PeptideProphet or MSFragger+Percolator) with about 1100+ protein groups.

Based on the above issue I am facing, I guess FragPipe would be able to performance NoEnzyme search successfully compared to PD?

Also can you provide me with your email address, I am thinking of potential collaboration with the use of MSFragger.

Lastly, I would like to thank you for your amazing MSFragger support!

Regards, Samy

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/13#issuecomment-679995545, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA54HPLW7WMWULVA4HDSCOVKPANCNFSM4QJK5RJQ .

-- Hui-Yin Chang, 張彙音 Assistant Professor, 助理教授 Department of Biomedical Sciences and Engineering, 生醫科學與工程學系 National Central University (Taiwan), 國立中央大學 (台灣)

[BenSamy2020]

Hi Huiyin,

I had sent an email to dr.chuiyin@gmail.com.

Regards, Parthiban