The St. Jude Center for Mass Spectrometry and Proteomics provides state-of-the-art mass spectrometry (MS)-based protein analysis services to researchers at St. Jude Children’s Research Hospital. Since its inception in 2001, the facility has supported more than 110 principal investigators from multiple departments. The services include protein intact mass characterization, small- and large-scale protein identification (e.g., affinity purification-mass spectrometry), post-translational modification analysis (e.g., phosphorylation, ubiquitination, methylation and acetylation), and comprehensive quantitative profiling of proteome and phosphoproteome directly from cells, tissues and even clinical specimens. Customized proteomics projects are also arranged upon consultation.
The major mass spectrometry platform is based on the high-resolution liquid chromatography (LC)-tandem MS. Facility staff members are highly experienced in all major quantitative MS approaches, such as label-free quantification (LFQ), stable isotope labeling with amino acids in cell culture (SILAC), and tandem mass tag (TMT). Using the latest method of multiplex TMT-LC/LC-MS/MS, the facility routinely profiles more than 10,000 proteins and 30,000 phosphorylation sites from up to 11 complex protein samples in a single experiment, with protein detection sensitivity below the nanogram level.
The proteomics facility is well equipped with cutting-edge instruments, hosting a total of seven modern mass spectrometers including one LC-TOF, two LTQ Orbitrap Elite, three Q Exactive HF, and one Orbitrap Fusion. All MS instruments are coupled with high-end LC systems, such as the nanoAcquity UPLC, EasynLC1000 and UltiMate 3000 nanoscale HPLC.
Proteomic data analysis is conducted with high-performance computing clusters, and an in-house developed software suite termed JUMP. The JUMP integrates numerous algorithms for sensitive protein identification, accurate quantification, and statistical inference of -omics datasets. The facility also has access to a large computer cluster maintained by St. Jude High Performance Computing Facility to further speed data processing.