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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. Expand
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
TLDR
A proteomic-scale analysis of protein acetylation suggests that it is an important biological regulatory mechanism and the regulatory scope of lysine acetylations is broad and comparable with that of other major posttranslational modifications. Expand
In-gel digestion for mass spectrometric characterization of proteins and proteomes
TLDR
This protocol is for the in-gel digestion of both silver and Coomassie-stained protein spots or bands and can be followed by MALDI-MS or LC-MS/MS analysis to identify proteins at sensitivities better than a few femtomoles of protein starting material. Expand
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
TLDR
A general mass spectrometric technology is developed and applied for identification and quantitation of phosphorylation sites as a function of stimulus, time, and subcellular location to provide a missing link in a global, integrative view of cellular regulation. Expand
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. Expand
Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap*S
TLDR
This work demonstrates sub-ppm mass accuracy on a linear ion trap coupled via a radio frequency-only storage trap to the orbitrap mass spectrometer (LTQ Orbitrap), and introduces a variable mass tolerance to improve certainty of peptide and small molecule identification. Expand
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. Expand
Higher-energy C-trap dissociation for peptide modification analysis
TLDR
Immonium ions generated via HCD pinpoint modifications such as phosphotyrosine with very high confidence are generated via higher-energy C-trap dissociation (HCD) and this work shows that an added octopole collision cell facilitates de novo sequencing. Expand
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
TLDR
Comparison of protein levels of essentially all endogenous proteins in haploid yeast cells to their diploid counterparts spans more than four orders of magnitude in protein abundance with no discrimination against membrane or low level regulatory proteins. Expand
Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers
TLDR
The authors' data reveal a highly adapted interplay between chromatin marks and their associated protein complexes, and reading specific trimethyl-lysine sites by specialized complexes appears to be a widespread mechanism to mediate gene expression. Expand
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