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MaxQuant and Perseus Bug Reporting
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LFQ intensity does not appear in the Peptides.txt file. #78

Open juseonmin opened 4 months ago

juseonmin commented 4 months ago

Describe the bug Hello,

I am currently using MaxQuant for data analysis and have encountered an issue after updating from version 2.0.3.0 to 2.5.2.0. Previously, the Peptides.txt file used to include LFQ intensity values, but this no longer seems to be the case after the update. Is this feature no longer supported?

I am using data obtained from an Ascend Orbitrap with Tune version 4.0. Interestingly, using MaxQuant version 2.0.3.0 with this data results in automatic termination of the software, preventing me from using this version. However, I would like to continue receiving LFQ intensity information in the Peptides.txt file while using version 2.5.2.0. Could you advise on how to resolve this issue?

Thank you for your assistance.

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CarloDeNart commented 4 months ago

By default LFQ intensities are still in the Peptides.txt file, and in the latest version too such a feature was not changed at all. Could you provide us the mqpar file?

juseonmin commented 4 months ago

Hello,

Thank you for your response. After hearing from you, I tried running the previous data with the new version 2.5.2.0, and I could verify that the LFQ column was successfully created in the peptides.txt file. However, it appears that the LFQ column is still not being generated for the new experimental data acquired with Ascend in version 2.5.2.0.

For comparison purposes, I have attached the column tables and the mqpar file. My experimental data involves two sets:

Data obtained from Orbitrap Eclipse, using Tune version below 4.0 Data obtained from Orbitrap Ascend, using Tune version 4.0 or above

With the first dataset, I was able to generate results using both MaxQuant versions 2.0.3.0 and 2.5.2.0. However, with the second dataset, results were only obtainable using the latter version. In all datasets, the LFQ column was properly formed in the ProteinGroups.txt file. Yet, in the case of dataset 2 with MaxQuant 2.5.2.0, the LFQ column was not formed in the Peptides.txt file.

I suspect there might be an issue with my settings, but I would greatly appreciate it if you could review the attached files and provide your insights.

Your program has been incredibly helpful, and I am thankful for the support it has provided.

Thank you for your time and assistance. I look forward to your response.

Best regards,

Seonmin Ju

2024년 5월 13일 (월) 오후 11:12, CarloDeNart @.***>님이 작성:

By default LFQ intensities are still in the Peptides.txt file, and in the latest version too such a feature was not changed at all. Could you provide us the mqpar file?

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juseonmin commented 4 months ago

I have also analyzed the data obtained using the Orbitrap Exploris 480 with a tune version similar to Ascend. As with the previous analysis, I reviewed the LFQ intensity in the protein groups file. However, I noticed that the LFQ intensity is not displayed in the peptides file.

Could you kindly verify this issue?

Thank you for your assistance.

oe480_newtune_ver2.5.2.0_tables.pdf oe480_newtune_ver2.5.2.0_mqpar.txt

zhenfu32 commented 2 months ago

Hello,

I am currently using MaxQuant version 2.6.2.0 for my proteinomics data analysis on a Linux server. I have encountered a similar issue where the peptides.txt file does not include the LFQ intensity and iBAQ columns, despite selecting the relevant parameters.

Steps to Reproduce:

In the "Group specific parameters" section, under "Label-free quantification", I selected "LFQ". In the "Global parameters" section, under "Label-free quantification", I checked "iBAQ". All other related parameters were kept at their default values. Results:

The proteinGroups.txt file correctly contains the intensity, LFQ intensity, and iBAQ columns. The peptides.txt file, however, only contains the intensity column, and the LFQ intensity and iBAQ columns are missing. I have attached my mqpar.xml file for reference. mqpar_v2.6.2.0.txt

Additional Information: I have attempted to resolve this issue but have been unsuccessful. I found a similar issue discussed on ResearchGate (https://www.researchgate.net/post/LFQ_intensities_missing_from_peptides_txt_file), where it was suggested that the problem might be related to changes in MaxQuant versions. Unfortunately, I was unable to find older versions of MaxQuant in the version archives on the official website.

Any assistance or insights into resolving this issue would be greatly appreciated. Thank you!

Best regards, Zhenfu