Bioinformatics methods for mass spectrometry-based proteomics data analysis

C Chen, J Hou, JJ Tanner, J Cheng - International journal of molecular …, 2020 - mdpi.com
Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous
progress in the understanding of cellular mechanisms, disease progression, and the …

Protein analysis by shotgun/bottom-up proteomics

Y Zhang, BR Fonslow, B Shan, MC Baek… - Chemical …, 2013 - ACS Publications
According to Genome Sequencing Project statistics (http://www. ncbi. nlm. nih.
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …

An introduction to mass spectrometry-based proteomics

SR Shuken - Journal of Proteome Research, 2023 - ACS Publications
Mass spectrometry is unmatched in its versatility for studying practically any aspect of the
proteome. Because the foundations of mass spectrometry-based proteomics are complex …

Characterization of SARS-CoV-2 proteins reveals Orf6 pathogenicity, subcellular localization, host interactions and attenuation by Selinexor

JG Lee, W Huang, H Lee, J van de Leemput, MA Kane… - Cell & bioscience, 2021 - Springer
Abstract Background SARS-CoV-2 causes COVID-19 which has a widely diverse disease
profile. The mechanisms underlying its pathogenicity remain unclear. We set out to identify …

Comet: an open‐source MS/MS sequence database search tool

JK Eng, TA Jahan, MR Hoopmann - Proteomics, 2013 - Wiley Online Library
Proteomics research routinely involves identifying peptides and proteins via MS/MS
sequence database search. Thus the database search engine is an integral tool in many …

[HTML][HTML] ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

T Xu, SK Park, JD Venable, JA Wohlschlegel… - Journal of …, 2015 - Elsevier
ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and
protein sequence databases has been developed. This algorithm uses a three tier scoring …

[HTML][HTML] A census of human soluble protein complexes

PC Havugimana, GT Hart, T Nepusz, H Yang… - Cell, 2012 - cell.com
Cellular processes often depend on stable physical associations between proteins. Despite
recent progress, knowledge of the composition of human protein complexes remains limited …

Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment

JC Chan, CP Morgan, N Adrian Leu, A Shetty… - Nature …, 2020 - nature.com
Extracellular vesicles (EVs) are a unique mode of intercellular communication capable of
incredible specificity in transmitting signals involved in cellular function, including germ cell …

Identification of splice variants and isoforms in transcriptomics and proteomics

T Su, MAR Hollas, RT Fellers… - Annual review of …, 2023 - annualreviews.org
Alternative splicing is pivotal to the regulation of gene expression and protein diversity in
eukaryotic cells. The detection of alternative splicing events requires specific omics …

Quantitative proteomic analysis of histone modifications

H Huang, S Lin, BA Garcia, Y Zhao - Chemical reviews, 2015 - ACS Publications
Several mechanisms have been proposed for histone marks to exert their functions,
including altering the physical properties of nucleosomes by neutralization of charge via …