Application of targeted mass spectrometry in bottom-up proteomics for systems biology research
NP Manes, A Nita-Lazar - Journal of proteomics, 2018 - Elsevier
The enormous diversity of proteoforms produces tremendous complexity within cellular
proteomes, facilitates intricate networks of molecular interactions, and constitutes a …
proteomes, facilitates intricate networks of molecular interactions, and constitutes a …
Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short …
The recent discovery of alternative open reading frames creates a need for suitable
analytical approaches to verify their translation and to characterize the corresponding gene …
analytical approaches to verify their translation and to characterize the corresponding gene …
CPPred: coding potential prediction based on the global description of RNA sequence
X Tong, S Liu - Nucleic acids research, 2019 - academic.oup.com
The rapid and accurate approach to distinguish between coding RNAs and ncRNAs has
been playing a critical role in analyzing thousands of novel transcripts, which have been …
been playing a critical role in analyzing thousands of novel transcripts, which have been …
Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions
MA Tufail, B Jordan, L Hadjeras, R Gelhausen… - Nature …, 2024 - nature.com
The mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1
is crucial for climate and environmental research due to its ability to produce methane. Here …
is crucial for climate and environmental research due to its ability to produce methane. Here …
Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats
M Schmid, D Frei, A Patrignani… - Nucleic acids …, 2018 - academic.oup.com
Generating a complete, de novo genome assembly for prokaryotes is often considered a
solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors …
solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors …
The role of micropeptides in biology
Micropeptides are small polypeptides coded by small open-reading frames. Progress in
computational biology and the analyses of large-scale transcriptomes and proteomes have …
computational biology and the analyses of large-scale transcriptomes and proteomes have …
A practical guide to small protein discovery and characterization using mass spectrometry
Small proteins of up to∼ 50 amino acids are an abundant class of biomolecules across all
domains of life. Yet due to the challenges inherent in their size, they are often missed in …
domains of life. Yet due to the challenges inherent in their size, they are often missed in …
False discovery rate: the Achilles' heel of proteogenomics
Proteogenomics refers to the integrated analysis of the genome and proteome that
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics
L Fancello, T Burger - Genome Biology, 2022 - Springer
Background Proteogenomics aims to identify variant or unknown proteins in bottom-up
proteomics, by searching transcriptome-or genome-derived custom protein databases …
proteomics, by searching transcriptome-or genome-derived custom protein databases …
Harnessing the microbiomes of suppressive composts for plant protection: from metagenomes to beneficial microorganisms and reliable diagnostics
Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often
only limited options for disease management are available. It has long been known that …
only limited options for disease management are available. It has long been known that …