Automatic Determination of Disulfide Bridges in Proteins

Sokolowska, Izabela; Wetie, Armand G. Ngounou; Woods, Alisa G.; Darie, Costel C.

doi:10.1177/2211068212454737

Cited by 39 publications

(24 citation statements)

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“…Magnification is ×15 000 (a), ×60 000 (b), and ×150 000 (c). (Figure adapted from Reference with permission from the publisher. )…”

Section: Methods To Detect Ppismentioning

confidence: 99%

“…SDS-PAGE is the most frequently used biochemical fractionation method for proteins. However, when SDS-PAGE is not compatible with the end goal of the experiment, methods that can be used to focus on only a set or subset of proteins within the proteome (subproteomes) can be built and used, based on a logical biochemical approach, and depending on the type of the sample to be analyzed [85][86][87][88][89][90][91][92][93]. Therefore, the use of the physicochemical properties of proteins and their PTMs (that would allow one substitute for the inability to use SDS-PAGE and/or to complement it) may be helpful to achieve the end goal.…”

Section: Sds-page Under Nr Conditions or Sds-page (Nr) For Investigatmentioning

confidence: 99%

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Investigation of stable and transient protein–protein interactions: Past, present, and future

et al. 2013

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This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs and organisms. The significance of post-translational modifications within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and mass spectrometry (MS)-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.

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“…Magnification is ×15 000 (a), ×60 000 (b), and ×150 000 (c). (Figure adapted from Reference with permission from the publisher. )…”

Section: Methods To Detect Ppismentioning

confidence: 99%

Section: Sds-page Under Nr Conditions or Sds-page (Nr) For Investigatmentioning

confidence: 99%

Investigation of stable and transient protein–protein interactions: Past, present, and future

et al. 2013

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“…For visualization of protein bands, the gel can be stained either with the dye coomassie blue or silver stained or by fluorescently labeling the samples before 2-DE. For mass spectrometry analysis, gel bands are removed, and undergo several other steps to generate peptides in bottom-up and shotgun proteomics [51, 53, 67, 68]. Compared to LC/MS, 2-DE methods are more reproducible and robust.…”

Section: Reviewmentioning

confidence: 99%

Mass spectrometry for the detection of potential psychiatric biomarkers

et al. 2013

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The search for molecules that can act as potential biomarkers is increasing in the scientific community, including in the field of psychiatry. The field of proteomics is evolving and its indispensability for identifying biomarkers is clear. Among proteomic tools, mass spectrometry is the core technique for qualitative and quantitative identification of protein markers. While significant progress has been made in the understanding of biomarkers for neurodegenerative diseases such as Alzheimer’s disease, multiple sclerosis and Parkinson’s disease, psychiatric disorders have not been as extensively investigated. Recent and successful applications of mass spectrometry-based proteomics in fields such as cardiovascular disease, cancer, infectious diseases and neurodegenerative disorders suggest a similar path for psychiatric disorders. In this brief review, we describe mass spectrometry and its use in psychiatric biomarker research and highlight some of the possible challenges of undertaking this type of work. Further, specific examples of candidate biomarkers are highlighted. A short comparison of proteomic with genomic methods for biomarker discovery research is presented. In summary, mass spectrometry-based techniques may greatly facilitate ongoing efforts to understand molecular mechanisms of psychiatric disorders.

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“…MS is a method that can reliably and comprehensively identify proteins and putative biomarkers [4,5,[12][13][14][15][16][17][18][19][20][21][22]. MS is already in use for newborn screening for several other disorders, including phenylketonuria, congenital hypothyroidism and cystic fibrosis [23].…”

Section: Introductionmentioning

confidence: 99%