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)
The following instructions apply to a SIMPATIQCO system with the following properties:
There are three methods to upload a file to SIMPATIQCO
Since there is no interface for this operation, one
has to add instruments manually. This is simple done by adding a line in the
SIMPATIQCO database. Open the tbl_instruments table and fill in the data
for the new instrument.
The name_long string will later appear in the SIMPATIQCO web interface. Note that the id is a primary key, so just count this number up and do not delete lines. If you want to remove an instrument, just set the "active" column to false.
If there is a column named "dev", set its value to false.
The column "order" just regulates the listing of the instruments from left to right on the simpatiqco main site.
All other columns are optional. The columns "calc_statistic_period" and "run_type_ids" will later be filled when you go trough the settings and run-type settings.
Each uploaded raw file will be analysed and the resulting data (raw file facts and search results) will be stored. To make these values comparable over time, the raw files need to be analysed in a certain way, which is not changing. The "run-types" hold these information, espacially the Mascot-search paramters. So each raw file is assigned to a certain run-type. Run-types can easily be created in the "Settings" page (see manual "Adding and removing of run-types" below). For better usability, the run-types can also be assigned to specific instruments. This has no impact on the statistic or what so ever, but is only a visual helper. For example, it is not necessary to make an ETD-run-type selectable for a non ETD instrument. This assigning is also done on the "Settings" page. The picture shows the self explaining matrix.Adding and removing of run-types
If your mascot-server connection works, you can add run-types with different search parameters. Navigate to the Settings pane, and scroll down to the Status area. If you see something like "Mascotserver: Connection OK" then your mascot-server is reachable. Scroll down to the "Run-type configuration" area, enter a Name for your new run-type, choose the settings available on your mascot-server, and click save.
The "Display in menu: group number" item, lets you choose in which group your run-type will appear, when a user clicks upload new raw file. This is just an optical feature for providing a better overview regarding the different run-types. There are 10 groups possible and each group can hold infinite numbers of run-types. If you want to move a run-type to another group or up/down within a group, just select it by clicking it, then two small arrows on the left will appear. An "OK" sign will appear on the left if your run-type was saved successfully. If not, check the input fields for possible implausible values e.g. letters in numerical input fields, or using a "," instead of a "." -depending on your mascot server settings.
It is not intended to ever remove a run-type, since every uploaded run is bound to the latter. Therefore, if you want to remove a run-type (make it disappear from the menu), just enter the SIMPATIQCO database, open tbl_run_types and set the active column to false.Peptide lists
On the Settings page you can create peptide lists to observe e.g. Retention times of certain peptides. Create a list (a peptide list is always bound to a certain run-type) e.g. "BSA peptides", then fill the list, by navigating to the search results. Click on the proteins which contain your desired peptides and click the "+" item. You will then be able to choose the peptide list which your peptide should be added to. To use your peptide lists, navigate to the Time-course Panel and select your run-type. If there are any peptide lists attached to it, they will appear, together with the available plots. If you click a peptide list, the corresponding plot for each peptide will appear for the last runs.Time-course: plotting long term data about proteins of interest
To observe certain values about a protein of interest over a long term e.g. the sequence coverage of Bovine Serum Albumin (BSA) in an everyday test run, you must tell the system, that you want to make e.g. BSA a protein of interest (POI). Do this by opening a search-result and click on the protein.
A little white diamond appears next to the protein name. When you click it, this protein will become a protein of interest for the run-type of this search result. It will be marked in green color from now on, and it will appear in the list of proteins you can select for monitoring long time values in the Database pane. If you want to remove the POI status from a protein, navigate to the Settings pane, scroll down to the Proteins Of Interest Pane, and find the corresponding cell (Protein name/Run-type) and click the X icon.Troubleshooting
First thing to do, log on to your server, and look what happens when the simpatiqco web site is accessed. Watch out for any error messages. If your uploaded runs deliver no results or you get error messages which don't explain enough there are ways of debugging. First, check the temp directory (e.g.: D:\temp) and open upload_log.txt. This file contains info on the latest upload and should like this:
[instrument_id] => 5
[run_type_id] => 24
[Filedata] => Array
[name] => 2012-02-15_100scans.RAW
[type] => application/octet-stream
[tmp_name] => D:\temp\php29E.tmp
[error] => 0
[size] => 3682034
php -c "C:\Program Files (x86)\EasyPHP-5.4.0RC4\apache\php.ini" D:\www\simpatiqco\inc\rawextractor.php 1244NOTE: Adapt the above code to your settings. If you made a standard installation, then EasyPHP is in the "Programm Files (x86)" directory and simpatiqco is on D:\www. The last paramter is the ID of your run. If the command succeds, you can watch what happens and when exactly the analyzis crashes.