Editorial for Special Issue: Approaches to Top-Down Proteomics: In Honour of Prof. Patrick H. O’Farrell

Coorssen, Jens R.; Yergey, Alfred L.

doi:10.3390/proteomes5030018

Cited by 4 publications

(8 citation statements)

References 11 publications

(11 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, while bottom-up may serve as a rapid, low-resolution scan of a proteome, it enables deep, high-resolution proteome analyses when paired with two-dimensional gel electrophoresis (2DE). The 2DE protocol was developed in 1975, essentially initiating the discipline of proteomics [ 92 , 93 ]. Since inception, this method has also received its share of criticism, mainly around original issues concerning the resolution of low abundance proteoforms with extreme p I and MW, and hydrophobic protein species [ 73 , 94 , 95 ].…”

Section: Discovery Proteomicsmentioning

confidence: 99%

Proteomes Are of Proteoforms: Embracing the Complexity

2021

View full text Add to dashboard Cite

Proteomes are complex—much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current ‘state-of-the-field’. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?

show abstract

Section: Discovery Proteomicsmentioning

confidence: 99%

Proteomes Are of Proteoforms: Embracing the Complexity

2021

View full text Add to dashboard Cite

show abstract

“…The serum proteome based cancer biomarkers are soluble molecules secreted (and/or shed off) into the blood stream by cancer cells or other cell types belonging to the tumor microenvironment. 23,[103][104][105] The quantification of such biomarker molecules is economic; such serum based noninvasive diagnostic assays may correlate with the oral precancerous or OSCC cancerous pathologies. [103][104][105] The five differential serum spots were identified as four proteins DNAJC13, SSFA2-IV, UPF0415, and KRT-1.…”

Section: Discussionmentioning

confidence: 99%

“…102 In head and neck cancers HPV16 genome exits in three states: episomes, integrated and hybrid episomes. 91 The [103][104][105] The five differential serum spots were identified as four proteins DNAJC13, SSFA2-IV, UPF0415, and KRT-1. Two amongst five serum protein spots were identified as SSFA2-IV.…”

Section: Discussionmentioning

confidence: 99%

“…Conjointly, the present work involved two‐dimensional gel electrophoresis based serum proteomic profiling of non‐addicted OSCC case and healthy control. The serum proteome based cancer biomarkers are soluble molecules secreted (and/or shed off) into the blood stream by cancer cells or other cell types belonging to the tumor microenvironment . The quantification of such biomarker molecules is economic; such serum based noninvasive diagnostic assays may correlate with the oral precancerous or OSCC cancerous pathologies .…”

Section: Discussionmentioning

confidence: 99%

“…serum proteomic profiling of non-addicted OSCC case and healthy control. The serum proteome based cancer biomarkers are soluble molecules secreted (and/or shed off) into the blood stream by cancer cells or other cell types belonging to the tumor microenvironment 23,[103][104][105]. …”

mentioning

confidence: 99%

See 2 more Smart Citations

Assessment of cellular and serum proteome from tongue squamous cell carcinoma patient lacking addictive proclivities for tobacco, betel nut, and alcohol: Case study

Khowal

Naqvi

Monga

et al. 2018

J of Cellular Biochemistry

View full text Add to dashboard Cite

The intriguing molecular pathways involved in oral carcinogenesis are still ambiguous. The oral squamous cell carcinoma (OSCC) ranks as the most common type constituting more than 90% of the globally diagnosed oral cancers cases. The elevation in the OSCC incidence rate during past 10 years has an alarming impression on human healthcare. The major challenges associated with OSCC include delayed diagnosis, high metastatic rates, and low 5-year survival rates. The present work foundations on reverse genetic strategy and involves the identification of genes showing expressional variability in an OSCC case lacking addictive proclivities for tobacco, betel nut, and/or alcohol, major etiologies. The expression modulations in the identified genes were analyzed in 16 patients comprising oral pre-cancer and cancer histo-pathologies. The genes SCCA1 and KRT1 were found to down regulate while DNAJC13, GIPC2, MRPL17, IG-Vreg, SSFA2, and UPF0415 upregulated in the oral pre-cancer and cancer pathologies, implicating the genes as crucial players in oral carcinogenesis.

show abstract

Sphingolipids modulate docking, Ca2+ sensitivity and membrane fusion of native cortical vesicles

Abbineni

Coorssen

2018

The International Journal of Biochemistry & Cell Biology

View full text Add to dashboard Cite

Editorial for Special Issue: Approaches to Top-Down Proteomics: In Honour of Prof. Patrick H. O’Farrell

Abstract: Presaging the current discipline of Proteomics, Prof Patrick H. O’Farrell recognized the critical need for detailed protein analyses to dissect and thereby understand molecular mechanisms. [...]

Cited by 4 publications

References 11 publications

Proteomes Are of Proteoforms: Embracing the Complexity

Proteomes Are of Proteoforms: Embracing the Complexity

Assessment of cellular and serum proteome from tongue squamous cell carcinoma patient lacking addictive proclivities for tobacco, betel nut, and alcohol: Case study

Sphingolipids modulate docking, Ca2+ sensitivity and membrane fusion of native cortical vesicles

Contact Info

Product

Resources

About