LFQ intensity does not appear in the Peptides.txt file.

[juseonmin]

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]

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]

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:

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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? — Reply to this email directly, view it on GitHub <#78 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AYBZBOYL6FFXYUVXC7U77EDZCDC23AVCNFSM6AAAAABHTZVZWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBXGY4DGMJVG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[juseonmin]

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