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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
TLDR
MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
Andromeda: a peptide search engine integrated into the MaxQuant environment.
TLDR
A novel peptide search engine using a probabilistic scoring model that can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases.
The Perseus computational platform for comprehensive analysis of (prote)omics data
TLDR
The Perseus software platform was developed to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data and it is anticipated that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ *
TLDR
A new intensity determination and normalization procedure called MaxLFQ is developed that is fully compatible with any peptide or protein separation prior to LC-MS analysis, which accurately detects the mixing ratio over the entire protein expression range, with greater precision for abundant proteins.
The PRIDE database and related tools and resources in 2019: improving support for quantification data
TLDR
Key statistics on the current data contents and volume of downloads are outlined, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas are outlined.
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
TLDR
This protocol explains step by step how to use MaxQuant on stable isotope labeling by amino acids in cell culture (SILAC) data obtained with double or triple labeling.
Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
TLDR
High-resolution mass spectrometry–based proteomics was applied to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics, finding that nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylated site occupancy in mitosis, suggesting that these proteins may be inactivated by phosphorylate in mitotic cells.
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
TLDR
A new method, 2D annotation enrichment, is described, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes.
System-Wide Changes to SUMO Modifications in Response to Heat Shock
TLDR
This comprehensive proteomic analysis of the substrates of a ubiquitin-like modifier (Ubl) identifies a pervasive role for SUMO proteins in the biologic response to hyperthermic stress.
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