ProDBWiki/DeveloperDocumentation/ImportMultiScans

Import Multi Scans

Overview

If you have a gel picture with many protein spots from a tissue, and you want to know what kind of proteins that are, you take a sample from the spots and analyse them with mass spectrometry. As a result you get a file with the peptide masses. Now you can import the files and connect them with the corresponding gel spots. This is a lot of work, especially if you have a large number of spots/files. Therefore you can use the Multi Files Importer. Here you can import all files from spots from one gel at once. You save all the files and the config-file from the spot selector in a compressed file. The compressed file has to be a .tgz-, .tar.gz-, .tar- or .zip-file. Also you have to observe that the compressed file has to be from a special form. This tool uploads all files at once and connects them automatically with the right gel spot. At the moment it only works for Maldi-Files.

How to use

At first you have to import a gel-picture and select the spots you want to analyse. In the config-file you find the the directories where the ms-files for one spot have to be saved (normally the mass spectrometer does it automatically). Be aware that the config file has to be in a specific format, described below. Now you need to save the config-file as geometry.config. After you selected the spots and send them into the mass spectrometer, you have to create a workstep for ms import and select all samples(spots) that were used by the spot selector. Then you will see all your selected samples, normally with the name SpotPicking(X). Now you can click on "Import Scan" and you will be forwarded to the Mass Spectra Data site. Here you find two sections: "Mass Spectra Browser" and "Mass Spectra Importer". In the second field (Mass Spectra Importer) you choose "Maldi" for the mass spectra type (it doesn't work correctly for Esi-files at the moment) and select "many" for the number of files. Now you can browse and insert your file into the file-window. After you click on "Import", the system starts importing the file. The file has to be a .tgz-, .tar.gz-, .tar- or .zip-file otherwise there will be an error. For the format of the file see the section below. The system automatically connects every maldi file with the corresponding sample. After you imported the file, you can select a sample from the field (Mass Spectra Browser) above and you will see the mass spectrum for this sample.

If you want to make a search with mascot or emowse against a database, you have to return to the Experiment Editor by clicking on the link on the left site of the web-page. There you click on Experiment Selection and choose the link Mass Spectra Data. From there you select MS for scan type and choose one or more scans for the search. To get to the search form you have to click on the "Peptide Mass Fingerprint" link.

Formats

Format of the Config File

The config file has to be in a special format. Only then the connection between the files and the samples can be made correctly. First of all, it is important that you save the config file, after you selected the spots on the gel, with the name geometry.config. Here is an example for a config file with 14 spots in it:

Comment_1	Pos_on_Scout	AutoX_Method	Spectrum_Directory	Spectrum_Filename	Probe_Geometry	Chip_on_Scout
************	************	************	************	************	************	************
standard	A:1	calibrate_sbd		Standard_A1		1
probe	A:1	measure_sbd		I_A_01		0
probe	B:1	measure_sbd		I_B_01		0
standard	C:1	calibrate_sbd		Standard_C1		1
probe	C:1	measure_sbd		I_C_01		0
probe	D:1	measure_sbd		I_D_01		0
standard	E:1	calibrate_sbd		Standard_E1		1
probe	E:1	measure_sbd		I_E_01		0
probe	F:1	measure_sbd		I_F_01		0
standard	G:1	calibrate_sbd		Standard_G1		1
probe	G:1	measure_sbd		I_G_01		0
probe	H:1	measure_sbd		I_H_01		0
probe	A:2	measure_sbd		I_A_02		0
probe	B:2	measure_sbd		I_B_02		0
probe	C:2	measure_sbd		I_C_02		0
probe	D:2	measure_sbd		I_D_02		0
probe	E:2	measure_sbd		I_E_02		0
probe	F:2	measure_sbd		I_F_02		0

This is a standart config file. It is automatically generated by ProDB. It is important that there is only the name of the Spectrum_Directory in the config file (forth tab) and not the whole path. Furthermore each row containing a spot has to start with the word probe and every row containing a calibration has to start with something else (default is standart). Normally, if you take the autogenerated file you don't have to change anything. Try to change as little as possible in the file.

Format of the compressed File

First create a directory (take any name you want) and copy all directorys (with the scan files in it) in the new directory. The geometry.config file has to be copied there, too. For example you create a directory with the name massensp and you have the directories from above with the maldi files in it. Now you copy the scan directories (I_A_01, I_B_01, ... , I_E_02, I_F_02) and the geometry.config in the directory massensp.

massensp: I_A_01
          I_B_01
          I_C_01
          I_D_01
          I_E_01
          I_F_01
          I_G_01
          I_H_01
          I_A_02
          I_B_02
          I_C_02
          I_D_02
          I_E_02
          I_F_02
          geometry.config

Now you compress the directory massensp (with tar, zip, ...) so that you get massensp.tgz, massensp.tar.gz, massensp.tar or massensp.zip. If you are working with linux or unix you can use one of the following commands (you have to be in the same directory as massensp):

.tgz and .tar.gz: tar -cvzf name.tgz directory -> tar -cvzf massensp.tgz massensp/ or tar -cvzf massensp.tar.gz massensp/
.tar:             tar -cvf name.tar directory -> tar -cvf massensp.tar massensp/
.zip:             zip -r name.zip directory -> zip -r massensp.zip massensp/

What did I do

For the this function I wrote a new modul: ImportMultiFiles. You can find it in prodb/share/www/cgi-bin/. This modul has two functions import_multifiles_maldi and import_multifiles_esi. But the second function doesn't work correctly at the moment.

The function import_multifiles_maldi is called by msscan.cgi(same directory). I modified the function parseMS (in msscan.cgi), so that it can differ between importing one and many files.

sub parseMS {
	my ($q, $tmpl, $session, $master, $probes) = @_;
	my $scans;

	#parses one scan
	if ($q->param('number')eq 'one') {
            ........normal import.........
        }

	#parses many scans (from a .tgz, .tar.gz,.tar and .zip File)
	elsif ($q->param('number')eq 'many') {
            .......imports many files.......
            ......calls the import function from ImportMultiFiles ......
             my $result=import_multifiles_maldi($master, $directory, $probes, $name);
        }

At first the function import_multifiles_maldi decompresses the uploaded file and saves it in /vol/tmp. Then it takes the geometry.config file and reads it. It saves the directories in a hash (%positionScan) with the number of the corresponding sample as key. Now it takes one scan after the other, loads the file up and parses it with the function parseMaldiFileXML or parseMaldiFile, depending on the file format of the scan, from MSTools.pm. It than gets all information for the scan from the parser and creates a new Scanobject and for every peak a new Peakobject. At last the import_multifiles_maldi removes the tempory file.

Author: Nicole de la Chaux