Answers.Body: <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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Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-08T11:54:21.017Z
Answers.LastActivityDate: 2023-05-08T11:54:21.017Z
Answers.UserDisplayName: jing zhao
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-08T11:59:02.427Z
Comments.Text: Thank you for your reply. I only changed the modification and added the fasta  raw file  in the configuration file, Other parameters were default.
Comments.UserDisplayName: jing zhao
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-12T14:18:10.130Z
Comments.Text: Dear @jingzhao thanks for posting back. Could you kindly "accept" your answer (green tick button) - it does help with our site stats
Comments.UserDisplayName: M__
Tags: <maxquant>
Title: maxquant error: Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array
ThreadText: # 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 @username_0 thanks for posting back. Could you kindly "accept" your answer (green tick button) - it does help with our site stats  
  
  ---
  
  ## 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)
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