ArticleCurrent protocols in bioinformatics2012
Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.
Article in Current protocols in bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.Journal of proteome research · 2023Article
- Binding of cytochrome P450 27C1, a retinoid desaturase, to its accessory protein adrenodoxin.Archives of biochemistry and biophysics · 2021Article
- Proteomic Identification and Meta-Analysis inPlants (Basel, Switzerland) · 2021Article
- Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium.Cell host & microbe · 2019Article
- Isotopic tagging of oxidized and reduced cysteines (iTORC) for detecting and quantifying sulfenic acids, disulfides, and free thiols in cells.The Journal of biological chemistry · 2019Article
- Synthesis and Characterization of Site-Specific OCurrent protocols in nucleic acid chemistry · 2019Article
- Sulfenylation of Human Liver and Kidney Microsomal Cytochromes P450 and Other Drug-Metabolizing Enzymes as a Response to Redox Alteration.Molecular & cellular proteomics : MCP · 2018Article
- Article
- Characterization of the Ovarian Tumor Peptidome.Vitamins and hormones · 2018Article
- Proteolytic processing of lysyl oxidase-like-2 in the extracellular matrix is required for crosslinking of basement membrane collagen IV.The Journal of biological chemistry · 2017Article
- Systematic and Quantitative Assessment of Hydrogen Peroxide Reactivity With Cysteines Across Human Proteomes.Molecular & cellular proteomics : MCP · 2017Article
- Human mitochondrial cytochrome P450 27C1 is localized in skin and preferentially desaturatesThe Journal of biological chemistry · 2017Article
- Heme-thiolate sulfenylation of human cytochrome P450 4A11 functions as a redox switch for catalytic inhibition.The Journal of biological chemistry · 2017Article
- Efficient Microscale Basic Reverse Phase Peptide Fractionation for Global and Targeted Proteomics.Journal of proteome research · 2016Article
- Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.Journal of proteome research · 2016Article
- An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics.Journal of the American Society for Mass Spectrometry · 2015Article
- Global, in situ, site-specific analysis of protein S-sulfenylation.Nature protocols · 2015Article
- Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes.Journal of proteome research · 2015Article
- Proteomic analysis of colon and rectal carcinoma using standard and customized databases.Scientific data · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The identification of peptides and proteins by LC-MS/MS requires the use of bioinformatics. Tools developed in the Tabb Laboratory contribute significant flexibility and discrimination to this process. The Bumbershoot tools (MyriMatch, DirecTag, TagRecon, and Pepitome) enable the identification of peptides represented by MS/MS scans. All of these tools can work directly from instrument capture files of multiple vendors, such as Thermo RAW format, or from standard XML-based formats, such as mzML or mzXML. Peptide identifications are written to mzIdentML or pepXML format. Protein assembly is handled by the IDPicker algorithm. Raw identifications are filtered to a confident set by use of the target-decoy strategy. IDPicker arranges large sets of input files into a hierarchy for reporting, and the software applies a parsimony algorithm to report the smallest possible number of proteins to explain the observed peptides. This protocol details the use of these tools for new users.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.