High-Sensitivity Proteome-Scale Searches for Crosslinked Peptides Using CRIMP 2.0.

Crosslinking mass spectrometry (XL-MS) is a valuable technique for generating point-to-point distance measurements in protein space. However, cell-based XL-MS experiments require efficient software that can detect crosslinked peptides with sensitivity and controlled error rates. Many algorithms implement a filtering strategy designed to reduce the size of the database prior to mounting a search for crosslinks, but concern has been expressed over the possibility of reduced sensitivity using these strategies. We present a new scoring method that uses a rapid presearch method and a concept inspired by computer vision algorithms to resolve crosslinks from other conflicting reaction products. Searches of several curated crosslink datasets demonstrate high crosslink detection rates, and even the most complex proteome-level searches (using cleavable or noncleavable crosslinkers) can be completed efficiently on a conventional desktop computer. The detection of protein-protein interactions is increased twofold through the inclusion of compositional terms in the scoring equation. The combined functionality is made available as CRIMP 2.0 in the Mass Spec Studio.

Investigating the Use of Dry Matter Intake and Energy Balance Prepartum as Predictors of Digestive Disorders Postpartum.

One objective was to evaluate the association of dry matter intake as a percentage of body weight (DMI%BW) and energy balance (EB) prepartum and postpartum, and energy-corrected milk (ECM) postpatum with digestive disorders postpartum. For this, ANOVA was used, and DMI%BW, EB, and ECM were the outcome variables, and left displaced abomasum (LDA), indigestion, and other digestive disorders (ODDZ) were the explanatory variables. The main objective was to evaluate prepartum DMI%BW and EB as predictors of digestive disorders. For this, logistic regression was used, and LDA, indigestion, and ODDZ were the outcome variables and DMI%BW and EB were the explanatory variables. Data from 689 cows from 11 experiments were compiled. Left displaced abomasum was not associated with prepartum DMI%BW or EB. Postpartum data were normalized to the day of the event (day 0). Cows that developed LDA had lesser postpartum DMI%BW on days -24, -23, -12, -7 to 0 and from days 1 to 8, 10 to 12, and 14 and 16, lesser postpartum EB from days -7 to -5, -3 to 0, and 12, and lesser postpartum energy-corrected milk on days -19, -2, -1, 0, 7, 9, 10, 15, and 17 relative to diagnosis than cows without LDA. Cows that developed indigestion had lesser prepartum DMI%BW and EB than cows without indigestion, and lesser postpartum DMI%BW on days -24, -1, 0, 1, and 2, and greater DMI%BW on day 26, lesser ECM on days -24, -2, -1, 0, 1, and 2 relative to diagnosis. Postpartum EB was not associated with indigestion postpartum. Cows that developed ODDZ had lesser prepartum DMI%BW on day -8 and from days -5 to -2, lesser prepartum EB on day -8 and from days -5 to -2, and lesser postpartum DMI%BW than cows without ODDZ. Each 0.1 percentage point decrease in the average DMI%BW and each Mcal decrease in the average EB in the last 3 days prepartum increased the odds of having indigestion by 9% each. Cutoffs for DMI%BW and EB during the last 3 days prepartum to predict indigestion were established and were ≤1.3%/day and ≤0.68 Mcal/day, respectively. In summary, measures of prepartum DMI%BW and EB were associated with indigestion and ODDZ postpartum and were predictors of indigestion postpartum, although the effect sizes were small.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Liver proteomic analysis of postpartum Holstein cows exposed to heat stress or cooling conditions during the dry period.

Heat stress negatively affects cow performance, compromises immune function, and increases susceptibility to metabolic disorders, particularly during the dry period and as cows transition from gestation to lactation. Metabolic adaptations of the liver are critical for successful transition, yet it is unclear how heat stress affects metabolic pathways within the liver at the proteomic level. The objective of this study was to investigate the liver proteome of postpartum cows that were cooled or heat stressed during the dry period to gain insight into how protein expression is altered by prior heat stress and may contribute to performance and disease outcomes. During the dry period, cows were either housed in shaded barns with fans and water soakers [cooled group (CL); n = 5] or in shaded barns lacking these cooling devices [heat-stressed group (HT); n = 5]. Liver biopsies were collected at 2 d postpartum, and protein content was analyzed by label-free quantitative shotgun proteomics (nanoscale liquid chromatography coupled to tandem mass spectrometry). In the most comprehensive bovine liver proteomics analysis completed to date, we identified 3,270 proteins, 75 of which were differentially expressed between HT and CL cows (fold change ±1.2). The top pathways differing between HT and CL cows were oxidative phosphorylation, mitochondrial dysfunction, farnesoid X receptor/retinoid X receptor (FXR/RXR) activation, and the methylmalonyl pathway. Cooling cows during the dry period likely improves ATP production, reduces oxidative stress, and prevents excessive accumulation of hepatic triglycerides and cholesterol, which may contribute to greater milk yield and lower susceptibility to transition-related diseases.