title: Current challenges in software solutions for mass spectrometry-based quantitative proteomics.
abstract: Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.
authors: Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, The Netherlands.
authors: Salvatore
authors: S
authors: Cappadona
authors: Peter R
authors: PR
authors: Baker
authors: Pedro R
authors: PR
authors: Cutillas
authors: Albert J R
authors: AJ
authors: Heck
authors: Bas
authors: B
authors: van Breukelen
mesh_terms: D003627:Data Interpretation, Statistical; D057225:Data Mining; D013058:Mass Spectrometry; D010446:Peptide Fragments / Q000737:chemistry; D010449:Peptide Mapping; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics; D059629:Signal-To-Noise Ratio; D012984:Software
chemical_list: D010446:Peptide Fragments; D020543:Proteome