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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!

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    $\begingroup$ Thank you for your reply. I only changed the modification and added the fasta raw file in the configuration file, Other parameters were default. $\endgroup$
    – jing zhao
    May 8, 2023 at 11:59
  • $\begingroup$ Dear @jingzhao thanks for posting back. Could you kindly "accept" your answer (green tick button) - it does help with our site stats $\endgroup$
    – M__
    Sep 12, 2023 at 14:18

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****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 enter image description here

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