In Brief This study presents SOMAscan assay proteomics data from human SF. SF was obtained from three groups, including knee joints with signs of mild degeneration. This group may represent early-stage knee OA, an underrepresented group in OA biomarker studies. Apart from conventional differential abundant analysis, we conducted network analysis of protein-protein dependencies using GGMs. Notably, network complexity was found to be lost in the graph representing early-stage OA, as compared to controls, suggesting a disruption in the regular protein interplay ..read more

In Brief For highly sensitive immune cell profiling in the tumor microenvironment, six immune cell subtype-specific spectral libraries covering 7815 proteins were established as a community resource. The library-assisted single-shot data-independent acquisition strategy offers deep coverage and identification of low-abundance immunobiologic process-related proteins in microscale tissue (1 μg), providing comprehensive coverage of surface markers and key signaling pathways. Application in colorectal cancer mouse models revealed an immunosuppressive status in mesenteric lymph nodes, confirmi ..read more

In Brief Cellular proteins have different ages - whereas some have been recently synthesized, others have existed in the cell for days. How a protein’s age influences its function is difficult to study. We developed a method named “proteome birthdating” that partitions proteins into discernible age groups. We examined the age-selectivity of ubiquitination and show that proteasomal targets consist mostly of young proteins. Proteome birthdating is useful for analyzing proteome turnover dynamics and investigating the functional consequences of protein age ..read more

In Brief The first proteome profiling of cerebrospinal fluid (CSF) from reversible cerebral vasoconstriction syndrome (RCVS) patients sheds light on the mysterious pathophysiology of the disease. A RCVS-CSF spectral library was constructed to facilitate deep personalized CSF profiling by data-independent acquisition. The findings reveal the first RCVS proteome and suggest a potential pathogenetic mechanism involving dysfunction of blood-brain barrier and neurovascular unit. Moreover, the study nominates biomarker candidates with mechanistic plausibility for RCVS, offering diagnostic and therap ..read more

In Brief Monoclonal antibody affinity purification and mass spectrometry were used to identify galectin-3-binding protein (LG3BP) as a binding partner of Sulf-2 in HNSCC cell lines conditioned media. Sulf-2 chondroitin sulfate side chain influences the binding to LG3BP, and we confirmed its importance by generating a mutant Sulf-2 protein. We have shown that the LG3BP non-competitively inhibits Sulf-2 enzymatic activity , and consequently addition of LG3BP to a spheroid cell culture inhibited the invasion of the HNSCC cells into Matrigel ..read more

In Brief Using quantitative proteomics, we analyzed multiple layers of epigenetic changes in WT and histone chaperone-deficient Arabidopsis plants, even after genotoxic stress. We discriminated many histone variants and reconstructed the combinatorial pattern of histone PTMs. Rapid changes in the PTM profiles and slower changes in the histone variant ratios and histone variant distribution give a new insight in the plants’ ability to compensate the deficiencies in chromatin structure ..read more

In Brief The biosynthetic regulation and initiation of protein O-linked mannose (O-Man) glycosylations has been dissected in genetically engineered human cell lines by a sensitive method for differential O-glycoproteomics. The results expand current knowledge on C- and O-Man glycoproteins and reveal how three unique (POMT1/POMT2, TMTC1-4, and TMEM260) biosynthetic pathways orchestrate domain-specific O-Man biosynthesis ..read more

In Brief The E3 ligase Cereblon (CRBN) is commonly used for protein degraders but carries with it the risk of degradation of additional proteins (CRBN neosubstrates) a molecular glue mechanism of action. Here, we curated a set of 25 proteins of interest associated with CRBN-related protein homeostasis and/or embryo/fetal development and developed a targeted mass spectrometry assay for monitoring them. We applied this to rabbit embryos that were exposed maternally to immunomodulatory drugs and report ..read more

In Brief T cells undergo a significant rearrangement of their proteome and phosphoproteome during activation while accumulating necessary cellular components for rapid cell division. Here, we describe the phosphorylation integrated thermal shift assay, which combines the measurement of protein and phosphorylation site abundance with the measurement of protein and phosphorylation site thermal stability. This assay may help determine which proteome and phosphoproteome changes are functionally relevant in T cell activation by identifying proteins/phosphorylation sites with altered biophysical sta ..read more

In Brief SARS-CoV-2's rapid global spread exposed PCR testing limitations. We addressed this through mass spectrometry, developing a proteomics workflow targeting nucleocapsid protein peptides. By developing a selective MRM3 strategy, we achieved higher sensitivity compared to conventional methods. Our first approach detected viral peptides in nasopharyngeal samples with a cycle threshold (Ct) value down to 35 with sensitivity and specificity of 94.2% and 100.0% specificity without immunopurification. Subsequent mass spectrometry iterations, capable of processing 400+ samples daily, demonstrat ..read more