proteominertm protein enrichment kit  (Bio-Rad)

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: Overlapping and unique proteins identified by native digestion, ProteoMiner Small‐Capacity Enrichment Kit, and PreOmics Enrich‐iST Kit. CSF samples were processed using these three methods, followed by LC–MS/MS, DDA, and MASCOT identification. The graph shows the overlap of proteins identified by MASCOT in both replicates for given method. The Venn diagram was generated using the ggVennDiagram package15 (v1.5.2) in R Studio16 (v4.1.2).

Article Snippet: To address this, enrichment techniques and kits have been developed, including ProteoMiner Enrichment Kits by Bio‐Rad and PreOmics Enrich‐iST by PreOmics.

Techniques: Liquid Chromatography with Mass Spectroscopy, Generated

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: The PreOmics Enrich‐iST Kit outperformed ProteoMiner in depleting HAPs. The bar chart shows the emPAI scores of known HAPs measured using three techniques. Each protein is represented by three bars corresponding to the three techniques: native digestion (‘Native’, blue), ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green) and PreOmics ENRICH‐iST Kit (‘PreOmics’, red). The y ‐axis represents the emPAI score, and the x ‐axis shows the proteins analysed. In most cases, the sample processed with the PreOmics ENRICH‐iST Kit exhibited lower emPAI scores across known HAPs. Values ( n = 2) are expressed as means and ± SD. Image made using ggplot2 (version 3.5.2).

Article Snippet: To address this, enrichment techniques and kits have been developed, including ProteoMiner Enrichment Kits by Bio‐Rad and PreOmics Enrich‐iST by PreOmics.

Techniques:

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: PreOmics ENRICH‐iST demonstrated superior enrichment efficiency, identifying more pathways at greater statistical significance as well as pathways relevant to neuropathologies. Comparison of FDR‐adjusted p values (−log 10 scale) showed the PreOmics ENRICH‐iST Kit (‘PreOmics’, red) generally achieved more significant values across the analysed GO pathways compared to the native digestion (‘Native’, blue) and ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green). Out of the 50 pathways analysed, 22 were identified at a lower FDR by PreOmics ENRICH‐iST. Dashed vertical lines indicate the mean –log 10 (FDR) for each technique (Native: 10.3 ± 3.76; PreOmics: 12.0 ± 5.63; ProteoMiner: 11.5 ± 4.55), with shaded regions representing ± 1 standard deviation and dotted lines marking the boundaries of each distribution. Image made using ggplot2 (version 3.5.2).

Article Snippet: To address this, enrichment techniques and kits have been developed, including ProteoMiner Enrichment Kits by Bio‐Rad and PreOmics Enrich‐iST by PreOmics.

Techniques: Comparison, Standard Deviation

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: Overlapping and unique proteins identified by native digestion, ProteoMiner Small‐Capacity Enrichment Kit, and PreOmics Enrich‐iST Kit. CSF samples were processed using these three methods, followed by LC–MS/MS, DDA, and MASCOT identification. The graph shows the overlap of proteins identified by MASCOT in both replicates for given method. The Venn diagram was generated using the ggVennDiagram package15 (v1.5.2) in R Studio16 (v4.1.2).

Article Snippet: The ProteoMiner enrichment (Bio‐Rad ProteoMiner Small‐Capacity Kit no. 163‐3006) was carried out using 1 mg of protein ( n = 2, technical replicates).

Techniques: Liquid Chromatography with Mass Spectroscopy, Generated

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: The PreOmics Enrich‐iST Kit outperformed ProteoMiner in depleting HAPs. The bar chart shows the emPAI scores of known HAPs measured using three techniques. Each protein is represented by three bars corresponding to the three techniques: native digestion (‘Native’, blue), ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green) and PreOmics ENRICH‐iST Kit (‘PreOmics’, red). The y ‐axis represents the emPAI score, and the x ‐axis shows the proteins analysed. In most cases, the sample processed with the PreOmics ENRICH‐iST Kit exhibited lower emPAI scores across known HAPs. Values ( n = 2) are expressed as means and ± SD. Image made using ggplot2 (version 3.5.2).

Article Snippet: The ProteoMiner enrichment (Bio‐Rad ProteoMiner Small‐Capacity Kit no. 163‐3006) was carried out using 1 mg of protein ( n = 2, technical replicates).

Techniques:

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: PreOmics ENRICH‐iST demonstrated superior enrichment efficiency, identifying more pathways at greater statistical significance as well as pathways relevant to neuropathologies. Comparison of FDR‐adjusted p values (−log 10 scale) showed the PreOmics ENRICH‐iST Kit (‘PreOmics’, red) generally achieved more significant values across the analysed GO pathways compared to the native digestion (‘Native’, blue) and ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green). Out of the 50 pathways analysed, 22 were identified at a lower FDR by PreOmics ENRICH‐iST. Dashed vertical lines indicate the mean –log 10 (FDR) for each technique (Native: 10.3 ± 3.76; PreOmics: 12.0 ± 5.63; ProteoMiner: 11.5 ± 4.55), with shaded regions representing ± 1 standard deviation and dotted lines marking the boundaries of each distribution. Image made using ggplot2 (version 3.5.2).

Article Snippet: The ProteoMiner enrichment (Bio‐Rad ProteoMiner Small‐Capacity Kit no. 163‐3006) was carried out using 1 mg of protein ( n = 2, technical replicates).

Techniques: Comparison, Standard Deviation

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: Overlapping and unique proteins identified by native digestion, ProteoMiner Small‐Capacity Enrichment Kit, and PreOmics Enrich‐iST Kit. CSF samples were processed using these three methods, followed by LC–MS/MS, DDA, and MASCOT identification. The graph shows the overlap of proteins identified by MASCOT in both replicates for given method. The Venn diagram was generated using the ggVennDiagram package15 (v1.5.2) in R Studio16 (v4.1.2).

Article Snippet: Here, we compared three different approaches to prepare CSF samples for proteomic LC–MS/MS analysis: our laboratory protocol for in‐solution trypsin digestion (native digestion; Anderson et al. ), Bio‐Rad's ProteoMiner Small‐Capacity Enrichment Kit, and the PreOmics’ PreOmics Enrich‐iST Kit.

Techniques: Liquid Chromatography with Mass Spectroscopy, Generated

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: The PreOmics Enrich‐iST Kit outperformed ProteoMiner in depleting HAPs. The bar chart shows the emPAI scores of known HAPs measured using three techniques. Each protein is represented by three bars corresponding to the three techniques: native digestion (‘Native’, blue), ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green) and PreOmics ENRICH‐iST Kit (‘PreOmics’, red). The y ‐axis represents the emPAI score, and the x ‐axis shows the proteins analysed. In most cases, the sample processed with the PreOmics ENRICH‐iST Kit exhibited lower emPAI scores across known HAPs. Values ( n = 2) are expressed as means and ± SD. Image made using ggplot2 (version 3.5.2).

Article Snippet: Here, we compared three different approaches to prepare CSF samples for proteomic LC–MS/MS analysis: our laboratory protocol for in‐solution trypsin digestion (native digestion; Anderson et al. ), Bio‐Rad's ProteoMiner Small‐Capacity Enrichment Kit, and the PreOmics’ PreOmics Enrich‐iST Kit.

Techniques:

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: PreOmics ENRICH‐iST demonstrated superior enrichment efficiency, identifying more pathways at greater statistical significance as well as pathways relevant to neuropathologies. Comparison of FDR‐adjusted p values (−log 10 scale) showed the PreOmics ENRICH‐iST Kit (‘PreOmics’, red) generally achieved more significant values across the analysed GO pathways compared to the native digestion (‘Native’, blue) and ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green). Out of the 50 pathways analysed, 22 were identified at a lower FDR by PreOmics ENRICH‐iST. Dashed vertical lines indicate the mean –log 10 (FDR) for each technique (Native: 10.3 ± 3.76; PreOmics: 12.0 ± 5.63; ProteoMiner: 11.5 ± 4.55), with shaded regions representing ± 1 standard deviation and dotted lines marking the boundaries of each distribution. Image made using ggplot2 (version 3.5.2).

Article Snippet: Here, we compared three different approaches to prepare CSF samples for proteomic LC–MS/MS analysis: our laboratory protocol for in‐solution trypsin digestion (native digestion; Anderson et al. ), Bio‐Rad's ProteoMiner Small‐Capacity Enrichment Kit, and the PreOmics’ PreOmics Enrich‐iST Kit.

Techniques: Comparison, Standard Deviation

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: Overlapping and unique proteins identified by native digestion, ProteoMiner Small‐Capacity Enrichment Kit, and PreOmics Enrich‐iST Kit. CSF samples were processed using these three methods, followed by LC–MS/MS, DDA, and MASCOT identification. The graph shows the overlap of proteins identified by MASCOT in both replicates for given method. The Venn diagram was generated using the ggVennDiagram package15 (v1.5.2) in R Studio16 (v4.1.2).

Article Snippet: Briefly, the ProteoMiner Small‐Capacity Enrichment Kit (Bio‐Rad) uses a combinatorial hexapeptide library bound to chromatographic beads to reduce HAPs in samples (Li ), whereby HAPs saturate their ligands and excess protein is washed away.

Techniques: Liquid Chromatography with Mass Spectroscopy, Generated

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: The PreOmics Enrich‐iST Kit outperformed ProteoMiner in depleting HAPs. The bar chart shows the emPAI scores of known HAPs measured using three techniques. Each protein is represented by three bars corresponding to the three techniques: native digestion (‘Native’, blue), ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green) and PreOmics ENRICH‐iST Kit (‘PreOmics’, red). The y ‐axis represents the emPAI score, and the x ‐axis shows the proteins analysed. In most cases, the sample processed with the PreOmics ENRICH‐iST Kit exhibited lower emPAI scores across known HAPs. Values ( n = 2) are expressed as means and ± SD. Image made using ggplot2 (version 3.5.2).

Article Snippet: Briefly, the ProteoMiner Small‐Capacity Enrichment Kit (Bio‐Rad) uses a combinatorial hexapeptide library bound to chromatographic beads to reduce HAPs in samples (Li ), whereby HAPs saturate their ligands and excess protein is washed away.

Techniques:

Journal: Veterinary Medicine and Science

Article Title: Evaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Cerebrospinal Fluid

doi: 10.1002/vms3.70933

Figure Lengend Snippet: PreOmics ENRICH‐iST demonstrated superior enrichment efficiency, identifying more pathways at greater statistical significance as well as pathways relevant to neuropathologies. Comparison of FDR‐adjusted p values (−log 10 scale) showed the PreOmics ENRICH‐iST Kit (‘PreOmics’, red) generally achieved more significant values across the analysed GO pathways compared to the native digestion (‘Native’, blue) and ProteoMiner Small‐Capacity Enrichment Kit (‘ProteoMiner’, green). Out of the 50 pathways analysed, 22 were identified at a lower FDR by PreOmics ENRICH‐iST. Dashed vertical lines indicate the mean –log 10 (FDR) for each technique (Native: 10.3 ± 3.76; PreOmics: 12.0 ± 5.63; ProteoMiner: 11.5 ± 4.55), with shaded regions representing ± 1 standard deviation and dotted lines marking the boundaries of each distribution. Image made using ggplot2 (version 3.5.2).

Article Snippet: Briefly, the ProteoMiner Small‐Capacity Enrichment Kit (Bio‐Rad) uses a combinatorial hexapeptide library bound to chromatographic beads to reduce HAPs in samples (Li ), whereby HAPs saturate their ligands and excess protein is washed away.

Techniques: Comparison, Standard Deviation