Geena 2
Build March 10, 2015.
This system is under active development,
please forgive us for possible errors and
send us your comments, criticisms and congratulations,
if any.

Welcome to Geena 2, a tool for MS spectra filtering, averaging and aligning.

(SSI - Standard Search Interface)

This is the Standard Search Interface (SSI). You may be interested in using the Quick Search Interface (QSI) that simplifies the use of Geena 2 by reducing the number of parameters to a very minimum or the Bright Search Interface (BSI) that allows you to tune averaging and alignment parameters, while leaving all remaining to their default values.

Using Geena 2 should be straightforward. Input and output data use a simple format. Nevertheless, should you have any problem, see the help or the information on data formats pages.

NB! This version includes a new feature. When a normalization peak is provided, it is used to calibrate m/z values.
In practice, for each spectrum all m/z values are recomputed by taking into account the difference between the teorethical and the actual m/z values of the normalization peak.

NB! Move your mouse over the icon for a contextual help.

 Job information
 
Job name:
 
Your email:
Country:
 
 Input data
 
Data origin: Upload file     Spectra data store
Data file:
(see information on data file format
and an example file)
 
Samples from spectra data store: All     Some
Which samples
(only if Some is checked):
 Filter and isotopic peaks join
 
Analysis range: From m/z to m/z
Normalization peak: No    Yes, at m/z
First abundance threshold: at lowest m/z (absolute value)
Last abundance threshold: at highest m/z (absolute value)
Intermediate thresholds: at m/z
at m/z
at m/z
at m/z
Maximum number of isotopic replicas:
Maximum delta between isotopic peaks: Da
 
 Computation and alignment of average spectra
 
Maximum delta for aligning replicates: Da
Minimum number of signals in replicates:
 
Maximum delta for aligning average spectra: Da
Minimum number of signals in average spectra:
 
Show standard deviation: No    Yes
 
 


For information, get in touch with:
Paolo Romano,
IRCCS Ospedale Policlinico San Martino,
Genoa, Italy
Click here to see my email address

If you use Geena, please cite the following paper:
Romano P et al.
Geena 2, improved automated analysis of MALDI/TOF mass spectra.
BMC Bioinformatics 2016, 17(Suppl 4):61
PMID: 26961516; DOI: 10.1186/s12859-016-0911-2