Sequence database search engines are bioinformatics algorithms that identify peptides from
tandem mass spectra using a reference protein sequence database. Two decades of …

In a global effort for scientific transparency, it has become feasible and good practice to
share experimental data supporting novel findings. Consequently, the amount of publicly …

Motivation BioContainers (biocontainers. pro) is an open-source and community-driven
framework which provides platform independent executable environments for bioinformatics …

Figure 1 PeptideShaker data-analysis cycle.(a) Data generated in-house or publicly
available from PRIDE can be used as input.(b) The sequence database is selected in …

The identification of proteins by mass spectrometry is a standard technique in the field of
proteomics, relying on search engines to perform the identifications of the acquired spectra …

Machine learning is a subdiscipline within artificial intelligence that focuses on algorithms
that allow computers to learn solving a (complex) problem from existing data. This ability can …

The field of computational proteomics is approaching the big data age, driven both by a
continuous growth in the number of samples analyzed per experiment as well as by the …

Mass-spectrometry-based proteomics has become the standard approach for identifying and
quantifying proteins. A vital step consists of analyzing experimentally generated mass …

In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three
different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode …

ABSTRACT The Proteomics Identifications database (PRIDE, http://www. ebi. ac. uk/pride) at
the European Bioinformatics Institute has become one of the main repositories of mass …