about the OSF repository

[jinaanna]

Another question, I have noticed that you have only uploaded the peptide quantification results but not protein quantification results in the OSF repository (https://doi.org/10.17605/OSF.IO/6G3UX). How do you cope with the result from Spectronaut? How to generate the protein quantification results in Spectronaut except the"Run pivot Report" function? Maybe some codes in R could finish this?

[vdemichev]

All DIA-NN reports contain protein quantities. Please see the PG.Normalised column. We don't recommend using Spectronaut. Specifically for the Nat Methods DIA-NN paper, we did not need protein reports from Spectronaut, so did not generate them. But in general, you can easily export protein quantities in Spectronaut, just need to select the respective columns.

Best, Vadim

[jinaanna]

I didn't figure out one question and I would like to consult you again. How do you compare the protein quantification precision using LFQbench with the peptide quantification results in Spectronaut? Does LFQbench support the extraction of protein quantification results from peptide results ? Could you please give me some guidance?

Jina		jina

@. | 签名由网易邮箱大师定制 On 10/5/2021 05:26，Vadim @.> wrote：

All DIA-NN reports contain protein quantities. Please see the PG.Normalised column. We don't recommend using Spectronaut. Specifically for the Nat Methods DIA-NN paper, we did not need protein reports from Spectronaut, so did not generate them. But in general, you can easily export protein quantities in Spectronaut, just need to select the respective columns.

Best, Vadim

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[jinaanna]

I didn't figure out one question and I would like to consult you again. How do you compare the protein quantification precision using LFQbench with the peptide quantification results in Spectronaut? Does LFQbench support the extraction of protein quantification results from peptide results ? Could you please give me some guidance?

Jina		jj

@. | 签名由网易邮箱大师定制 On 10/5/2021 @.> wrote： I didn't figure out one question and I would like to consult you again. How do you compare the protein quantification precision using LFQbench with the peptide quantification results in Spectronaut? Does LFQbench support the extraction of protein quantification results from peptide results ? Could you please give me some guidance?

Jina		jina

@. | 签名由网易邮箱大师定制 On 10/5/2021 05:26，Vadim @.> wrote：

All DIA-NN reports contain protein quantities. Please see the PG.Normalised column. We don't recommend using Spectronaut. Specifically for the Nat Methods DIA-NN paper, we did not need protein reports from Spectronaut, so did not generate them. But in general, you can easily export protein quantities in Spectronaut, just need to select the respective columns.

Best, Vadim

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.