Error when uploading evidence file to MSstatsShiny

Dominika Lewandowska

unread,

Oct 31, 2023, 9:39:39 AM10/31/23

to MSstats

Hi there,

I'm trying to run MSStats for the first time, using MSstatsShiny. It seems I can't upload my evidence file from MaxQuant even though it is below the size limit ( 180 MB). The error I'm getting says: <html> <head><title>413 Request Entity Too Large</title></head> <body> <center><h1>413

Any ideas on how to solve it?

Many thanks,

Dominika

Devon Kohler

unread,

Oct 31, 2023, 10:13:33 AM10/31/23

to MSstats

Hi Dominika,

We have lowered the file size recently, in an attempt to keep the server up. It has very low computational resources so really should be used to test smaller files. I would recommend downloading the application locally:

1. Download R and RStudio - How to. Note R version must be >= 4.3
2. Intall the package via Bioconductor

3. Run the app by typing "MSstatsShiny::launch_MSstatsShiny()" in the console.

In the meantime I will update the documentation to reflect the new upload limit.

Best,

Devon

Dominika Lewandowska

unread,

Oct 31, 2023, 11:02:21 AM10/31/23

to MSstats

Hi Devon,

Many thanks for your prompt reply. I will try to run the app in the R Studio.

Dominika

Dominika Lewandowska

unread,

Oct 31, 2023, 12:13:29 PM10/31/23

to MSstats

Hi again,

I ran MSstatsShiny in the console, no problem with the evidence file upload. However I'm getting an error message on the annotation file. It's attached here so someone can have a look.

Warning: Error in .checkAnnotation: ** Columns Run, Condition, BioReplicate missing in the annotation. Please check the annotation file.

Thank you!

Dominika

HS_annotation.txt

Devon Kohler

unread,

Oct 31, 2023, 12:46:10 PM10/31/23

to MSstats

Hi Dominika,

Can you try to upload the annotation file as a csv? Attached below.

Devon

HS_annotation.csv

Dominika Lewandowska

unread,

Nov 1, 2023, 7:33:07 AM11/1/23

to MSstats

Hi Devon,

I tried the csv file from you. I'm still getting an error:

Warning: Error in .checkAnnotation: ** Columns BioReplicate missing in the annotation. Please check the annotation file.

Thank you so much for your help :)

Dominika

Devon Kohler

unread,

Nov 1, 2023, 4:14:40 PM11/1/23

to MSstats

Hi Dominika,

I think the issue is just that the column has a lower case R (Bioreplicate) in your file. We should probably ignore capitalization in the package, but I've attached one that I think should work now.

Devon

HS_annotation.csv

Dominika Lewandowska

unread,

Nov 2, 2023, 8:33:34 AM11/2/23

to MSstats

Hi Devon,

It works! Thank you for finding a simple solution. :)

Best,

Dominika

Reply all

Reply to author

Forward