Quantifying homologous proteins and proteoforms
Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases. To avoid these biases, we developed and implemented a first-principles model (HIquant) for quantifying proteoform stoichiometries. We characterized when MS data allow inferring proteoform stoichiometries by HIquant, derived an algorithm for optimal inference, and demonstrated experimentally high accuracy in quantifying fractional PTM occupancy without using external standards, even in the challenging case of the histone modification code. HIquant server is implemented at: https://web.northeastern.edu/slavov/2014_HIquant/
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
Ensembles of phalanxes across assessment metrics for robust ranking of homologous proteins
Two proteins are homologous if they have a common evolutionary origin, and the binary classification problem is to identify proteins in a candidate set that are homologous to a particular native protein. The feature (exp…
Binary ClassificationGeneral ClassificationProteomics Standards Initiatives ProForma 2.0 Unifying the encoding of Proteoforms and Peptidoforms
There is the need to represent in a standard manner all the possible variations of a protein or peptide primary sequence, including both artefactual and post-translational modifications of peptides and proteins. With tha…
Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains
The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and funct…
Efficiently Predicting Mutational Effect on Homologous Proteins by Evolution Encoding
Predicting protein properties is paramount for biological and medical advancements. Current protein engineering mutates on a typical protein, called the wild-type, to construct a family of homologous proteins and study t…
On the Mechanism of Homology Search by RecA Protein Filaments
Genetic stability is a key factor in maintaining, survival and reproduction of biological cells. It relies on many processes, but one of the most important is a {\it homologous recombination}, in which the repair of brea…