Journal: Antibiotics

Article Title: Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database

doi: 10.3390/antibiotics9110757

Figure Lengend Snippet: Workflow of the methodologies used to profile the whole proteome of the posterior salivary glands from the cephalopod Octopus vulgaris : ( a ) Sampling, dissection, and protein extraction of the posterior salivary glands (PSGs) from three adult specimens of Octopus vulgaris (Ov) corresponding to three biological replicates (Ov1_PSG, Ov2_PSG, Ov3_PSG); ( b ) Sample preparation protocols for LC-MS/MS analyses (FASP: Filter Aided Sample Preparation and ISD: In solution digestion), and the corresponding two technical replicates for each specimen (biological replicate); ( c ) Resulting 12 LTQ raw files from LC-MS/MS peptide sequencing using a nanoLC-MS/MS, composed by an Ultimate 3000 liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Scientific, Bremen, Germany); ( d ) Protein identification and quantitative analyses (MaxQuant freeware v1.6.2.3), downstream analyses (Perseus v1.6.2.3) and leading proteins annotation (BLASTp program against UniProtKB/Swiss-Prot and nr database).

Article Snippet: The strategy employed was based on homology search using a local BLAST with BLASTp program against the “UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase” (accessed 13 May 2019) [ ], “UniProtKB/Swiss-Prot Tox-Prot” ( http://www.uniprot.org/program/Toxins ; accessed 13 May 2019) [ ], and against the National Center for Biotechnology Information (NCBI) non-redundant protein database (nr database: ftp://ftp.ncbi.nlm.nih.gov/blast/db ; accessed 25 June 2018), setting a cut-off e-value of 1e−3.

Techniques: Sampling, Dissection, Protein Extraction, Sample Prep, Liquid Chromatography with Mass Spectroscopy, Sequencing, Tandem Mass Spectroscopy, Liquid Chromatography, Mass Spectrometry

Journal: PLoS ONE

Article Title: Targeted Next-Generation Sequencing of Plasma DNA from Cancer Patients: Factors Influencing Consistency with Tumour DNA and Prospective Investigation of Its Utility for Diagnosis

doi: 10.1371/journal.pone.0162809

Figure Lengend Snippet: Lung cancer ctDNA sequencing.

Article Snippet: Sequencing of ctDNA from 12 lung cancer patients identified 22 non-synonymous variants , with some of the mutations predicted or known to affect protein function and some of which are actionable, as annotated in the Jackson Laboratory Clinical Knowledgebase, https://ckb.jax.org/ [ ] and ClinVar database, http://www.ncbi.nlm.nih.gov/clinvar/ [ ].

Techniques: Sequencing, Mutagenesis, Variant Assay, Clinical Proteomics, Ligand Binding Assay, Phospho-proteomics, Migration, Cell Culture, Activation Assay, Activity Assay, Protein-Protein interactions, Residue, Ubiquitin Proteomics