Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect

Cociorva, Daniel; Tabb, David L.

doi:10.1002/0471250953.bi1304s16

Cited by 213 publications

(200 citation statements)

References 7 publications

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“…No enzyme specificity was considered for any search. SEQUEST results were assembled and filtered using the DTASelect (version 2.0) program (Tabb et al 2002;Cociorva et al 2006). DTASelect 2.0 uses a linear discriminant analysis to dynamically set XCorr and DeltaCN thresholds for the entire data set to achieve a userspecified false-positive rate.…”

Section: Mass Spectrometry Analysismentioning

confidence: 99%

Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing

Lardelli¹,

Thompson²,

Yates³

et al. 2010

RNA

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Eukaryotic pre-mRNA splicing is a complex process requiring the precise timing and action of >100 trans-acting factors. It has been known for some time that the two steps of splicing chemistry require three DEAH-box RNA helicase-like proteins; however, their mechanism of action at these steps has remained elusive. Spliceosomes arrested in vivo at the three helicase checkpoints were purified, and first step-arrested spliceosomes were functionally characterized. We show that the first step of splicing requires a novel ATP-independent conformational change. Prp2p then catalyzes an ATP-dependent rearrangement displacing the SF3a and SF3b complexes from the branchpoint within the spliceosome. We propose a model in which SF3 prevents premature nucleophilic attack of the chemically reactive hydroxyl of the branchpoint adenosine prior to the first transesterification. When the spliceosome attains the proper conformation and upon the function of Prp2p, SF3 is displaced from the branchpoint allowing first step chemistry to occur.

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Section: Mass Spectrometry Analysismentioning

confidence: 99%

Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing

Lardelli¹,

Thompson²,

Yates³

et al. 2010

RNA

Self Cite

160

194

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“…Cold Spring Harbor Laboratory Press on May 12, 2018 -Published by rnajournal.cshlp.org Downloaded from (Tabb et al 2002;Cociorva et al 2006). Filtering criteria for positive protein identifications were the identification of two unique peptides with Xcorr values of 2.0 for plus 1 spectra, 2.2 for plus 2 spectra, and 3.75 for plus 3 spectra.…”

Section: Mass Spectrometrymentioning

confidence: 99%

The zipcode-binding protein ZBP1 influences the subcellular location of the Ro 60-kDa autoantigen and the noncoding Y3 RNA

Sim¹,

Yao²,

Weinberg³

et al. 2011

RNA

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The Ro 60-kDa autoantigen, a ring-shaped RNA-binding protein, traffics between the nucleus and cytoplasm in vertebrate cells. In some vertebrate nuclei, Ro binds misfolded noncoding RNAs and may function in quality control. In the cytoplasm, Ro binds noncoding RNAs called Y RNAs. Y RNA binding blocks a nuclear accumulation signal, retaining Ro in the cytoplasm. Following UV irradiation, this signal becomes accessible, allowing Ro to accumulate in nuclei. To investigate how other cellular components influence the function and subcellular location of Ro, we identified several proteins that copurify with the mouse Ro protein. Here, we report that the zipcode-binding protein ZBP1 influences the subcellular localization of both Ro and the Y3 RNA. Binding of ZBP1 to the Ro/Y3 complex increases after UV irradiation and requires the Y3 RNA. Despite the lack of an identifiable CRM1-dependent export signal, nuclear export of Ro is sensitive to the CRM1 inhibitor leptomycin B. In agreement with a previous report, we find that ZBP1 export is partly dependent on CRM1. Both Ro and Y3 RNA accumulate in nuclei when ZBP1 is depleted. Our data indicate that ZBP1 may function as an adapter to export the Ro/Y3 RNA complex from nuclei.

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“…No enzyme specificity was considered for any search. SEQUEST results were assembled and filtered using the DTASelect (version 2.0) program (Tabb et al, 2002;Cociorva et al, 2007). The false positive rates (5% in this analysis) are estimated by the program from the number and quality of spectral matches to the decoy database.…”

Section: Multidimensional Protein Identification Technology (Mudpit)mentioning

confidence: 99%

dFMRP and Caprin, translational regulators of synaptic plasticity, control the cell cycle at the Drosophila mid-blastula transition

et al. 2010

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SUMMARYThe molecular mechanisms driving the conserved metazoan developmental shift referred to as the mid-blastula transition (MBT) remain mysterious. Typically, cleavage divisions give way to longer asynchronous cell cycles with the acquisition of a gap phase. In Drosophila, rapid synchronous nuclear divisions must pause at the MBT to allow the formation of a cellular blastoderm through a special form of cytokinesis termed cellularization. Drosophila Fragile X mental retardation protein (dFMRP; FMR1), a transcriptspecific translational regulator, is required for cellularization. The role of FMRP has been most extensively studied in the nervous system because the loss of FMRP activity in neurons causes the misexpression of specific mRNAs required for synaptic plasticity, resulting in mental retardation and autism in humans. Here, we show that in the early embryo dFMRP associates specifically with Caprin, another transcript-specific translational regulator implicated in synaptic plasticity, and with eIF4G, a key regulator of translational initiation. dFMRP and Caprin collaborate to control the cell cycle at the MBT by directly mediating the normal repression of maternal Cyclin B mRNA and the activation of zygotic frühstart mRNA. These findings identify two new targets of dFMRP regulation and implicate conserved translational regulatory mechanisms in processes as diverse as learning, memory and early embryonic development.KEY WORDS: Cyclin B, Fragile X syndrome, Frühstart (Z600), Drosophila dFMRP and Caprin, translational regulators of synaptic plasticity, control the cell cycle at the Drosophila

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Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect

Cited by 213 publications

References 7 publications

Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing

Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing

The zipcode-binding protein ZBP1 influences the subcellular location of the Ro 60-kDa autoantigen and the noncoding Y3 RNA

dFMRP and Caprin, translational regulators of synaptic plasticity, control the cell cycle at the Drosophila mid-blastula transition

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