Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment. These coordinates calibrate protein databases or spectrum libraries to a specific mass spectrometer and chromatography setup, facilitating DIA-only pipelines and the reuse of global resource libraries. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect 20–25% more peptides from DIA experiments than with data dependent acquisition-based spectrum libraries alone.

SUMMARY Triple-negative breast cancer is a heterogeneous disease characterized by poor clinical outcomes and a shortage of targeted treatment options. To discover molecular features of triple-negative breast cancer, we performed quantitative proteomics analysis of twenty human-derived breast cell lines and four primary breast tumors to a depth of more than 12,000 distinct proteins. We used this data to identify breast cancer subtypes at the protein level and demonstrate the precise quantification of biomarkers, signaling proteins, and biological pathways by mass spectrometry. We integrated proteomics data with exome sequence resources to identify genomic aberrations that affect protein expression. We performed a high-throughput drug screen to identify protein markers of drug sensitivity and understand the mechanisms of drug resistance. The genome and proteome provide complementary information that, when combined, provide a powerful engine for therapeutic discovery. This resource is available to the cancer research community to catalyze further analysis and investigation.

The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding of cellular decision‐making has been limited by the small number of simultaneously monitored phospho‐regulatory events. Here, we have estimated changes in activity in 215 human kinases in 399 conditions derived from a large compilation of phosphopeptide quantifications. This atlas identifies commonly regulated kinases as those that are central in the signaling network and defines the logic relationships between kinase pairs. Co‐regulation along the conditions predicts kinase–complex and kinase–substrate associations. Additionally, the kinase regulation profile acts as a molecular fingerprint to identify related and opposing signaling states. Using this atlas, we identified essential mediators of stem cell differentiation, modulators of Salmonella infection, and new targets of AKT1. This provides a global view of human phosphorylation‐based signaling and the necessary context to better understand kinase‐driven decision‐making.

Systematic approaches to study cellular signaling require new phosphoproteomic techniques that reproducibly measure the same phosphopeptides across multiple replicates, conditions, and time points. Here we present a method to mine information from large-scale, heterogeneous phosphoproteomics datasets to rapidly generate robust targeted assays. We demonstrate the performance of our method by interrogating the IGF-1/AKT signaling pathway; and show that even rarely observed phosphorylation events can be consistently detected and precisely quantified.

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Lipid deposition in the liver is associated with metabolic disorders including fatty liver disease, type II diabetes, and hepatocellular cancer. The enzymes acetyl-CoA carboxylase 1 (ACC1) and ACC2 are powerful regulators of hepatic fat storage; therefore, their inhibition is expected to prevent the development of fatty liver. In this study we generated liver-specific ACC1 and ACC2 double knockout (LDKO) mice to determine how the loss of ACC activity affects liver fat metabolism and whole-body physiology. Characterization of LDKO mice revealed unexpected phenotypes of increased hepatic triglyceride and decreased fat oxidation. We also observed that chronic ACC inhibition led to hyper-acetylation of proteins in the extra-mitochondrial space. In sum, these data reveal the existence of a compensatory pathway that protects hepatic fat stores when ACC enzymes are inhibited. Furthermore, we identified an important role for ACC enzymes in the regulation of protein acetylation in the extra-mitochondrial space.

Cell Reports 10, February 17, 2015; 944-956) In the published version of this manuscript, there was an error in Figure S4. The original scanned image file of the film contained six lanes, with the wild-type sample run in duplicate at either end of the gel. While the sixth lane was cropped out of the image of the film probed with anti-Dnmt3L antibody, it was accidentally included in the image of the film probed with anti-Ezh2 antibody.The corrected figure is below. The authors regret the error.

Proteins can be phosphorylated at neighboring sites resulting in different functional states, and studying the regulation of these sites has been challenging. Here we present Thesaurus, a search engine that detects and quantifies phosphopeptide positional isomers from parallel reaction monitoring and data independent acquisition mass spectrometry experiments. We apply Thesaurus to analyze phosphorylation events in the PI3K/AKT signaling pathway and show neighboring sites with distinct regulation.Hundreds of thousands of amino acids in thousands of proteins are estimated to be actively phosphorylated in every human cell (1). Many proteins are phosphorylated at neighboring sites (2) and over half of sites in multi-phosphorylated proteins are within four amino acids of each other (3). Several well-studied proteins make use of neighboring phosphorylation sites to act as switches (MAPK (4), CDC4 (5)), timers (PER ( 6)) or as negative inhibition toggles (IRS1 ( 7)) but global analysis of these phosphorylation clusters has remained impractical. Tandem mass spectrometry (MS/MS) of tryptic peptides is a key tool in discovering and quantifying sites of protein phosphorylation. Typical phosphoproteomic workflows use data dependent acquisition (DDA) to collect MS/MS spectra based on precursor m/z as peptides chromatographically elute. Site localization software tools such as Ascore (8) assign the most likely phosphorylation position for each peptide using sitespecific fragment ions. To increase the number of distinct peptides that are sampled, DDA Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: