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Recent large scale cancer genome sequencing projects have identified spectrum of driver genomic alterations in HNSCC including CDKN2A, TP53, PIK3CA, NOTCH1, HRAS, FBXW7, PTEN, NFE2L2, FAT1, and CASP8 [ 2– 4].
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The Bacterial Proteogenomic Pipeline detected 47 peptides found in pseudo proteins with at least 10 distinctive identified spectra, of which 2 elongate known proteins and 45 belong to new standalone proteins, 4 of these peptides are not proteotypic, but could be associated to more than one pseudo protein.
It brings the total percentage of identified spectra to ≈ 22.6 % at 1% FDR [ Cheung et al.., (2012) identified 6% of spectra at 2% FDR].
For the Bayesian type of analyses [5], one assumes the existence of two score distributions: one for the score of correctly identified spectra, in terms of best hit, and another for the score of incorrectly identified spectra.
These concepts together contribute to the accuracy of the method and the increased number of identified spectra.
The number of identified spectra per proteome is the naïve observed abundance estimate.
As expected, pMatch significantly outperformed SpectraST in detecting unanticipated PTMs and increasing the number of identified spectra.
Its value represents the percentage of peptide spectra assigned to VAPA/B out of all identified spectra.
Here, we identified the spectrum of IDH mutations in human enchondromas and chondrosarcomas and studied their effects in mice.
Here we have identified a spectrum of chromosome anomalies in embryos of zebrafish homozygous for a hypomorphic mutation in Mps1, a kinase required for the mitotic checkpoint.
Open-ended interviews identified a spectrum of issues unique to adults with PCD.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com