<p>****this was the xml file that i configured to maxquant. i changed modification and added the fastq and raw file. Other parameters were default. however, 'Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array' was reported when I run the command '<em>maquant mq.xml</em>'. but, When I only kept the N modification, the program ran successfully, but a small amount of peptides were identified.
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CC BY-SA 4.0
2023-05-08T11:54:21.017Z
2023-05-08T11:54:21.017Z
jing zhao
<p>An error occurred while I was running the program maxquant (2.0.3):</p>
<p>Reading search engine results (SP)</p>
<p>Unhandled Exception:
System.Exception: Exception during execution of external process: 1228404
Unhandled Exception:
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at MsLib.Search.AndromedaPeptide.FromString (System.String line, BaseLibS.Ms.Data.Protein.ProteinSet proteinSet) [0x000a9] in :0
at MsLib.Search.AndromedaQuerySp.Add (System.Int32 count, System.String line, BaseLibS.Ms.Data.Protein.ProteinSet proteinSet, System.Int32 minLength) [0x00001] in :0</p>
<p>[ERROR] FATAL UNHANDLED EXCEPTION: System.IndexOutOfRangeException: Index was outside the bounds of the array.
at MsLib.Search.AndromedaPeptide.FromString (System.String line, BaseLibS.Ms.Data.Protein.ProteinSet proteinSet) [0x000a9] in :0</p>
<p>how can i fix it, thank your very much!</p>

CC BY-SA 4.0
2023-05-08T11:59:02.427Z
Thank you for your reply. I only changed the modification and added the fasta  raw file  in the configuration file, Other parameters were default.
jing zhao
CC BY-SA 4.0
2023-09-12T14:18:10.130Z
Dear @jingzhao thanks for posting back. Could you kindly "accept" your answer (green tick button) - it does help with our site stats
M__
<maxquant>
maxquant error: Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array
# maxquant error: Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array

(Asked by: username_0 on 2023-05-05)

An error occurred while I was running the program maxquant (2.0.3):

Reading search engine results (SP)

Unhandled Exception:
System.Exception: Exception during execution of external process: 1228404
Unhandled Exception:
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at MsLib.Search.AndromedaPeptide.FromString (System.String line, BaseLibS.Ms.Data.Protein.ProteinSet proteinSet) [0x000a9] in :0
at MsLib.Search.AndromedaQuerySp.Add (System.Int32 count, System.String line, BaseLibS.Ms.Data.Protein.ProteinSet proteinSet, System.Int32 minLength) [0x00001] in :0

[ERROR] FATAL UNHANDLED EXCEPTION: System.IndexOutOfRangeException: Index was outside the bounds of the array.
at MsLib.Search.AndromedaPeptide.FromString (System.String line, BaseLibS.Ms.Data.Protein.ProteinSet proteinSet) [0x000a9] in :0

how can i fix it, thank your very much!

**Tags:** maxquant
> **Comments:**
> **username_0**: Thank you for your reply. I only changed the modification and added the fasta  raw file  in the configuration file, Other parameters were default.  
> **username_1**: Dear @jingzhao thanks for posting back. Could you kindly "accept" your answer (green tick button) - it does help with our site stats  

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## 1 answers

### Answer by username_0 on 2023-05-08. Score: 1

\*\*\*\*this was the xml file that i configured to maxquant. i changed modification and added the fastq and raw file. Other parameters were default. however, 'Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array' was reported when I run the command '*maquant mq.xml*'. but, When I only kept the N modification, the program ran successfully, but a small amount of peptides were identified.
[![enter image description here](https://i.sstatic.net/wCo8e.png)](https://i.sstatic.net/wCo8e.png)
[![enter image description here](https://i.sstatic.net/zUA57.png)](https://i.sstatic.net/zUA57.png)


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