skip to main content

Attention:

The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 11:00 PM ET on Friday, September 13 until 2:00 AM ET on Saturday, September 14 due to maintenance. We apologize for the inconvenience.


Title: Characterizing the sarcoplasmic proteome of aged pork chops classified by purge loss
Abstract Unpredictable variation in quality, including fresh pork water-holding capacity, remains challenging to pork processors and customers. Defining the diverse factors that influence fresh pork water-holding capacity is necessary to make progress in refining pork quality prediction methods. The objective was to utilize liquid chromatography and mass spectrometry coupled with tandem mass tag (TMT) multiplexing to evaluate the sarcoplasmic proteome of aged pork loins classified by purge loss. Fresh commercial pork loins were collected, aged 12 or 14 d postmortem, and pork quality and sensory attributes were evaluated. Chops were classified into Low (N = 27, average purge = 0.33%), Intermediate (N = 27, average purge = 0.72%), or High (N = 27, average purge = 1.19%) chop purge groups. Proteins soluble in a low-ionic strength buffer were extracted, digested with trypsin, labeled with 11-plex isobaric TMT reagents, and detected using a Q-Exactive Mass Spectrometer. Between the Low and High purge groups, 40 proteins were differentially (P < 0.05) abundant. The Low purge group had a greater abundance of proteins classified as structural and contractile, sarcoplasmic reticulum and calcium regulating, chaperone, and citric acid cycle enzymes than the High purge group. The presence of myofibrillar proteins in the aged sarcoplasmic proteome is likely due to postmortem degradation. These observations support our hypothesis that pork chops with low purge have a greater abundance of structural proteins in the soluble protein fraction. Together, these and other proteins in the aged sarcoplasmic proteome may be biomarkers of pork water-holding capacity. Additional research should establish the utility of these proteins as biomarkers early postmortem and over subsequent aging periods.  more » « less
Award ID(s):
1828942
NSF-PAR ID:
10440908
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Journal of Animal Science
Volume:
101
ISSN:
0021-8812
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Fresh pork tenderness contributes to consumer satisfaction with the eating experience. Postmortem proteolysis of proteins within and between myofibrils has been closely linked with pork tenderness development. A clear understanding of the molecular features associated with pork tenderness development will provide additional targets and open the door to new solutions to improve and make pork tenderness development more consistent. Therefore, the objective was to utilize liquid chromatography and mass spectrometry with tandem mass tag (TMT) multiplexing to evaluate myofibrillar sub-proteome differences between pork chops of different instrumental star probe values. Pork loins (N = 120) were collected from a commercial harvest facility at 24 h postmortem. Quality and sensory attributes were evaluated at 24 h postmortem and after ~2 weeks of postmortem aging. Pork chops were grouped into 4 groups based on instrumental star probe value (group A,x¯ = 4.23 kg, 3.43 to 4.55 kg; group B,x¯ = 4.79 kg, 4.66 to 5.00 kg; group C,x¯ = 5.43 kg, 5.20 to 5.64 kg; group D,x¯ = 6.21 kg, 5.70 to 7.41 kg; n = 25 per group). Myofibrillar proteins from the samples aged ~2 wk were fractionated, washed, and solubilized in 8.3 M urea, 2 M thiourea, and 1% dithiothreitol. Proteins were digested with trypsin, labeled with 11-plex isobaric TMT reagents, and identified and quantified using a Q-Exactive Mass Spectrometer. Between groups A and D, 54 protein groups were differentially abundant (adjusted P < 0.05). Group A had a greater abundance of proteins related to the thick and thin filament and a lesser abundance of Z-line-associated proteins and metabolic enzymes than group D chops. These data highlight that distinct myofibrillar sub-proteomes are associated with pork chops of different tenderness values. Future research should evaluate changes immediately and earlier postmortem to further elucidate myofibrillar sub-proteome differences over the postmortem aging period.

     
    more » « less
  2. The development of fresh meat quality is dictated by biochemical changes during the perimortem and postmortem period. Lipid and protein oxidation in postmortem skeletal muscle and meat products is detrimental to product quality. The mechanisms that influence lipid and protein oxidation in fresh meat remain unelucidated. Peroxiredoxins are thiol-specific antioxidant proteins that are highly reactive and abundant and may be involved in limiting oxidation early postmortem. This review aims to provide a background on oxidation in skeletal muscle, peroxiredoxins, a summary of proteomic experiments associating peroxiredoxins and meat quality, and the importance of context from proteomic methods and results. Additional controlled experiments considering the cellular conditions of postmortem skeletal muscle are necessary to further understand the contribution of peroxiredoxins to fresh meat quality development. 
    more » « less
  3. Abstract

    Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress‐induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep‐coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low‐quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label‐free quantitation of 3426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of single systems from a laboratory‐raised with two field‐collected populations revealed (1) a more unique proteome in the laboratory‐raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were distinct in laboratory‐cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate's deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research onB. schlosseriwith proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.

     
    more » « less
  4. Abstract

    De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors2, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.

     
    more » « less
  5. Purpose

    The aim of this study is to identify the potential cerebrospinal fluid (CSF) biomarkers for Alzheimer's disease and to evaluate these markers on independent CSF samples using parallel reaction monitoring (PRM) assays.

    Experimental Design

    High‐Resolution mass spectrometry and tandem mass tag (TMT) multiplexing technology are employed to identify potential biomarkers for Alzheimer's disease. Some of the identified potential biomarkers are validated using PRM assays.

    Results

    A total of 2327 proteins are identified in the CSF of which 139 are observed to be significantly altered in the CSF of AD patients. The proteins altered in AD includes a number of known AD marker such as MAPT, NPTX2, VGF, GFAP, and NCAM1 as well as novel biomarkers such as PKM and YWHAG. These findings are validated in a separate set of CSF specimens from AD dementia patients and controls. NPTX2, in combination with PKM or YWHAG, leads to the best results with AUCs of 0.935 and 0.933, respectively.

    Conclusions and Clinical Relevance

    The proteins that are found to be altered in the CSF of patients with AD could be used for monitoring disease progression and therapeutic response and perhaps also for early detection once they are validated in larger studies.

     
    more » « less