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A guided tour of the Trans-Proteomic Pipeline

A guided tour of the Trans-Proteomic Pipeline,10.1002/pmic.200900375,Proteomics,Eric W. Deutsch,Luis Mendoza,David Shteynberg,Terry Farrah,Henry Lam,N

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A guided tour of the Trans-Proteomic Pipeline   (Citations: 12)
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Eric W. Deutsch, Luis Mendoza, David Shteynberg, Terry Farrah, Henry Lam, Natalie Tasman, Zhi Sun, Erik Nilsson, Brian Pratt, Bryan Prazen, Jimmy K. Eng, Daniel B. Martinhttp://academic.research.microsoft.com/io.ashx?type=5&id=34281797&selfId1=0&selfId2=0&maxNumber=12&query=
Journal: Proteomics , vol. 10, no. 6, pp. 1150-1159, 2010
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    • ...Concentrated urinary protein (W4 and W5) were run in triplicate on fresh SDS-PAGE gels. The gels were stained with Coomassie Blue and the ∼20 kDa bands of interest were excised and then subjected to in-gel digestion. Briefly, the gel pieces were de-stained and proteins within gel pieces were reduced with 10 mM dithiothreitol, alkylated with 55 mM iodoacetamide, washed with 50 mM ammonium bicarbonate, pH 7.9 and then digested for 14 hours at 37°C with trypsin (1∶20) before being extracted into a 60% acetonitrile, 0.1% formic acid solution.. The digested protein was then subjected to reverse phase LC-MS/MS using an 1100 Series HPLC (Agilent Technologies, Boblingen, Germany) coupled with a QStar Elite Quadrupole – Time Of Flight Mass Spectrometer (Applied Biosystems, Foster City, CA, USA). The resulting peptide mass spectra were analysed using the MASCOT search algorithm against the Ludwig Non-Redundant database and subsequently validated using the Trans Proteomic Pipeline (TPP) and the Peptide Prophet tool ...

    Tony J. Parker, et al. A Fragment of the LG3 Peptide of Endorepellin Is Present in the Urine ...

    • ...) ...

    Ting-Lei Gu, et al. Survey of Activated FLT3 Signaling in Leukemia

    • ... In brief, samples were collected with an LTQ – Orbitrap hybrid mass spectrometer, using a top-ten method, a dynamic exclusion repeat count of 1, and a repeat duration of 30 sec. MS spectra were collected in the Orbitrap component of the mass spectrometer and MS/MS spectra was collected in the LTQ. Sequest (Thermo Fisher Scientific) searches were done against the NCBI human database released on July 02, 2009, (containing 37,391 proteins), allowing for tyrosine phosphorylation (Y+80) and oxidized methionine (M+16) as differential modifications. The PeptideProphet probability threshold was chosen to give a false positive rate of 5% for the peptide identifications...

    Ting-Lei Gu, et al. Survey of Tyrosine Kinase Signaling Reveals ROS Kinase Fusions in Huma...

    • ...MS/MS spectra were converted into MGF peak list files using tools in the Trans-Proteome Pipeline ...

    Juan D. Chavez, et al. Quantitative Proteomic and Interaction Network Analysis of Cisplatin R...

    • ...All peptide identifications across the 5 samples of each disease group (PDAC, MCP and SCP) were assembled into a single pepXML file ...

    Sheng Pan, et al. Proteomics Portrait of Archival Lesions of Chronic Pancreatitis

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