Premium
Selymatra: A web application for protein‐profiling analysis of mass spectra
Author(s) -
Nardone Davide,
Ciaramella Angelo,
Cerreta Mariangela,
Pulcrano Salvatore,
Bellenchi Gian C.,
Leone Linda,
Manco Giuseppe,
Febbraio Ferdinando
Publication year - 2022
Publication title -
biotechnology and applied biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.468
H-Index - 70
eISSN - 1470-8744
pISSN - 0885-4513
DOI - 10.1002/bab.2249
Subject(s) - mass spectrometry , mass spectrum , profiling (computer programming) , matrix assisted laser desorption/ionization , computational biology , chemistry , computer science , time of flight mass spectrometry , ionization , chromatography , analytical chemistry (journal) , biological system , data mining , bioinformatics , desorption , biology , ion , organic chemistry , adsorption , operating system
Surface enhanced laser desorption/ionization‐time of flight (SELDI‐TOF) mass spectrometry is a variant of the matrix‐assisted laser desorption/ionization‐time of flight (MALDI‐TOF) mass spectrometry. It is used in many cases especially for the analysis of protein profiling and for preliminary screening of biomarkers in complex samples. Unfortunately, these analyses are time consuming and protein identification is generally strictly limited. SELDI‐TOF analysis of mass spectra (SELYMATRA) is a web application (WA) developed to reduce these limitations by (i) automating the identification processes and (ii) introducing the possibility to predict proteins in complex mixtures from cells and tissues. The WA architectural pattern is the model‐view‐controller, commonly used in software development. The WA compares the mass value between two mass spectra (sample vs. control) to extract differences, and, according to the set parameters, it queries a local database to predict most likely proteins based on their masses and different expression amplification. The WA was validated in a cellular model overexpressing a tagged NURR1 receptor, being able to recognize the tagged protein in the profiling of transformed cells. A help page, including a description of parameters for WA use, is available on the website.