FragmentationAnalyzer currently supports three input formats:
In addition any files that can be converted to the supported text file format can be used. (See the importing data section for details on how to import data.)
Opening Data Sets
After starting the tool the data selection dialog will be shown. (The
dialog can also be opened from the File menu by selection 'Open'.) You
can either import new data sets from one of the three supported formats,
or use one of the already imported data sets. For this tutorial we will
use the example data set provided with the tool. See the
Import Data section for details on how to
import data. For now, select 'example data set' in the list of
available data sets and click on 'Open Data Set'.
The tool will now open the data set. Note that depending on the
size of the data set this can take some time. When finished a dialog
verifying that the data has been opened will be shown and the drop
down menus in the left part of the screen will be updated with the
data from the opened data set.
Selecting Search Parameters
To perform a search select the properties of the identifications
you are searching for in the lists. For example: instrument as ESI-QUAD-TOF,
N-term as NH2, C-term as COOH and charge as 2. The numbers behind the
terms are the total number of occurrences of that particular term in
the data set. Note that these numbers are for the whole data set and
not for the subset of the data set that you are currently selecting.
So even though all your selections have a high occurrence number, this
does not automatically result in identifications matching all your
selections. Leave the modification selection empty for now.
General Search
There are two search options available: general search or modification
search. We will first look at general search which basically returns
all identifications matching all the selected parameters. Click on
the 'Search' button in the lower left corner to start the search.
(Again note that depending on the size of the data set the process
might take some time completing.)
Search Results
When the search is completed a dialog presenting the main findings
will be shown, number of matches etc, and the results will be
inserted into the 'Search Results' table at the upper right part
of the screen. The results are sorted on the number of occurrences
of each identification, such that the most frequent are at the top
of the list.
Individual Spectra
Select a subset of the identifications by clicking in the rightmost
column of the table. Then select an analysis type in the 'Select Analysis Type'
drop down menu. First try 'List Individual Identifications'. Then
click the 'Analyze / Plot' button to the right of the drop down menu.
The list of individual spectra is then shown in the 'Individual Spectra'
table in the middle of the right part of the screen.
Analyze/Plot
Select a couple of the items in this table and again select an
analysis type in the 'Select Analysis Type' drop down menu for
the 'Individual Spectra' table, for example 'View Spectra'. Then
click the 'Analyze / Plot' button for the 'Individual Spectra' table.
The 'Search Results' and 'Individual Spectra' section will then
close and the 'Plot / Analyses' section will be expanded showing
the just created plot(s). The closed sections can easily be opened
again by clicking on the section header. Clicking ones more will
again close the section. Make sure that the 'Plot / Analyses' section
is visible before continuing.
Resizing Plots
In the plots section each plot is located in its own separate
frame. The frames can be resized and maximized individually. To
maximize a plot click on the plots maximize button in the upper
right corner (or double click on the title bar).
Plot Types
Currently nine different plot types are supported:
ms_lims
For ms-lims one
logs on to the ms_lims database via a dialog
in the tool using ones normal login details. When connected all the
required details about the identifications will be downloaded, while
some details, e.g., the fragment ion information, is not downloaded
but extracted when needed. The database connection will therefore
be required during the use of the tool. Please note that depending
on the size of the database the process of importing data from
ms_lims might take a while. However, the progress of the import
will be monitored closely and presented to the user.
Mascot Dat Files
When importing Mascot dat files
one simply selects the set of dat
files to import and select the Mascot confidence level to use
for the identifications. Only identifications above the selected
confidence will be imported.
OMSSA OMX Files
Importing OMSSA
omx files is done in the same way as for Mascot dat
files (except for the setting of the Mascot confidence level of course).
However, the instrument name is not included in the omx file and has
to be provided manually by the user for each imported file. Also note
that the omx file includes very little details about the amino acid
modifications, only a number <1>, <2> etc. The OMMSA
installation folder (containing the mods.xml and usermods.xml files)
therefore also has to be provided.
When a data set is imported into FragmentationAnalyzer it is divided into three parts:
Either spectrum file name or spectrum id has to be provided, but the
other can be set to "null".
fragmentIons.txt
fragmentIons.txt is also a tab separated consisting of one row per
fragment ion with the following elements:
The following fragment ion type names are recommended and will result in the best integration with the tool:
Spectra Folder
For non-ms_lims data sets the spectra are stored as
pkl files in a folder
called 'spectra'. One file per spectrum. The first line in each file contains
the precursor m/z, intensity and charge. Next follows one line per peak
in the spectrum with the m/z and intensity values.
For more details see the example data set or the source code.