Mass spectrometry, Protein Chemistry Facility
Research Institute of Molecular Pathology (IMP)
Institute of molecular biotechnology of the Austrian Academy of Sciences (IMBA)
Gregor Mendel Institute of Molecular Plant Biology (GMI)

PD-Nodes SimpatiQCo Software Tools Publications

SimpatiQCo About Download Installation Manual FAQ's

I already have Apache/PHP/IIS running, how can i use my setup?

PHP: Just make sure that you use a version >= 5.4
Apache: Config your apache httpd.conf like the one which comes with simpatiqco.
IIS: Please do follow the installation guide and install simpatiqco with apache. To run apache parallel to IIS open the apache httpd.conf and set the listening port to e.g. 8080. You can then contact simpatiqco by going to e.g.: localhost:8080/simpatiqco.

How to add modifications for the Mascot search.

You can add any modification from your Mascot server as a variable modification in simpatiqco.
Firstly, create a runtype in simpatiqco which uses Mascot as search engine and save it. By default, no modifications are searched. If you want to add modifications to your search do the following:
Check which modifications your Mascot server provides (the exact string is necessary). You can do this in the Mascot search web interface (see screenshot below) or in every other program (e.g. Proteome Discoverer) which connects to your Mascot server.

A modification string may look like this:

Oxidation (M)

Now open pgAdminIII. Open the simpatiqco database and navigate to Schemas->public->Tables->tbl_run_types.
Select the table and click on "View the data in the selected object." in the top menue of pgAdminIII.
A table with the runtypes will appear. In the row of your runtype, go to the column 'mods' and double click in the field.

Now enter the modifications, use the exact modification string like on your Mascot server. If you add more than one, separate them with a comma. Use no spaces between the modifications and don't append a comma at the end.
Press F5 to update the table and exit pgAdminIII.
That's it, every sample started with this runtype will be searched with the modifications you entered.

How to automatically copy and process files after acquisition.

When starting a batch on your instrument, run a bat file when the acquisition is finished. Enter the path and name in the "post acquisition" field. For example: "D:\simpatiqco.bat %R". The %R will hold the raw file name.

The bat file can look like this:

Simple version:

d:\mpause.exe 20
d:\mpause.exe 5

Extended version, autoapply a run-type if a certain tag (e.g. BSA) is found in the rawfile name:

echo OFF
REM wait 20s so that raw file writing is complete before copying to hot folder
d:\mpause.exe 20

REM avoid spaces in path and file name and keep the length of the QC file name
REM constant, e.g. len(120201OT1_CCBSAPP04.raw) = 23
set m=%1%
REM keep file name but remove path
set m=%m:~-23%

REM "BSA" in the file name identifies QC run to be processed with run type id 2
set m1=%m:BSA=1%
REM copy file to hot folder, prefix rtid2 so that the file will be processed using run type id2 nethod
IF NOT %m%==%m1% copy "%1" "\\YOURSERVER\hot\YOURINSTRUMENT\rtid2_%m%"

d:\mpause.exe 5

Use mpause.exe (can be found in SIMPATIQCO/hotupload) to create a short pause after acquisition (so that writing of the file is truly complete before copying starts). The example provided checks if the filename contains the substring "BSA". If this is the case, the raw file is copied to the hot folder, and an rtid-tag is added as a prefix to the file name (here run-type id 2). This tag is required for SimpatiQCo to select the appropriate method for automatic processing. Alternatively you may specify the rtid-tag already in the file name. You may have to make the "hot" directory shared to use the network path starting with "\\" to copy the raw files to the hot folder. Of course, set the copy paramters to your system (your server and your instrument name). For troubleshooting, check if you can open the directory "\\YOUR-SERVER\hot\YOUR-INSTRUMENT" from another computer and if you are able to copy files to it. Remember that the YOUR-INSTRUMENT folder structure within the hot folder is created automatically when first starting the service in SIMPATIQCO (and any files present in an existing "hot" folder structure at this timepoint would be removed). Therefore do not change the folder structure manually. Copy the bat file and mpause.exe to e.g.: "D:" and give it a try. For troubleshooting, you can watch SIMPATIQCO monitor and work in the hot folder when logging on to your SIMPATIQCO server.