Error on peptide validator

[hkweon]

Hi,

I was running Open MSFragger search on PD2.2. After a successful processing analysis of 12 LC-HCD-MS2, the consensus analysis fails with a peptide validator error. See the error message lines below. I could successfully finish another proteomic sample data, 12 LC-HCD, using the same MSFragger work flows and parameters. Can anyone help on this issue, or share experiences with the same issue? I appreciate your help. Thank you.

Hye Kyong

11:48 AM | (2):Peptide Validator | Warning | Error while running qvality on PSMs for 20210405_Samp_Band1-12_MSFragger-TrGlu node MSFragger(25). 11:48 AM | (2):Peptide Validator | Error | qvality: The following exception is raised during the execution of qvality.exe: The exit code of qvality was 1. (The expected exit code is 0). Consider, that the DynamicPropertyAccessor`2 value distribution is not usable for qvality.

[huiyinc]

Hi Hye,

Could you please share us your data (including the mzML and fasta files), so we can take a look of the issue? Thank you.

Huiyin

hkweon @.***> 於 2021年4月20日 下午11:02 寫道：



Hi,

I was running Open MSFragger search on PD2.2. After a successful processing analysis of 12 LC-HCD-MS2, the consensus analysis fails with a peptide validator error. See the error message lines below. I could successfully finish another proteomic sample data, 12 LC-HCD, using the same MSFragger work flows and parameters. Can anyone help on this issue, or share experiences with the same issue? I appreciate your help. Thank you.

Hye Kyong

11:48 AM | (2):Peptide Validator | Warning | Error while running qvality on PSMs for 20210405_Samp_Band1-12_MSFragger-TrGlu node MSFragger(25). 11:48 AM | (2):Peptide Validator | Error | qvality: The following exception is raised during the execution of qvality.exe: The exit code of qvality was

1. (The expected exit code is 0). Consider, that the DynamicPropertyAccessor`2 value distribution is not usable for qvality.

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[hkweon]

Hi,

First, thank you for your reply. Can I share the files with you in a UM-dropbox? Thank you.

Hye Kyong Kweon

On Apr 20, 2021, at 11:10 PM, chuiyin @.***> wrote:

 Hi Hye,

Could you please share us your data (including the mzML and fasta files), so we can take a look of the issue? Thank you.

Huiyin

hkweon @.***> 於 2021年4月20日 下午11:02 寫道：



Hi,

I was running Open MSFragger search on PD2.2. After a successful processing analysis of 12 LC-HCD-MS2, the consensus analysis fails with a peptide validator error. See the error message lines below. I could successfully finish another proteomic sample data, 12 LC-HCD, using the same MSFragger work flows and parameters. Can anyone help on this issue, or share experiences with the same issue? I appreciate your help. Thank you.

Hye Kyong

11:48 AM | (2):Peptide Validator | Warning | Error while running qvality on PSMs for 20210405_Samp_Band1-12_MSFragger-TrGlu node MSFragger(25). 11:48 AM | (2):Peptide Validator | Error | qvality: The following exception is raised during the execution of qvality.exe: The exit code of qvality was

1. (The expected exit code is 0). Consider, that the DynamicPropertyAccessor`2 value distribution is not usable for qvality.

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[sarah-haynes]

Hi Hye Kyong, can you upload your files here: https://umich.app.box.com/f/b57aacbe764842e69bf5c2811705385c

Thanks! Sarah

[hkweon]

Hi Sarah,

I just uploaded files. In case, RAW files are shared as well. Combination of Glu-C and trypsin was used to prepare peptides. Also a closed search showed high human protein contamination in samples. Thank you for your support in advance. Hye Kyong

On Wed, Apr 21, 2021 at 12:51 PM Sarah Haynes @.***> wrote:

Hi Hye Kyong, can you upload your files here: https://umich.app.box.com/f/b57aacbe764842e69bf5c2811705385c

Thanks! Sarah

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--

Hye Kyong Kweon, Ph.D.

Research Lab Specialist, Senior Mass Spectrometry Center Department of Chemistry University of Michigan, Ann Arbor @.***

[sarah-haynes]

Thanks Hye Kyong! If you get a chance, it might be helpful to have your PD workflow files as well.

[hkweon]

Hi Sarah,

Workflow files have been uploaded. They are not different from the provided MSFragger template workflows but modified with appropriate parameters for the samples. Thank you. Hye Kyong

On Wed, Apr 21, 2021 at 1:23 PM Sarah Haynes @.***> wrote:

Thanks Hye Kyong! If you get a chance, it might be helpful to have your PD workflow files as well.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-824229324, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6K5OXON33YCXRYRM35XXLTJ4CZHANCNFSM43ILGG6A .

--

Hye Kyong Kweon, Ph.D.

Research Lab Specialist, Senior Mass Spectrometry Center Department of Chemistry University of Michigan, Ann Arbor @.***

[huiyinc]

Hi Hye Kyong,

Sorry for the late reply. It takes me some time to try to figure out a solution. Unfortunately, I couldn't find one. After several attempts, I found out that all the peptides were filtered out in the node of Peptide Validator (even using a loose FDR, e.g., 5%). That's the reason for the issue. My assumption is that perhaps both target and decoy peptides have the similar score distribution such that the threshold is too high and all the peptides are removed. I will pull out the information from the msf file to check it. PD is primarily designed for closed search (not for open search), so there are some issues that need to be addressed (which I am working on). Maybe you can use FragPipe for the open search, and I will keep you posted if we have any improvements in the future. Thank you!

Huiyin

hkweon @.***> 於 2021年4月22日 週四 上午1:53寫道：

Hi Sarah,

Workflow files have been uploaded. They are not different from the provided MSFragger template workflows but modified with appropriate parameters for the samples. Thank you. Hye Kyong

On Wed, Apr 21, 2021 at 1:23 PM Sarah Haynes @.***> wrote:

Thanks Hye Kyong! If you get a chance, it might be helpful to have your PD workflow files as well.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-824229324, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AD6K5OXON33YCXRYRM35XXLTJ4CZHANCNFSM43ILGG6A

.

--

Hye Kyong Kweon, Ph.D.

Research Lab Specialist, Senior Mass Spectrometry Center Department of Chemistry University of Michigan, Ann Arbor @.***

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-824247161, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAYCQNQDMK5IPXDODNLTJ4GKZANCNFSM43ILGG6A .

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[hkweon]

Hi HuiYin,

Thank you for investigating the data. The sample data were collected with high rates of human contamination, simple target protein pool (His and V5 pull down), and peptides from two proteases. I am speculating all these factors are collectively contributing to the high FDR. I will try Fragpipe if it can handle the data set. Thank you for working on this.

Hye Kyong

On Tue, Apr 27, 2021 at 8:53 AM chuiyin @.***> wrote:

Hi Hye Kyong,

Sorry for the late reply. It takes me some time to try to figure out a solution. Unfortunately, I couldn't find one. After several attempts, I found out that all the peptides were filtered out in the node of Peptide Validator (even using a loose FDR, e.g., 5%). That's the reason for the issue. My assumption is that perhaps both target and decoy peptides have the similar score distribution such that the threshold is too high and all the peptides are removed. I will pull out the information from the msf file to check it. PD is primarily designed for closed search (not for open search), so there are some issues that need to be addressed (which I am working on). Maybe you can use FragPipe for the open search, and I will keep you posted if we have any improvements in the future. Thank you!

Huiyin

hkweon @.***> 於 2021年4月22日 週四 上午1:53寫道：

Hi Sarah,

Workflow files have been uploaded. They are not different from the provided MSFragger template workflows but modified with appropriate parameters for the samples. Thank you. Hye Kyong

On Wed, Apr 21, 2021 at 1:23 PM Sarah Haynes @.***> wrote:

Thanks Hye Kyong! If you get a chance, it might be helpful to have your PD workflow files as well.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-824229324 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AD6K5OXON33YCXRYRM35XXLTJ4CZHANCNFSM43ILGG6A

.

--

Hye Kyong Kweon, Ph.D.

Research Lab Specialist, Senior Mass Spectrometry Center Department of Chemistry University of Michigan, Ann Arbor @.***

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-824247161, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALAWWAYCQNQDMK5IPXDODNLTJ4GKZANCNFSM43ILGG6A

.

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

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--

Hye Kyong Kweon, Ph.D.

Research Lab Specialist, Senior Mass Spectrometry Center Department of Chemistry University of Michigan, Ann Arbor @.***

[huiyinc]

Hi Hye Kyong,

No problem at all!

Huiyin

從我的iPhone傳送

hkweon @.***> 於 2021年4月27日 下午9:34 寫道：

 Hi HuiYin,

Thank you for investigating the data. The sample data were collected with high rates of human contamination, simple target protein pool (His and V5 pull down), and peptides from two proteases. I am speculating all these factors are collectively contributing to the high FDR. I will try Fragpipe if it can handle the data set. Thank you for working on this.

Hye Kyong

On Tue, Apr 27, 2021 at 8:53 AM chuiyin @.***> wrote:

Hi Hye Kyong,

Sorry for the late reply. It takes me some time to try to figure out a solution. Unfortunately, I couldn't find one. After several attempts, I found out that all the peptides were filtered out in the node of Peptide Validator (even using a loose FDR, e.g., 5%). That's the reason for the issue. My assumption is that perhaps both target and decoy peptides have the similar score distribution such that the threshold is too high and all the peptides are removed. I will pull out the information from the msf file to check it. PD is primarily designed for closed search (not for open search), so there are some issues that need to be addressed (which I am working on). Maybe you can use FragPipe for the open search, and I will keep you posted if we have any improvements in the future. Thank you!

Huiyin

hkweon @.***> 於 2021年4月22日 週四 上午1:53寫道：

Hi Sarah,

Workflow files have been uploaded. They are not different from the provided MSFragger template workflows but modified with appropriate parameters for the samples. Thank you. Hye Kyong

On Wed, Apr 21, 2021 at 1:23 PM Sarah Haynes @.***> wrote:

Thanks Hye Kyong! If you get a chance, it might be helpful to have your PD workflow files as well.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-824229324 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AD6K5OXON33YCXRYRM35XXLTJ4CZHANCNFSM43ILGG6A

.

--

Hye Kyong Kweon, Ph.D.

Research Lab Specialist, Senior Mass Spectrometry Center Department of Chemistry University of Michigan, Ann Arbor @.***

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-824247161, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALAWWAYCQNQDMK5IPXDODNLTJ4GKZANCNFSM43ILGG6A

.

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/19#issuecomment-827583273, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6K5OUMLLBH6D233W4KHXDTK2XWHANCNFSM43ILGG6A .

--

Hye Kyong Kweon, Ph.D.

Research Lab Specialist, Senior Mass Spectrometry Center Department of Chemistry University of Michigan, Ann Arbor @.*** — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.