MaxQuant error at label free normalization step

[abak...@gmail.com]

I had a successful run with my set of samples and I wanted to run my samples one more time with min. ratio count set to 1. However, this time MQ gave an error at the "label free normalization" step. I checked the raw WIFF file, and the LC-MS/MS run seems to be fine, without an interruption. I copied the files once again from our server and it still gave the same error. I would be happy to share any kind of file, if you think you can help. 

Best,

Ahmet

[Nazlıcan Altınışık]

I have same problem at the same step as well. Is there anyone can help ?

21 Temmuz 2016 Perşembe 12:36:16 UTC+3 tarihinde abak...@gmail.com yazdı:

[Ireshyn Govender]

Hi All

I also have the same problem - I am trying to run samples that I have already run before. It gives the error all the time even though these samples ran perfectly fine before. This was on an older version of MaxQuant as well. 

Any help will be appreciated.

Thank you!

Ireshyn G.

[Ireshyn Govender]

Hi Ahmet

How did you resolve this issue?

Thank you in advance.

Kind regards,

Ireshyn Govender

On Thursday, 21 July 2016 11:36:16 UTC+2, abak...@gmail.com wrote:

[tao....@umaryland.edu]

I had the same issue. The possible reason is one of your raw files could be corrupted or do not have good chromatogram. I checked my raw files one by one and found one file I cannot open in the xcalibur. Then I replaced this file and make sure it can be opened properly. Then no issue with maxquant search. Good luck

[Xinbi Li]

I have the same issue here. After reading the error message, I realize the error might occur by including one blank in the data process, which would cause some issues in the normalization. After remove it, everything works fine. 

[Scutenaire Jeremy]

Hi, 

I have the 1.6.7.0 version of the software and I got the same issue at normalization step. I open each of my files with the viewer of MaxQuant but nothing looks anormal. How do you know if there is one blank in the file? 

What if I skip the normalization step? 

Thank you. 

[Ireshyn Govender]

In my experience, if one (or more) run is very different from the rest - this issue occurs.

Perhaps check your runs in a viewer e.g. PeakView, then omit the run(s) that are different from the rest in terms of signal from your analysis. Run the remaining files in MQ and the error shouldn't come up again.

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[Katelyn Ludwig]

I am having a similar problem, but under my description it just says the file folder and "label free_normalization 0 Label free_normalization" and then it cuts off. I'm searching 180 files and it keeps happening. All files open fine in xcalibur, and most have searched fine in smaller searches. I did a small search that failed, repeated it exactly the same, and it went through. Any advice? It is very frustrating as it happens ~6 hours into the search. Thanks!

On Tuesday, July 30, 2019 at 9:54:02 AM UTC-4, Ireshyn Govender wrote:

In my experience, if one (or more) run is very different from the rest - this issue occurs.

Perhaps check your runs in a viewer e.g. PeakView, then omit the run(s) that are different from the rest in terms of signal from your analysis. Run the remaining files in MQ and the error shouldn't come up again.

On Tue, Jul 30, 2019 at 2:59 PM Scutenaire Jeremy <jeremy.s...@gmail.com> wrote:

Hi, 

I have the 1.6.7.0 version of the software and I got the same issue at normalization step. I open each of my files with the viewer of MaxQuant but nothing looks anormal. How do you know if there is one blank in the file? 

What if I skip the normalization step? 

Thank you. 

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[César Rivera]

Hi Katelyn.

Did you manage to solve your problem?

Today the same thing happened to me.

[Katelyn Ludwig]

Hi Cesar,

No, I never got it fixed unfortunately.