Multi-Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins.

Lysosomes, the main degradative organelles of mammalian cells, play a key role in the regulation of metabolism. It is becoming more and more apparent that they are highly active, diverse, and involved in a large variety of processes. The essential role of lysosomes is exemplified by the detrimental consequences of their malfunction, which can result in lysosomal storage disorders, neurodegenerative diseases, and cancer.

Generation of Antibodies Targeting Cleavable Cross-Linkers.

Chemical cross-linking has become a powerful tool for the analysis of protein structures and interactions by mass spectrometry. A particular strength of this approach is the ability to investigate native states in vivo, investigating intact organelles, cells, or tissues. For such applications, the cleavable cross-linkers disuccinimidyl sulfoxide (DSSO) and disuccinimidyl dibutyric urea (DSBU) are gaining increasing popularity, as they allow for the analysis of complex mixtures.

Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics.

Lysosomes are the main degradative organelles of cells and involved in a variety of processes including the recycling of macromolecules, storage of compounds, and metabolic signaling. Despite an increasing interest in the proteomic analysis of lysosomes, no systematic study of sample preparation protocols for lysosome enriched fractions has been performed to date. In the current study, we used samples enriched for lysosomes by paramagnetic nanoparticles and systematically evaluated experimental parameters for the analysis of the lysosomal proteome.

A Comprehensive High-Resolution Targeted Workflow for the Deep Profiling of Sphingolipids.

Sphingolipids make up a highly diverse group of biomolecules that not only are membrane components but also are involved in various cellular functions such as signaling and protein sorting. To obtain a quantitative view of the sphingolipidome, sensitive, accurate, and comprehensive methods are needed. Here, we present a targeted reversed-phase liquid chromatography-high-resolution mass spectrometry-based workflow that significantly increases the accuracy of measured sphingolipids by resolving nearly isobaric and isobaric species; this is accomplished by a use of (i) an optimized extraction procedure, (ii) a segmented gradient, and (iii) parallel reaction monitoring of a sphingolipid specific fragmentation pattern.

Transcriptional coexpression network reveals the involvement of varying stem cell features with different dysregulations in different gastric cancer subtypes.

Despite the advancements in the cancer therapeutics, gastric cancer ranks as the second most common cancers with high global mortality rate. Integrative functional genomic investigation is a powerful approach to understand the major dysregulations and to identify the potential targets toward the development of targeted therapeutics for various cancers. Intestinal and diffuse type gastric tumors remain the major subtypes and the molecular determinants and drivers of these distinct subtypes remain unidentified.