Simple, efficient and thorough shotgun proteomic analysis with PatternLab V

MDM Santos, DB Lima, JSG Fischer, MA Clasen… - Nature protocols, 2022 - nature.com
Shotgun proteomics aims to identify and quantify the thousands of proteins in complex
mixtures such as cell and tissue lysates and biological fluids. This approach uses liquid …

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

PC Carvalho, DB Lima, FV Leprevost, MDM Santos… - Nature protocols, 2016 - nature.com
PatternLab for proteomics is an integrated computational environment that unifies several
previously published modules for the analysis of shotgun proteomic data. The contained …

DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization

SJ Papp, AL Huber, SD Jordan, A Kriebs, M Nguyen… - Elife, 2015 - elifesciences.org
The circadian transcriptional repressors cryptochrome 1 (Cry1) and 2 (Cry2) evolved from
photolyases, bacterial light-activated DNA repair enzymes. In this study, we report that while …

Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue

MRO Trugilho, ED Hottz, GVF Brunoro… - PLoS …, 2017 - journals.plos.org
Dengue is the most prevalent human arbovirus disease worldwide. Dengue virus (DENV)
infection causes syndromes varying from self-limiting febrile illness to severe dengue …

Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins

V Schwämmle, T Verano-Braga, P Roepstorff - Journal of proteomics, 2015 - Elsevier
The investigation of post-translational modifications (PTMs) represents one of the main
research focuses for the study of protein function and cell signaling. Mass spectrometry …

Taking the shortcut for high-throughput shotgun proteomic analysis of bacteria

EM Hartmann, F Allain, JC Gaillard, O Pible… - … : methods and protocols, 2014 - Springer
Currently, proteomic tools are able to establish a complete list of the most abundant proteins
present in a sample, providing the opportunity to study at high resolution the physiology of …

Benchmarking quantitative label-free LC–MS data processing workflows using a complex spiked proteomic standard dataset

C Ramus, A Hovasse, M Marcellin, AM Hesse… - Journal of …, 2016 - Elsevier
Proteomic workflows based on nanoLC–MS/MS data-dependent-acquisition analysis have
progressed tremendously in recent years. High-resolution and fast sequencing instruments …

Proteomics reveals differentially regulated pathways when comparing grade 2 and 4 astrocytomas

DCA Verissimo, AC Camillo-Andrade, MDM Santos… - Plos one, 2023 - journals.plos.org
Astrocytic tumors are known for their high progression capacity and high mortality rates; in
this regard, proteins correlated to prognosis can aid medical conduct. Although several …

Mitofusin 1 silencing decreases the senescent associated secretory phenotype, promotes immune cell recruitment and delays melanoma tumor growth after …

D Tarallo, J Martínez, A Leyva, A Mónaco, C Perroni… - Scientific Reports, 2024 - nature.com
Cellular senescence is a therapy endpoint in melanoma, and the senescence-associated
secretory phenotype (SASP) can affect tumor growth and microenvironment, influencing …

Mebendazole Inhibits Histoplasma capsulatum In Vitro Growth and Decreases Mitochondrion and Cytoskeleton Protein Levels

MA Almeida, AR Bernardes-Engemann, RA Coelho… - Journal of Fungi, 2023 - mdpi.com
Histoplasmosis is a frequent mycosis in people living with HIV/AIDS and other
immunocompromised hosts. Histoplasmosis has high rates of mortality in these patients if …