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LiP-MS is an approach based on limited proteolysis that can be used to probe structural changes in proteins. This update highlights recent changes to the method to improve throughput, proteome coverage and data analysis.
PatternLab is a unified computational environment for analyzing shotgun proteomic data. Version 5 provides modules for preparing sequence databases, protein identification, statistical filtering and in-depth result browsing.
Chemicals are used to induce sporadic and inflammation-associated colon tumor growth in mouse models. When combined with p53 deficiency, tumor development is promoted, including the growth of invasive cancers and lymph node metastasis.
Here the authors describe an updated protocol for single-stranded sequencing library preparation suitable for highly degraded DNA from ancient remains or other sources. The procedure can be performed manually or in an automated fashion.
Here the authors provide an update to their 2013 protocol for using the PANTHER classification system, detailing how to analyze genome-wide experimental data with the newest version of PANTHER (v.14.0), with improvements in the areas of data quality, data coverage, statistical algorithms and user experience.
The COBRA toolbox provides quality-controlled reconstruction, modeling, topological analysis, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data.
This protocol update describes silica-based approaches for purification of DNA from ancient bone, tooth and sediment samples. The optimized buffers yield short DNA fragments compatible with high-throughput sequencing library preparation.
MaxQuant is a platform for mass spectrometry-based proteomics data analysis. It includes a peptide database search engine, called Andromeda, and expanding capability to handle data from most quantitative proteomics experiments.
