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pFindStudio / pGlyco2

pGlyco is a software tool dedicated for the analysis of intact glycopeptides/glycoproteins using mass spectrometry.
http://pfind.ict.ac.cn/software/pGlyco/
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Not finding any Peptides or Glycopeptides #14

Open NitinCCRC opened 6 years ago

NitinCCRC commented 6 years ago

Hi, I just downloaded version 2.1.2 and received the license from you. I started the simple N-glycopeptide search but it did not give me any results. I followed all the instructions but still, no peptides found. As soon as I start to search it gives me an error saying Glycodb has stopped working. I am not sure what is wrong. Following is the result report Converting N in N-X-S/T/C to J ----Source fasta = C:\Users\Nitin Supekar\Desktop\Pglyco\IgG.fasta ----Target fasta = C:\Users\Nitin Supekar\Desktop\Pglyco\IgG.fasta.N2J

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 /       pParse2.0 (x64) from pFind Studio     \
/        Email  :  pfind@ict.ac.cn              \
\        Website:  http://pfind.ict.ac.cn       /
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[pParse] Calling pXtract to export MS1 and MS2 files... [pXtract] The software will expire in 01/01/2019 [pXtract] Begin to extract G:\For_Software\Antibody_Trypticdigest_HCDpdCID.raw [pXtract] pXtract tries to use MSFileReader [pXtract] : MSFileReader should be 32/64 bit version corresponding to pFind. [pParse] MS1list completes. [pParse] Processing Antibody_Trypticdigest_HCDpdCID.MS1 [pParse] MS1 Or MS2 files not completely extracted! Antibody_Trypticdigest_HCDpdCID [pParse] Calling pXtract to export MS1 and MS2 files... [pXtract] The software will expire in 01/01/2019 [pXtract] Begin to extract G:\For_Software\Antibody_Trypticdigest_HCDpdCID.raw [pXtract] pXtract tries to use MSFileReader [pXtract] : MSFileReader should be 32/64 bit version corresponding to pFind.

[pParse] Dear User: pParse.exe failed to open G:\For_Software\Antibody_Trypticdigest_HCDpdCID.ms2, this file does not exist any more!

[pParse] pParse has encountered a problem and will exit. Retry with correct parameters. Contact pparse@ict.ac.cn for help.

[pGlyco Info] License will be expired in 2019/01/01 [pGlyco Info] Loading glycan database ... [pGlyco Info] Ion Indexing ... Process 1: [Complete] 100% [==================================================] [pGlyco Info] Estimating FDR ... Fitting glycan part ... target GlyScore pep is none Fitting peptide part ... [pGlyco Info] Inferring proteins ... Reading pGlyco results ... [pGlyco Info] Combining all results to: ----C:\Users\Nitin Supekar\Desktop\Pglyco\pGlyco_task_2018-06-29-09-45-26\pGlycoDB-GP-FDR-Pro.txt [pGlyco Info] Task Complete!

jalew188 commented 6 years ago

@NitinCCRC You should install MSFileReader (both 32 and 64 bit version) to access raw files.

We now have an "MSFileReader-free" raw reader, but it will take a few weeks to test it.