However, deriving meaning from peak lists spanning dozens or hundreds of samples is no simple task.
The program MS-Screener (Version 1.0.1) was applied to evaluate large datasets of peak lists.
The final peak lists were saved in plain text format and Mascot Generic Format (MGF).
In addition, the peak lists were evaluated by the program MS-Screener.
To create peak lists of the spectra, the BioTyper software was used as described above.
Subsequently, ESI-PMF peak lists were submitted to our Mascot search engine or Protein Prospector.
Recalibration was performed using a Perl script which adjusted precursor masses in the peak lists.
Peaks exceeding a threshold signal-to-noise ratio of 3 were exported to peak lists.
Peak lists were generated using ProteinLynx, part of MassLynx v 4.0.
Peak lists for database searching were created using Mascot Distiller (Version 1; MatrixScience, London, UK).
Assessing the rate of false positives in the peak lists is a challenging task.
