agalactiae or LPS in vitro. Further, after induction with mouse anti-tilapia IgM monoclonal antibody in vitro, OnSHP1 was significantly up-regulated in leukocytes. When spleen leukocytes treated with PTP Inhibitor II in vitro, the phosphorylation level of OnSHP1 at the phosphorylation sites (Y535 and Y557) and the cytoplasmic free Ca2+ concentration were up-regulated significantly. Overall, the findings of this study indicate that SHP1 gets involved in host defense against bacterial infection and BCR signaling pathway in Nile tilapia. Bursicon (burs) is a neuropeptide hormone consisting of two cystine-knot proteins (burs α and burs β), and burs α-β is responsible for cuticle tanning in insects. Further studies show that burs homodimers induce prophylactic immunity. Here, we investigated the hypothesis that burs homodimers act in regulating immunity in the red swamp crayfish Procambarus clarkii. We found that burs α and burs β are expressed in neural system of crayfish. Treating crayfish with recombinant burs-homodimer proteins led to up-regulation of several anti-microbial peptide (AMP) genes, and RNAi-mediated knockdown of burs led to decreased expression of AMP genes. The burs proteins also facilitated bacterial clearance and decreased crayfish mortality upon bacterial infection. Furthermore, burs proteins activated the transcriptional factor Relish, and knockdown of Relish abolished the influence of recombinant burs homodimers on AMP induction. We infer the burs homodimers induce expression of AMP genes via Relish in crayfish and this study extends this immune signaling pathway from insects to crustaceans. Micropterus Salmoides rhabdovirus (MSRV), as a common aquatic animal virus, can cause lethal and epidemic diseases in the cultivation of largemouth bass. In this study, we reported a kind of immersion single-walled carbon nanotubes-loaded subunit vaccine which composited by glycoprotein (G) of MSRV, and evaluated its protective effect on largemouth bass. The results showed that a stronger immune response including serum antibody levels, enzyme activities (superoxide dismutase, acid phosphatase, alkaline phosphatase and total antioxidant capacity), complement C3 content and immune-related genes (IgM, TGF-β, IL-1β, IL-8, TNF-α, CD4) expression can be induced obviously with single-walled carbon nanotubes-glycoprotein (SWCNTs-G) groups compared with G groups when largemouth bass were vaccinated. After bath immunization with G or SWCNTs-G for 28 days, fish were challenged with a lethal dose of MSRV. The survival rates for control group (PBS), SWCNTs group (40 mg L-1), pure G protein groups (40 mg L-1) and three SWCNTs-G groups (5 mg L-1, 10 mg L-1 and 40 mg L-1) were 0%, 0%, 39.5%, 36.7%, 43.6%and 70.1%, respectively. Importantly, with the assistance of SWCNTs, the immune protective rate of the SWCNTs-G group (40 mg L-1) increased by approximately 30.6%. This study suggested that SWCNTs-G is a promising immersion subunit vaccine candidate against the death caused by MSRV. Animal management practices may influence the animal’s susceptibility to stress, with detrimental effects on the ultimate meat quality. In this field, proteomics is a promising tool that reveals the biological pathways underpinning the effect of animal’s pre-slaughter stress (PSS) on the ultimate meat quality. The objective of this work was to study the effect of a pre-slaughter procedure that may promote stress, such as mixing unfamiliar animals during the transport and lairage period, on the post-mortem muscle proteome of young bulls reared under two different farm management systems (Intensive or Extensive). Comparative proteomics and biochemical analysis reveal the effect of PSS on biochemical pathways involved in the meat colour development, muscle redox status, energy metabolism and autophagy. This work highlights the potential of some muscle proteins such as Beclin-1 (autophagy marker), CKM (biomarker of energy transduction) and proteins of the energy metabolism (ALDOA, PYGM, PGM1, PKM, GPI) as potential biomarkers to discriminate beef samples according to the incidence of PSS. SIGNIFICANCE Meat scientists are interested in the study of individual animal-based measurements that allow the detection of stress situations which could have negative effects on meat quality. In this context, the mechanisms underlying the adverse effects of pre-slaughter stress on the post-mortem muscle metabolism need to be elucidated in order to understand how animal stress may influence the conversion of muscle into meat. In this work, the study of proteome changes in the post-mortem muscle has allowed the identification of significant biomarkers of these processes that could be used as tools for detecting inappropriate strategies that may induce increased animal stress and, in consequence, may compromise the ultimate beef quality. Quantitative crosslinking mass spectrometry (QCLMS) reveals structural details of protein conformations in solution. QCLMS can benefit from data-independent acquisition (DIA), which maximises accuracy, reproducibility and throughput of the approach. This DIA-QCLMS protocol comprises of three main sections sample preparation, spectral library generation and quantitation. The DIA-QCLMS workflow supports isotope-labelling as well as label-free quantitation strategies, uses xiSEARCH for crosslink identification, and xiDIA-Library to create a spectral library for a peptide-centric quantitative approach. We integrated Spectronaut, a leading quantitation software, to analyse DIA data. Spectronaut supports DIA-QCLMS data to quantify crosslinks. It can be used to reveal the structural dynamics of proteins and protein complexes, even against a complex background. In combination with photoactivatable crosslinkers (photo-DIA-QCLMS), the workflow can increase data density and better capture protein dynamics due to short reaction times. Additionally, this can reveal conformational changes caused by environmental influences that would otherwise affect crosslinking itself, such as changing pH conditions. SIGNIFICANCE This protocol is an detailed step-by-step description on how to implement our previously published DIA-QCLMS workflow (Müller et al. Mol Cell Proteomics. GW 501516 datasheet 2019 Apr;18(4)786-795). It includes sample preparation for QCLMS, Optimization of DIA strategies, implementation of the Spectronaut software and required python scripts and guideline on how to analyse quantitative crosslinking data. The DIA-QCLMS workflow widen the scope for a range of new crosslinking applications and this step-by-step protocol enhances the accessibility to a broad scientific user base. V.