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J. Biol. Chem. 287, 21599-21614. Proteomic analysis of wild-type and mutant huntingtin-associated proteins in mouse brains identifies unique interactions and involvement in protein synthesis. 2012

Culver, B.P., Savas, J.N., Park, S.K., Choi, J.H., Zheng, S., Zeitlin, S.O., Yates, J.R., and Tanese, N.

Notes: These authors analyzed and compared affinity-purified protein complexes from brain homogenates of wild type and huntingtin (Htt) mutant mice by mass spectrometry. Brain tissue from FLAG-tagged wild-type and Htt mice was homogenized in HEPES buffer supplemented with protease inhibitors and RNasin®. After affinity purification, protein complexes were digested using Sequencing-Grade Modified Trypsin and ProteaseMAX™ Trypsin Enhancer prior to mass-spectrometry analysis. (4227)

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5, 163–71. Barley as a green factory for the production of functional Flt3 ligand. 2010

Erlendsson, L.S., Muench, M.O., Hellman, U., Hrafnkelsdóttir, S.M., Jonsson, A., Balmer, Y., Mäntylä, E. and Orvar, B.L.

Notes: The authors explore barley (Hordeum vulgare) as a means of expressing recombinant human Flt3 ligand, which is a growth factor involved in proliferation and differentiation of stem cells and development of various immune cells. As part of their quality control, they performed in-gel proteolytic digestion and mass spectrometry. The recombinant Flt3 ligand was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, followed by Coomassie® blue staining, excision of the protein band, destaining, drying of the gel slice and digestion with Sequencing Grade Modified Trypsin at 30°C overnight prior to mass spectrometry. To test biological activity, the authors treated human acute myeloid leukemia cells with Flt3 expressed in barley or a commercial source of Flt3 then measured cell proliferation using the CellTiter 96® AQueous One Solution Cell Proliferation Assay. (4352)

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Cancer Res. 67, 3239–3253. Gene and protein expression profiling of human ovarian cancer cells treated with the heat shock protein 90 inhibitor 17-allylamino-17-demethoxygeldanamycin. 2007

Maloney, A., Clarke, P.A., Naaby-Hansen, S., Stein, R., Koopman, J.O., Akpan, A., Yang, A., Zvelebil, M., Cramer, R., Stimson, L., Aherne, W., Banerji, U., Judson, I., Sharp, S., Powers, M., Debilly, E., Salmons, J., Walton, M., Burlingame, A., Waterfield, M. and Workman, P.

Notes: For protein expression profiling of cancer cells treated with 17-allylamino-17-demethoxygeldanamycin (17AAG), a compound with known antitumor activity, lysates were prepared from A2780 cells, a human ovarian adenocarcinoma cell line, and subjected to two-dimensional protein analysis. The spots that varied in intensity in 17AAG-treated cells when compared to control cells were excised and the protein gel slice was reduced, alkylated and in-gel digested using Sequencing Grade Modified Trypsin. (3601)

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J. Biol. Chem. 281, 2114–9. On the mechanism of mitochondrial uncoupling protein 1 function. 2006

Breen, E.P., Gouin, S.G., Murphy, A.F., Haines, L.R., Jackson, A.M., Pearson, T.W., Murphy, P.V. and Porter, R.K.

Notes: Native uncoupling protein 1 (UCP 1) was purified from rat mitochondria by hydroxyapatite chromatography, separated by SDS-PAGE and the band stained with Coomassie® Brilliant Blue G-250. The 30–33kDa UCP 1 band was excised, destained, dehydrated, reduced and alkylated. The protein was then digested overnight with 40µl of 20ng/µl Sequencing Grade Modified Trypsin. The resulting peptides were extracted and analyzed by mass spectrometry. (3331)

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FEBS J. 273, 568-576. Prohibitin attenuates insulin-stimulated glucose and fatty acid oxidation in adipose tissue by inhibition of pyruvate carboxylase 2006

Vessal, M., Mishra, S., Moulik, S. and Murphy, L.J.

Notes: Prohibitin (PHB-1) is a multifunctional protein that is located in the mitochondria and plasma membrane and is secreted by adipocytes. Previously PHB-1 was shown to function as a chaperone protein for newly made subunits of mitochondrial respiratory enzymes. This paper describes a role for exogenous PHB-1 in the modulation of insulin-stimulated glucose and fatty acid oxidation. To identify PHB-1 binding partners, His-tagged PHB-1 was incubated with adipocytes. Membranes were solubilized and proteins separated by electrophoresis. Silver-stained bands were excised and destained before treatment with sequencing grade Trypsin. The tryptic peptides were analyzed by HPLC and Mass Spectrometry. (3634)

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Eukaryot. Cell 5, 1990–2000. The Tetrahymena thermophila phagosome proteome. 2006

Jacobs, M.E., DeSouza, L.V., Samaranayake, H., Pearlman, R.E., Siu, K.W., and Klobutcher, L.A.

Notes: The authors wanted to learn more about the proteins that comprise the Tetrahymena
phagosome proteome. Proteins were isolated from phagosome preparations, denatured by adding 5mM dithiothreitol and heating to 60°C for 1 hour. The samples were cooled to room temperature and alkylated by incubation with 10mM iodoacetamide for 1 hour protected from light. Sequencing Grade Modified Trypsin, at a 1:20 concentration (wt/wt) with an equal volume of 50mM ammonium bicarbonate, was added to the sample and incubated overnight at 37°C. Each sample was analyzed by two-dimensional liquid chromatography–tandem mass spectrometry (LC-MS/MS). Whole-cell Tetrahymena DNA was isolated using the Wizard® Genomic DNA Purification Kit protocol for isolating genomic DNA from plant tissue omitting the use of liquid nitrogen with mortar and pestle. The isolated DNA was then used for restriction digestion, ligation and sequencing. (3680)

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J. Biol. Chem. 280, 18498–503. Asparagine deamidation perturbs antigen presentation on class II major histocompatibility complex molecules. 2005

Moss, C.X., Matthews, S.P., Lamont, D.J., and Watts, C.

Notes: The authors used tetanus toxin C fragment (TTCF) antigen as a model to show that asparagine deamidation interferes with processing by asparagine endopeptidase (AEP) and can influence antigen presentation in T cells. The level of iso-aspartic acid, a product of Asn deamidation, in aged TTCF was quantitated using the IsoQuant® Isoaspartate Detection Kit. Asn deamidation was confirmed by tryptic digestion using Sequencing Grade Modified Trypsin, followed by MALDI-TOF mass spectrometry. The observed sizes of two tryptic peptides were one mass unit larger than expected, consistent with the fact that Asn deamidation leads to a gain of one mass unit. (3664)

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Infect. Immun. 73, 4853–63. Surfaceome of Leptospira spp. 2005

Cullen, P.A., Xu, X., Matsunaga, J., Sanchez, Y., Ko, A.I., Haake, D.A., and Adler, B.

Notes: To identify proteins expressed on the cell surface of various strains of Leptospira, the authors labeled intact Leptospira cells with biotin, solubilized the cells with Triton® X-100, then captured the biotinylated proteins using the SoftLink™ Soft Release Avidin Resin. The captured products were analyzed by one- and two-dimensional gel electrophoresis. The spots were excised and washed with 50mM ammonium bicarbonate /100% acetonitrile. The gel pieces were then dried, rehydrated in a solution containing 12ng of Sequencing Grade Modified Trypsin, and incubated in 50mM ammonium bicarbonate overnight at 37°C. The proteins were concentrated, desalted and subjected to MALDI-TOF mass spectrometry to identify the individual proteins of the Leptospira surfaceome. (3661)

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J. Biol. Chem. 279(21), 22228-35. Identification of a novel PDX-1 binding site in the human insulin gene enhancer. 2004

Le Lay, J., Matsuoka, T.A., Henderson, E. and Stein, R.

Notes: The GG2 element located upstream of the human insulin gene was mutated and cloned into a firefly luciferase construct. Two pancreatic mouse cell lines, ßTC-3 and Min6, were co-transfected with the various GG2 luciferase vectors using phRL-TK Vector as a normalization control. Luciferase expression was then assessed using the Dual-Luciferase® Reporter Assay System. Three factors known to affect insulin gene expression were transcribed and translated using the TNT® Coupled Reticulocyte Lysate System. The proteins were then used in a gel-shift assay with several DNA element oligos. A 38-40 kDa protein that bound to the GG2 element was identified.  This protein was isolated by DNA affinity chromatography, run on a SDS-PAGE gel and digested with 0.01µg/µl Sequencing Grade Modified Trypsin. Digestion products were then analyzed by Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and TOF/TOF tandem mass spectrometry. (3116)

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J. Gen. Virol. 85(Pt 7), 2111-21. Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus. 2004

Jiang, D. and Ghabrial, S.A.

Notes: The authors cloned and sequenced the dsRNA from Penicillium chrysogenum virus (PcV) and analyzed the gene products of the segmented virus. After reverse transcription followed by PCR to confirm the 5’ and 3’ ends of the dsRNA segments, RT-PCR was used to amplify the complete cDNAs for the four viral segments.The products were cloned into pGEM®-T Vector after A-tailing. To confirm the ORFs predicted for each of the four segments, the cDNAs were added to TNT® T7 Quick Coupled Transcription/Translation System reactions that included radiolabeled methionine. The resulting proteins ranged in size from 94-128 kDa and were separated on an 8% SDS-PAGE gel and analyzed by autoradiography. Gradient-purified PcV virions were digested with Sequencing Grade Modified Trypsin at 37°C for 18 hours and the digestion products were separated by reverse-phase HPLC on a C18 column. Two highly resolved peptides were selected for amino acid sequencing by automated Edman degradation. (3089)

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J. Biol. Chem. 279, 9321–9330. Nek9, a novel FACT-associated protein, modulates interphase progression. 2004

Tan B.C.M. and Lee, S.C.

Notes: Promega’s Sequencing Grade Modified Trypsin was used to perform in-gel digests of Coomassie® blue-stained proteins that associated with Nek-9 in Nek-9 immunoprecipitates from HeLa cell extracts.  Digestions were performed on dried 7.5 or 10% polyacrylamide gel slices and peptide fragments were analyzed by Electrospray mass spectrometry. The two analyzed proteins were sequenced and determined to be SSRP1 and FACT140.  (3057)

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J. Biol. Chem. 274, 10618-10624. Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1. 1999

Desterro, J.M.P., Rodriguez, M.S., Kemp, G.D., Hay, R.T.

Notes: To clone the SUMO coupling enzyme, the SUMO peptide was attached to a column, and HeLa extracts were run through the column. Eluted proteins were separated by SDS-PAGE, stained and the appropriate bands were cut from the gel. The gel bands were then digested with an in-gel trypsinization protocol using the Sequencing-Grade Modified Trypsin. The resultant bands were separated by HPLC, sequenced and the full sequences were obtained from the ATCC database. The SUMO-1 Activating enzyme was found to contain two subunits, SAE-1 (38kDa) and SAE-2 (72kDa). These subunites were expressed in vitro using the TNT® Coupled Wheat Germ Extract System and found to interact. (1226)

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J. Biol. Chem. 273, 26078-26086. Cloning and disruption of caPLB1, a phopholipase B gene involved in the pathogenicity of Candida albicans. 1998

Leidich, S.D., Ibrahim, A.S., Fu, Y., Koul, A., Jessup, C., Vitullo, J., Fonzi, W., Mirbod, F., Nakashima, S., Nozawa, Y., Ghannoum, M.A.

Notes: The Sequencing Grade Modified Trypsin was used to digest a protein isolated from a gel slice. The protein was isolated by a referenced method. The isolated protein was dehydrated and then digested overnight at 37°C in 75µl of 200mM NH4HCO3 containing 2.5µg of the modified trypsin. The resulting peptides were recovered by extraction with 60% acetonitrile and 0.1% trifluoroacetic acid and subsequent HPLC to isolate individual fragments for sequencing. (0824)

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J. Biol. Chem. 273, 673-676. Evidence of viral capsid dynamics using limited proteolysis and mass spectrometry. 1998

Bothner, B., Dong, X.F., Bibbs, L., Johnson, J.E., Siuzdak, G.

Notes: Flock House Virus (1mg/ml) was digested with Sequencing Grade Modified Trypsin in a reaction with a 1:3000 enzyme to virus ratio in a 10-20µl volume. At each time point, 0.5µl of the reaction was removed and placed on a MALDI analysis plate. The resulting cleavage products were treated with the exprotease carboxypeptidase YY to obtain c-terminal sequence information. (1389)

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Biol. Reprod. 59, 743-752. Large-format, two-dimensional polyacrylamide gel electrophoresis of ovine periimplantation uterine luminal fluid proteins: Identification of aldose reductase, cytoplasmic actin and transferrin as conceptus-synthesized proteins 1998

Lee, R.S.F., Wheeler, T.T., Peterson, A.J.

Notes: The Sequencing Grade Modified Trypsin was used to digest a protein on a nitrocellulose membrane. Digestion prior to protein sequencing are referenced. (0815)

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J. Biol. Chem. 273, 21585-21593. Purification and characterization of human NTH1, a homolog of Eschericia coli endonuclease III: Direct identification of Lys-212 as the active nucleophilic residue. 1998

Ikeda, S., Biswas, T., Roy, R., Izumi, T., Boldogh, I., Kurosky, A., Seki, S., Mitra, S.

Notes: Complexes of the protein NTH1 and an oligonucleotide were covalently crosslinked. The complex (12nmol) was resolved by ion-exchange chromatography and dialyzed against 50mM NH4HCO3. The complex was boiled for 5 minutes and digested with 20µg each of Sequencing Grade Modified Trypsin and Sequencing Grade Endoproteinase Glu-C (discontinued) at 37°C for 2 hours, and the digest was repeated for an additional 48 hours. The resulting peptides were resolved by HPLC and peptides sequenced. (0991)

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J. Biol. Chem. 273, 26014-26025. RGSZ1, a GZ-selective RGS protein in brain: Structure, membrane association, regulation by GalphaZ, phosphorylation and relationship to a GZ GTPase-activating protein subfamily. 1998

Wang, J., Ducret, A, Tu, Y., Kozasa, T., Aebersold, R., Rose, E.

Notes: The Sequencing Grade Modified Trypsin was used to digest proteins directly on nitrocellulose by referenced methods. Briefly, nitrocellulose bands were excised, cut in 1mm squares, and incubated for 18 hours at 37°C in 15-20µl of 15mM N-ethylmorpholine, 5mM acetic acid, 1% Zwittergent 3-16 that contained 1µg of Sequencing Grade Modified Trypsin. (0201)

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J. Biol. Chem. 272, 27218-27223. cDNA cloning, tissue distribution, and identification of the catalytic triad of monoglyceride lipase. Evolutionary relationship to esterases, lysophospholipases, and haloperoxidases. 1997

Karlsson, M., Contreras, J.A., Hellman, U., Tornqvist, H., Holm, C.

Notes: Tryptic peptides, produced with Sequencing Grade Modified Trypsin, of the purified lipase were used to generate primers for RT-PCR. The largest amplimer was purified and used to screen a lambda gt11 library. The isolated 303 amino acid clone and site-specific mutants were put into the pCI-neo Mammalian Expression Vector and expressed in COS cells. The transiently expressed proteins were assayed for esterase and lipase activity. (0960)

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J. Biol. Chem. 272, 13743-13749. Isolation and characterization of a new member of the scavenger receptor superfamily, glycoprotein-340 (gp-340) as a lung surfactant protein-D binding molecule. 1997

Holmskov, U., Lawson, P., Teisner, B., Tornoe, I., Willis, A.C., Morgan, C., Koch, C., Reid, K.B.

Notes: Sequencing Grade Modified Trypsin was used to obtain sequence data from excised gel bands. (1010)

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J. Biol. Chem. 272, 14850-14859. The type II transforming growth factor-β receptor autophosphorylates not only on serine and threonine but also on tyrosine residues. 1997

Lawler, S., Feng, X.H., Chen, R.H., Maruoka, E.M., Turck, C.W., Griswold-Prenner, I., Derynck, R.

Notes: The authors used Sequencing Grade Modified Trypsin for peptide mapping. (0847)

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J. Biol. Chem. 272, 21793-21802. Topography of the photosystem I core proteins of the cyanobacterium Synechocystis sp. PCC 6803. 1997

Sun, J., Xu, Q., Chitnis, V.P., Jin, P., Chitnis, P.R.

Notes: The authors used Sequencing Grade Modified Trypsin for analysis of membrane topology of proteins (PsaA and PsaB) of photosystem I. (2192)

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J. Biol. Chem. 271, 7745-7751. Characterization of distinct nuclear and mitochondrial forms of human deoxyuridine triphosphate nucleotidohydrolase. 1996

Ladner, R.D., NcNulty, D.E., Carr, S.A., Roberts, G.D., and Caradonna, S.J.

Notes: Sequencing Grade Modified Trypsin was used to generate tryptic peptides from an SDS-PAGE gel slice. The gel slice was subjected to reduction and alkylation prior to digestion. Extensive detail of the procedure is given. (0869)

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