The role of protein and peptide separation before mass spectrometry analysis in clinical proteomics

Camerini, Serena; Mauri, Pierluigi

doi:10.1016/j.chroma.2014.12.035

Cited by 65 publications

(54 citation statements)

References 100 publications

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“…Reproduction, Fertility and Development G in methodologies may have contributed to the differences in identified proteins between the studies chosen for our metaanalysis, a comprehensive analysis of the issues and limitations relevant to proteomic methodologies is beyond the scope of this article and the reader is referred to the following excellent reviews (Lumbreras et al 2009;Camerini and Mauri 2015;Larance and Lamond 2015;Schey et al 2015). The different range of proteins found in placenta-derived exosomes is intriguing.…”

Section: Placenta-derived Extracellular Vesiclesmentioning

confidence: 96%

“…Other sources of variation in the identified proteins between these research groups could also be related to the choice of different methodologies employed for exosome protein sample preparation, sample separation and digestion techniques and protein identification software (Camerini and Mauri 2015;Schey et al 2015). For example, contaminants in cell culture media, particularly albumin, and sucrose gradients used to isolate extracellular vesicles of a particular size, can introduce components that may interfere with protein identification analysis (Schey et al 2015).…”

Section: Proteinsmentioning

confidence: 98%

“…For example, contaminants in cell culture media, particularly albumin, and sucrose gradients used to isolate extracellular vesicles of a particular size, can introduce components that may interfere with protein identification analysis (Schey et al 2015). In addition, samples are not efficiently separated or digested in 1D gels, while in-solution digestion requires complete solubilisation of the sample proteins (Camerini and Mauri 2015); both these methodologies can lead to reduced recovery of proteins available for analysis. While differences …”

Section: Proteinsmentioning

confidence: 99%

See 2 more Smart Citations

Placenta-derived extracellular vesicles: their cargo and possible functions

Familari

Cronqvist

Masoumi

et al. 2017

Reprod. Fertil. Dev.

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The literature on extracellular vesicles consists of rapidly expanding and often contradictory information. In this paper we attempt to review what is currently known regarding extracellular vesicles released specifically from human placental syncytiotrophoblast cells with a focus on the common but complex pregnancy-associated syndrome pre-eclampsia, where the level of syncytiotrophoblast extracellular vesicle release is significantly increased. We review common methods for syncytiotrophoblast extracellular vesicle derivation and isolation and we discuss the cargo of syncytiotrophoblast extracellular vesicles including proteins, RNA and lipids and their possible functions. A meta-analysis of available trophoblast-derived extracellular vesicle proteomic datasets revealed only three proteins in common: albumin, fibronectin-1 and plasminogen activator inhibitor-1, suggesting some variability in vesicle cargo, most likely reflecting stage and cell type of origin. We discuss the possible sources of variability that may have led to the low number of common markers, which has led us to speculate that markers and density in common use may not be strict criteria for identifying and isolating placenta-derived exosomes.

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Section: Placenta-derived Extracellular Vesiclesmentioning

confidence: 96%

Section: Proteinsmentioning

confidence: 98%

Section: Proteinsmentioning

confidence: 99%

See 1 more Smart Citation

Placenta-derived extracellular vesicles: their cargo and possible functions

Familari

Cronqvist

Masoumi

et al. 2017

Reprod. Fertil. Dev.

View full text Add to dashboard Cite

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“…Perhaps one of the major limitations of the technology is the unknown or unproven ability for a MS test to consistently provide the same answer across laboratories [114][115][116]. Due to the low sensitivity of MS relative to immunoassay, much larger volumes (or smaller dilutions) are typically required and thus sample preparation and the removal of background or matrix proteins becomes particularly important [117]. In addition to a wide variety of instrument platforms with different performance characteristics and multiple sample preparation techniques can be used, each with its own advantages and disadvantages.…”

Section: The Challenges In Employing Ms Assays In Clinical Laboratoriesmentioning

confidence: 99%

The clinical utility of mass spectrometry based protein assays

Lassman

McAvoy

Chappell

et al. 2016

Clinica Chimica Acta

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“…However, reproducibility and variable dynamic ranges, of highly complex samples pose a humungous challenge. Highly abundant proteins cause 'the suppression effect' which could make it difficult, rather impossible for the detection of low represented molecules [36]. In order to break down the complexity and enable enrichment of low abundant species, fractionation is of prior importance.…”

Section: Fractionationmentioning

confidence: 99%

Proteomics as a multifaceted tool in medicine and environmental assessment

Kuruvilla¹

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Proteomics is evolving as a multi-faceted tool for addressing various biochemical and biomedical queries in the field of scientific research. This involves various stages, ranging from sample preparation to data analysis and biological interpretation. Sample preparation involves isolating proteins from the sample source, purifying and digesting them to initiate shotgun proteomics. Shotgun proteomics identifies proteins by bottom-up proteomic approaches where proteins are identified from the fragmentation spectra of their own peptides.Paper I: deals with the simplification of functional characterization for nanoparticles intended for use in biomedicine. Proteomics was constructive in differentiating and semi-quantifying the surface of protein corona. This could be beneficial in predicting the interactions between nanoparticles and a biological entity like the cell or a receptor protein and provide initial valuable information related to targeting, uptake and safety.Paper II: deals with understanding effects of TiO2 nanoparticles on endothelial cells. A combinatorial approach, involving transcriptomics and proteomics was used to identify aberrations in the permeability and integrity of endothelial cells and tissues. Our study also investigated the correlation of size and how they motivated a differential cellular response. In case of intravenous entry for nanoparticles in targeted drug delivery systems, endothelial cells are the first barrier encountered by these drug carriers. This evaluation involving endothelial cell response could be very instrumental during the designing of NP based drug delivery systems.Paper III: Pharmaceuticals and its metabolites could be very hazardous, especially if its disposal is not managed properly. Since water bodies are the ultimate sink, these chemicals could end up there, culminating in toxicity and other 'mixture effects' in combination with other factors. To evaluate the effects of the pharmaceutical, propranolol and climatic factors like low salinity conditions, a microcosm exposure was designed and shotgun proteomics helped understand its impact on mussel gills. In this study too, a combination of transcriptomics and proteomics unveiled molecular mechanisms altered in response to stressors, both individually and in combination.Paper IV: An interplay of various factors like EBF1 and PAX5 determines B-cell lineage and commitment. This might have been materialized by direct and transient proteinprotein interactions. A unique method called BioID helped screen relevant interactions in living cells by the application of a promiscuous biotin ligase enzyme capable of tagging proteins through biotinylation based on a proximity radius. Biotinylation of endogenous proteins enabled their selective isolation by exploiting the high affinity of biotin and streptavidin on streptavidin coated agarose beads, leading to their identification by mass spectrometry. The biotinylated proteins were potential candidate interactors of EBF1 and PAX5, which were later confirmed by sequencing tec...

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The role of protein and peptide separation before mass spectrometry analysis in clinical proteomics

Cited by 65 publications

References 100 publications

Placenta-derived extracellular vesicles: their cargo and possible functions

Placenta-derived extracellular vesicles: their cargo and possible functions

The clinical utility of mass spectrometry based protein assays

Proteomics as a multifaceted tool in medicine and environmental assessment

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