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Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
TLDR
A statistical model is presented to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST, demonstrating that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides. Expand
A statistical model for identifying proteins by tandem mass spectrometry.
TLDR
A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample, and it is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications. Expand
Molecular characterization of mitochondrial apoptosis-inducing factor
TLDR
The identification and cloning of an apoptosis-inducing factor, AIF, which is sufficient to induce apoptosis of isolated nuclei is reported, indicating that AIF is a mitochondrial effector of apoptotic cell death. Expand
Mass spectrometry-based proteomics
TLDR
The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine. Expand
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
TLDR
An approach for the accurate quantification and concurrent sequence identification of the individual proteins within complex mixtures based on isotope-coded affinity tags and tandem mass spectrometry is described. Expand
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis*
TLDR
A new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest is presented, using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. Expand
Correlation between Protein and mRNA Abundance in Yeast
TLDR
The results clearly delineate the technical boundaries of current approaches for quantitative analysis of protein expression and reveal that simple deduction from mRNA transcript analysis is insufficient to predict protein expression levels from quantitative mRNA data. Expand
Crucial Step in Cholesterol Homeostasis Sterols Promote Binding of SCAP to INSIG-1, a Membrane Protein that Facilitates Retention of SREBPs in ER
TLDR
By facilitating sterol-dependent ER retention of SCAP, INSIG-1 plays a central role in cholesterol homeostasis. Expand
Orm family proteins mediate sphingolipid homeostasis
TLDR
The function in sphingolipid metabolism of the ORM genes is revealed—a conserved gene family that includes ORMDL3, which has recently been identified as a potential risk factor for childhood asthma. Expand
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
TLDR
The Trans‐Proteomic Pipeline is described, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels, and enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a range of different database search programs. Expand
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