FAQ

How to install MSFileReader?

Please first manually uninstall the old version of MSFileReader, before installing the new version.

1. Go to https://thermo.flexnetoperations.com/control/thmo/RegisterMemberToAccount to register with Thermo and be able to download MSFileReader. If you have registered before, you can go directly to https://thermo.flexnetoperations.com/control/thmo/login to login.

2. Once you are registered and logged in, you can download MSFileReader 3.0 SP2 (or below) from the Thermo web site. It is currently under “Utility Software”. The latest version we support (as of 2018-01-21) is MSFileReader 3.0 SP2, available since Apr 11, 2016. pLink 2 has been tested with MS File Reader 3.0 SP2 or below.
   Attention: MSFileReader 3.1 SP2/SP4 CAN NOT run properly with pLink 2 now. Please DO NOT install this version of MSFileReader when using pLink 2.

3. Right-click on the installer and "Run as Administrator"

   

4. Install it accepting defaults.
   (Attention: The installer will install MS Visual C++ 2008 & 2010 Redistributable simultaneously. Please accept adding the additional installation features.)

   

5. If given the option, install both 32-bit and 64-bit versions.

   

6. After the installation of MS File Reader, you can use pLink 2 to read data from the raw file and check if the installation of MS File Reader succeeds.

• If the installation fails, you can get some messages from pLink 2. Please see the example below.

	  *********************************************
	 /       pParse2.0 (x64) from pFind Studio     \
	/        Email  :  pfind@ict.ac.cn              \
	\        Website:  http://pfind.ict.ac.cn       /
	  *********************************************

[pParse] Calling pXtract to export MS1 and MS2 files... 
[pXtract] The software will expire in 01/01/2019
[pXtract] Begin to extract C:\Data\BL21-osmoticI-LTG-1M.raw
[pXtract] pXtract tries to use MSFileReader 
[pXtract] <Exception>: MSFileReader should be 32/64 bit version corresponding to pFind.
[pParse] MS1list completes. 
[pParse] Processing BL21-osmoticI-LTG-1M.MS1 
[pParse] MS1 Or MS2 files not completely extracted! BL21-osmoticI-LTG-1M 
[pParse] Calling pXtract to export MS1 and MS2 files... 
[pXtract] The software will expire in 01/01/2019
[pXtract] Begin to extract C:\Data\BL21-osmoticI-LTG-1M.raw
[pXtract] pXtract tries to use MSFileReader 
[pXtract] <Exception>: MSFileReader should be 32/64 bit version corresponding to pFind.

[pParse] 
Dear User:
 pParse.exe failed to open C:\Data\BL21-osmoticI-LTG-1M.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. 

• If the installation succeeds, you can also get some messages from pLink 2. Please see the example below.

	  *********************************************
	 /       pParse2.0 (x64) from pFind Studio     \
	/        Email  :  pfind@ict.ac.cn              \
	\        Website:  http://pfind.ict.ac.cn       /
	  *********************************************

[pParse] Calling pXtract to export MS1 and MS2 files... 
[pXtract] The software will expire in 01/01/2019
[pXtract] Begin to extract C:\Data\BL21-osmoticI-LTG-1M.raw
[pXtract] pXtract tries to use MSFileReader 
[pXtract] <Output files>: 100.00%
[pXtract] Output Files Completed!
[pXtract] == == == Time elapsed: 48.331s. == == ==
[pParse] MS1list completes. 
[pParse] Processing BL21-osmoticI-LTG-1M.MS1 
[pParse] Loading MS1 and MS2 files... 
[pParse] Loading MS1 Spectra Number: 6567 
[pParse] Loading MS2 Spectra Number: 34350 
[pParse] Writing MS1 to PF... 

[pParse] <Exporting HCDFT>: 100%

[pParse] Evaluting by the classifier... 
[pParse] Filtering by the threshold... 

[pParse] <Writing MGF>: 100%
[pParse] Writing CSV... 
[pParse] Releasing resources... 
[pParse] Saving CSV to disk... 
[pParse] Exported 80405 precursors. 
[pParse] Found 0 duplicate scans. 
[pParse]  == == == Time elapsed: 85 seconds. == == == =  
[pLink] Welcome to use pLink v2.2.1650, it will be expired on 20190101
[pLink] Search Engine initializing...