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The determination of the site specific glycosylation level usually combines glycosylated-proteins/glycosylated-peptides enrichment strategy, since separation of the glycosylated-proteins/ glycosylated-peptides from the backgrounds can reduce the sample complexity to a large extent.
Due to the wide dynamic range of individual proteins in cells, which presumably varies over five to six orders of magnitude [ 2], a key requirement for a comprehensive proteome analysis is to reduce sample complexity to a level that permits access to low abundance proteins.
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Joint observability and sampling complexity are established, extending Shannon's sampling theorem and our recent results on sampling complexity to joint estimation problems.
To decrease sample complexity and to increase the sensitivity of detection we used the CPLL technology.
To reduce the sample complexity and to enrich low abundant bZIP63-binding proteins before kinase identification, we affinity purified plant protein extracts on immobilized bZIP63.
Recent method development efforts focused on pre- or post-FASP fractionation to reduce the sample complexity and to improve proteome coverage.
Decreased sample complexity due to sample fractionation has previously been shown to alleviate the compression of ratios, which has been identified as a problem in iTRAQ based quantitation [ 34– 34].
For proteomics, we applied a similar work-flow, whereby chromatographic separation was used to amplify bacterial products via reduction of the sample complexity prior to MS analysis, and construction and interrogation of a smaller custom database (rather than complex databases, ie NCBI or SwissProt) was used for selective analysis of bacterial peptides.
Here we demonstrate that the reduction of sample complexity prior to analysis improves proteome coverage and the resolution of LAP.
Several enrichment and fractionation steps can be introduced at protein or peptide level in this general workflow when sample complexity has to be reduced or when a specific subset of proteins/peptides should be analysed (i.e. organelle specific proteome [ 2, 3] or substoichiometric post-translational modified peptides [ 4]).
An alternative approach to reduce sample complexity further is to use selective primers for PCR amplification as was shown recently in the 2b-RAD-seq protocol (Wang et al. 2012).
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