Direct Maximization of Protein Identifications from Tandem Mass Spectra
نویسندگان
چکیده
منابع مشابه
Direct Maximization of Protein Identifications from Tandem Mass Spectra*□S
The goal of many shotgun proteomics experiments is to determine the protein complement of a complex biological mixture. For many mixtures, most methodological approaches fall significantly short of this goal. Existing solutions to this problem typically subdivide the task into two stages: first identifying a collection of peptides with a low false discovery rate and then inferring from the pept...
متن کاملDirect maximization of protein identifications from tandem mass spectra.
The goal of many shotgun proteomics experiments is to determine the protein complement of a complex biological mixture. For many mixtures, most methodological approaches fall significantly short of this goal. Existing solutions to this problem typically subdivide the task into two stages: first identifying a collection of peptides with a low false discovery rate and then inferring from the pept...
متن کاملSupplement to “Direct maximization of protein identifications from tandem mass spectra”
We are given a set of observed spectra S = {s1, . . . , sNS} and a database D of target and decoy proteins against which we perform a database search. The search produces a set of peptide-spectrum matches (PSMs). Denoting the set of peptides as E1, . . . , ENE , the PSMs are written as the tuples (Ei, sj) ∈ M, each representing a match of peptide i to spectrum j. Note that, in general, we may o...
متن کاملProtein Identification from Tandem Mass Spectra with Probabilistic Language Modeling
This paper presents an interdisciplinary investigation of statistical information retrieval (IR) techniques for protein identification from tandem mass spectra, a challenging problem in proteomic data analysis. We formulate the task as an IR problem, by constructing a “query vector” whose elements are system-predicted peptides with confidence scores based on spectrum analysis of the input sampl...
متن کاملProtein Identification from Tandem Mass Spectra by Database Searching.
Protein identification from tandem mass spectra is one of the most versatile and widely used proteomics workflows, able to identify proteins, characterize post-translational modifications, and provide semiquantitative measurements of relative protein abundance. This manuscript describes the concepts, prerequisites, and methods required to analyze a tandem mass spectrometry dataset in order to i...
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ژورنال
عنوان ژورنال: Molecular & Cellular Proteomics
سال: 2012
ISSN: 1535-9476
DOI: 10.1074/mcp.m111.012161