Title [pLink] the format of .mgf file is not compatible with pLink
Priority question Status finished
Superseder Nosy List MichaelB, ctarn
Assigned To ctarn Keywords

Created on 2021-05-18.09:05:34 by MichaelB, last changed by ctarn.

File name Uploaded Type Edit Remove
ProblemMGFfile.mgf MichaelB, 2021-05-18.14:31:33 application/octet-stream
pLinkProblem.png MichaelB, 2021-05-18.09:05:34 image/png
pLinkProblem2.png MichaelB, 2021-05-18.14:23:48 image/png
msg68 (view) Author: ctarn Date: 2021-05-18.14:55:00

Thanks. The format of the .mgf file is not compatible with pLink since each row of the 
peaks list contains three numbers instead of just two (m/z & intensity).

May I ask that what's the original format of the data? I would recommend you to use the 
original data directly if it is acceptable by pLink; or try to convert the format using 
other tools.
msg67 (view) Author: MichaelB Date: 2021-05-18.14:30:35
Please find attached MGF file. Thank you.
msg66 (view) Author: MichaelB Date: 2021-05-18.14:23:48
Thank you - I have now done that - please see attached screenshot. The output 
says problems with the MGF file. However, the same MGF file works fine when 
converted to mzML with MSConvertGUI and viewed in mMass.
msg65 (view) Author: ctarn Date: 2021-05-18.13:34:27
Hi, issue 8 is a guide of how to run pLink in command line mode (CMD) on Windows OS. 
pLink for UNIX/MacOS is not released yet. Thanks you very much.
msg64 (view) Author: MichaelB Date: 2021-05-18.13:32:00
Hi, where can I download pLink for UNIX/MacOS so I can run it on the command 
line, please?
msg63 (view) Author: ctarn Date: 2021-05-18.12:12:14
Hi, Please try to run pLink in Command line mode and sent us the output. Please refer 
to issue 8.
msg62 (view) Author: MichaelB Date: 2021-05-18.09:05:34
Hi, I am trying to use pLink to detect SS bonds in mass spec data. After I set 
up the fields with a .mgf file and .fasta database and click START, pLink 
gives some output (see screenshot) and then crashes. Please can you assist?
Date User Action Args
2021-05-19 10:17:24ctarnsetpriority: urgent -> question
status: chatting -> finished
2021-05-18 14:57:30ctarnsettitle: pLink crashes on searching -> [pLink] the format of .mgf file is not compatible with pLink
2021-05-18 14:55:03ctarnsetmessages: + msg68
2021-05-18 14:31:33MichaelBsetfiles: + ProblemMGFfile.mgf
2021-05-18 14:30:54MichaelBsetfiles: - Alan200310half.mgf
2021-05-18 14:30:45MichaelBsetfiles: + Alan200310half.mgf
messages: + msg67
2021-05-18 14:23:51MichaelBsetfiles: + pLinkProblem2.png
messages: + msg66
2021-05-18 13:34:30ctarnsetmessages: + msg65
2021-05-18 13:32:03MichaelBsetmessages: + msg64
2021-05-18 12:12:17ctarnsetassignedto: ctarn
messages: + msg63
status: unread -> chatting
nosy: + ctarn
2021-05-18 09:05:37MichaelBcreate