Geena 2: Spectra Analysis

Geena 2
Build August 31, 2021. This system is under active development,
please forgive us for possible errors and
send us your comments, criticisms and congratulations,
if any. the authors

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 Contextual help icon for a contextual help.

Job information

Reference name for your analysis, you may change it. It is included within the name of result files. Job name:

Provide a valid email address, results will be sent by email Your email:

Your country, for information and statistics only Country:

Input data

Specify the origin of your data, either a properly formatted file (see information on file formats) or the database. Data origin: Upload file Spectra data store

You must select a properly formatted file from your computer. This file must be uploaded to the server but it is removed as soon as it is used. Data file:
(see information on data file format
and an example file)

You must specify which samples should be included in the analysis: if you select All, then all samples in the database will be taken into account, if you select Some, only samples selected in the following field will be analysed. Samples from spectra data store: All Some

You must select the samples (each including one or more spectra, from the database. This is a multiple secelct field: use CTRL key + left mouse button to select single values in the list or SHIFT key + left mouse button to select a range of consecutive values in the list. Which samples
(only if Some is checked):

Filter and isotopic peaks join

You must define the m/z range for the analysis: all peaks not included in this range won't be taken into account Analysis range: From m/z to m/z

A standard signal may be added to sera before spectrometry for normalization aims. Select this option if your experiment included this component and you want to normalize data. You must also specify the corresponding m/z value. Normalization peak: No Yes, at m/z

Minimum abundance value at the lowest m/z value of the range (interpolation is applied for intermediate m/z values). Peaks having lower abundance values won't be included in the analysis. Put this value to 0 if you don't want to filter peaks. First abundance threshold: at lowest m/z (absolute value)

Minimum abundance value at the highest m/z value of the range (interpolation is applied for intermediate m/z values). Peaks having lower abundance values won't be included in the analysis. Put this value to 0 if you don't want to filter peaks. Last abundance threshold: at highest m/z (absolute value)

Minimum abundance value at intermediate m/z values (interpolation is applied for intermediate m/z values). Peaks having lower abundance values won't be included in the analysis. Intermediate thresholds: at m/z

at m/z

at m/z

at m/z

Maximum number of isotopic replicas:

Maximum allowed delta between isotopic peaks. Isotopic peaks are selected when their m/z value differ by no more than 1+delta Da and by no less than 1-delta Da. 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 allowed delta between corresponding peaks in average spectra. Peaks are aligned and related m/z alignment values are computed when their m/z value differ by no more than ± delta Da. Maximum delta for aligning average spectra: Da

Minimum number of signals that is needed to include peaks of average spectra in the final alignment. Put 1 to include all peaks. Minimum number of signals in average spectra:

Show standard deviation values for averaging and alignment. 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

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