For questions: paulo at



YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra).  YADA also enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.

YADA is part of the PatternLab for proteomics project. If using YADA please site:

Carvalho PC, Xu T, Han X, Cociorva D, Barbosa VC, Yates JR, III. YADA: A tool for taking the most out of high resolution mass spectra. Bioinformatics, 25: 2734-2736, 2009.

[Click here to go to the download page]


Main Screen

YADA's main interface. Everything can be accomplished through here. All other tabs are extras! Just select what you want to do and how. One should choose from the pre-existing default configurations for Bittum up, Middle Down, Top Down, or pick the Geek Mode to unlock the control panel enabling every aspect of the software to be customized.

Control Panel

Every aspect of YADA can be controled here, even though the default setings should be appropriate for the great majority of the jobs.

Peak filtering parameters
MS1 Min Intensity: Any ion below this threshold will be eliminated.
MS2 Min Intensity: Any ion below this threshold will be eliminated.
FT-MS Filtering PPM: if peaks are monotonically increasing within an isotope, and are within such ppm, the least intense will be eliminated.
The Gaussian filter only kick in realy noisy spectra and fits two log-normal distributions in an intensity histogram; one for noise peaks and one for "real peaks". The noise threshold can then be automaticaly determined by that of the optimal Bayesian classifier.

Envelope detection parameters
PPM: This is not the PPM of your instrument, It is mainly used to to integrate peaks near isotopic signals.
Str MS1: Stringency for detecting MS1 envelopes according to normalized dotproduct of integrated and theoretical signal.
Str MS2: Stringency for detecting MS2 envelopes according to normalized dotproduct of integrated and theoretical signal. Usualy there is less noise in the MS2, so a lower value can be used.
Max Charge: The maximum charge state to consider.
Cluster Decon: A clustering threshold for coalising deisotoped and decharged peaks.
Conv: A clustering threshold for coalising convoluted peaks.

MS1 Correction Parameters
Tolerance for multiple envelopes: This defines the bounds for classifying ions as precursor ions.. The center of the window is defined by the fragmented precursor ion peak.
Stringency MS1 Correction: The envelopes will only be considered for MS2 monoisotopic assignment or inclusion of multiple ions if above this stringency.

Output parameters
ITMS and FTMS: If checked, both spectra will be included in the output file. ITMS spectra are not deisotoped and decharged.
Min no. peaks / spectrum: If there are less deconvoluted peaks than the number specified, the spectrum is not outputed.
Max no. peaks / spectrum: If there are more envelopes than the number specified, only the highes scoring ones will be used to detect the monoisotopic peaks and be outputed.



The MSChopper splits big files to enable a more eficient memory management. This should be used especialy on computers that have a small RAM (<2GB).

Single Spectrum Deconvolution

This is a single spectrum deisotoping and decharging toy. It can be used to get a feeling of YADA's parameters. Copy a spectrum from Excalibur, paste in in the indicated area and press the Go! button.


Envelope Generator

YADA uses a regressor to quickly obtain theoretical isotopic envelopes, and therefore aproximations; but very good ones. Use this tool to see how YADA is working unde the hood and geretating isotopic envelopes for a given mass.

Spectrum Filter

Use this tool to get a feeling of how YADA's automatic peak filtering algorithm does its job. Use the interactive spectrum viewer to zoom in the envelopes.