rapigest Waters Corporation Search Results


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  • 99
    Waters Corporation rapigest
    Workflow for large-scale quantitative phosphoproteomics of synaptosomes. Synaptosomal proteins were extracted by lysis of synaptosomes and acetone precipitation. The protein pellets were dried, resuspended in 1% <t>RapiGest</t> buffer and digested by trypsin. Peptides were labeled with heavy and light dimethyl labeling ( Boersema et al., 2009 ). To obtain pair-wise comparisons between the three conditions, samples were mixed with a ratio of 1:1. The mixed peptides were separated by strong cation exchange (SCX) chromatography, with the eluate being divided into 12 fractions. Phosphopeptides in each fraction were separately enriched by TiO 2 microbeads ( Larsen et al., 2005 ) and subjected for mass spectrometry analysis. DOI: http://dx.doi.org/10.7554/eLife.14530.005
    Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 99/100, based on 122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 122 article reviews
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    rapigest - by Bioz Stars, 2020-02
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    99
    Waters Corporation rapigest sf
    MALDI MS spectra of ungroomed fingermarks digested with and without <t>RapiGest</t> SF. The proteolytic solution was applied by spray-coat. (a) MALDI MS spectrum generated using a 20 μg/mL trypsin solution containing. RapiGest SF at 0.1% concentration; (b) MALDI MS spectrum generated using a 20 μg/mL trypsin solution with no RapiGest SF. Panels (c) and (d) display a zoom in the regions between 1500-2400 m / z for the spectra in panels (a) and (b) respectively
    Rapigest Sf, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 99/100, based on 1045 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rapigest sf/product/Waters Corporation
    Average 99 stars, based on 1045 article reviews
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    99
    Waters Corporation rapigest sf reagent
    MALDI MS spectra of ungroomed fingermarks digested with and without <t>RapiGest</t> SF. The proteolytic solution was applied by spray-coat. (a) MALDI MS spectrum generated using a 20 μg/mL trypsin solution containing. RapiGest SF at 0.1% concentration; (b) MALDI MS spectrum generated using a 20 μg/mL trypsin solution with no RapiGest SF. Panels (c) and (d) display a zoom in the regions between 1500-2400 m / z for the spectra in panels (a) and (b) respectively
    Rapigest Sf Reagent, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 99/100, based on 153 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rapigest sf reagent/product/Waters Corporation
    Average 99 stars, based on 153 article reviews
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    rapigest sf reagent - by Bioz Stars, 2020-02
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    80
    Waters Corporation acid labile surfactant rapigest
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Acid Labile Surfactant Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 80/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Waters Corporation rapigest anionic surfactant
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Rapigest Anionic Surfactant, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 79/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Waters Corporation digestion enhancer rapigest
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Digestion Enhancer Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 89/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Waters Corporation acid cleavable surfactant rapigest
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Acid Cleavable Surfactant Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 89/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Waters Corporation rapigest sf solution
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Rapigest Sf Solution, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 99/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Waters Corporation rapigest bottle
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Rapigest Bottle, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Waters Corporation digestion buffer
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Digestion Buffer, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 99/100, based on 49 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    81
    Waters Corporation rapigest buffer
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Rapigest Buffer, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 81/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Waters Corporation rapidgest
    Membrane protein identifications comparing 1% SDC, 0.15% <t>RapiGest</t> SF, and 60% methanol solubilization.
    Rapidgest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 80/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 80 stars, based on 11 article reviews
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    91
    Waters Corporation detergent rapigest
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Detergent Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 91/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    75
    Waters Corporation rapigest sf protocol
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Rapigest Sf Protocol, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 75/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Waters Corporation rapigest sf powder
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Rapigest Sf Powder, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 80/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Waters Corporation rapigest rg
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Rapigest Rg, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Waters Corporation rg surfactant
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Rg Surfactant, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 78/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Waters Corporation rapidgest sf
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Rapidgest Sf, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Waters Corporation rapigest sm
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Rapigest Sm, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 77/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Waters Corporation acid labile detergent rapigest
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Acid Labile Detergent Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Waters Corporation buffer b
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Buffer B, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 99/100, based on 267 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Waters Corporation rapigest sf protein solubilization reagent
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Rapigest Sf Protein Solubilization Reagent, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 77/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    82
    Waters Corporation cleavable detergent rapigest sf surfactant
    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.
    Cleavable Detergent Rapigest Sf Surfactant, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 82/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    Waters Corporation acid degradable detergent rapigest
    In solution digestion leads to stable results in label-free proteomics. ( a ) The distribution maximum of coefficients of variation (CV) of the selected protocols varies between 0.075 and 0.2. CV values obtained for protocol triplicates are shown as two-dimensional distribution histograms (‘violin plots’). Quantification in DDA experiments was consistent over the dynamic range, as CV values only marginally changed when filtering by peptides according to their abundance (80%, 60%, 40% or 20%). CV likelihood maxima of all protocols were below 20%, while RapidACN led to the most reproducible results (CV = 7%) (n = 3). ( b ) Stability in a quantification experiment is improved by data-independent acquisition. CV values for the same set of peptides measured with SWATH and DDA using the <t>RapiGest</t> protocol, as shown in a two-dimensional distribution histogram. Whereas there was a high signal variation in DDA acquisition, the variation could be largely reduced in SWATH acquisition. ( c ) In solution protocols yield the highest number of peptides suitable for label-free quantification. The number of peptides with a CV
    Acid Degradable Detergent Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 76/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Waters Corporation rapigest sf surfacant
    In solution digestion leads to stable results in label-free proteomics. ( a ) The distribution maximum of coefficients of variation (CV) of the selected protocols varies between 0.075 and 0.2. CV values obtained for protocol triplicates are shown as two-dimensional distribution histograms (‘violin plots’). Quantification in DDA experiments was consistent over the dynamic range, as CV values only marginally changed when filtering by peptides according to their abundance (80%, 60%, 40% or 20%). CV likelihood maxima of all protocols were below 20%, while RapidACN led to the most reproducible results (CV = 7%) (n = 3). ( b ) Stability in a quantification experiment is improved by data-independent acquisition. CV values for the same set of peptides measured with SWATH and DDA using the <t>RapiGest</t> protocol, as shown in a two-dimensional distribution histogram. Whereas there was a high signal variation in DDA acquisition, the variation could be largely reduced in SWATH acquisition. ( c ) In solution protocols yield the highest number of peptides suitable for label-free quantification. The number of peptides with a CV
    Rapigest Sf Surfacant, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rapigest sf surfacant/product/Waters Corporation
    Average 85 stars, based on 3 article reviews
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    Waters Corporation rapigest acid cleavable detergent
    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.
    Rapigest Acid Cleavable Detergent, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 80/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.
    In Solution Urea Rapigest, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.
    Rapigest Sf Rsf Detergent, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.
    Acid Labile Surfactant, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 99/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.
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    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.
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    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with <t>Rapigest,</t> trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.
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    Image Search Results


    Workflow for large-scale quantitative phosphoproteomics of synaptosomes. Synaptosomal proteins were extracted by lysis of synaptosomes and acetone precipitation. The protein pellets were dried, resuspended in 1% RapiGest buffer and digested by trypsin. Peptides were labeled with heavy and light dimethyl labeling ( Boersema et al., 2009 ). To obtain pair-wise comparisons between the three conditions, samples were mixed with a ratio of 1:1. The mixed peptides were separated by strong cation exchange (SCX) chromatography, with the eluate being divided into 12 fractions. Phosphopeptides in each fraction were separately enriched by TiO 2 microbeads ( Larsen et al., 2005 ) and subjected for mass spectrometry analysis. DOI: http://dx.doi.org/10.7554/eLife.14530.005

    Journal: eLife

    Article Title: Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis

    doi: 10.7554/eLife.14530

    Figure Lengend Snippet: Workflow for large-scale quantitative phosphoproteomics of synaptosomes. Synaptosomal proteins were extracted by lysis of synaptosomes and acetone precipitation. The protein pellets were dried, resuspended in 1% RapiGest buffer and digested by trypsin. Peptides were labeled with heavy and light dimethyl labeling ( Boersema et al., 2009 ). To obtain pair-wise comparisons between the three conditions, samples were mixed with a ratio of 1:1. The mixed peptides were separated by strong cation exchange (SCX) chromatography, with the eluate being divided into 12 fractions. Phosphopeptides in each fraction were separately enriched by TiO 2 microbeads ( Larsen et al., 2005 ) and subjected for mass spectrometry analysis. DOI: http://dx.doi.org/10.7554/eLife.14530.005

    Article Snippet: The remaining chemicals and reagents were purchased from individual supplier: sequencing grade modified trypsin (Promega, Madison, WI), formaldehyde (D2, 98%, CD2 O, Cambridge Isotope Laboratories, Andover, MA), ammonium hydroxide (NH4 OH, BAKER ANALYZED, Deventer, the Netherlands), PMSF (AppliChem, Darmstadt, Germany), 2-Amino-2-hydroxymethyl-propane-1,3-diol (Tris, VWR International, Leuven, Belgium), Rapigest (Waters, Milford, MA), titanium dioxide beads (TiO2 , GL Sciences Inc., Tokyo, Japan).

    Techniques: Lysis, Labeling, Chromatography, Mass Spectrometry

    MALDI MS spectra of ungroomed fingermarks digested with and without RapiGest SF. The proteolytic solution was applied by spray-coat. (a) MALDI MS spectrum generated using a 20 μg/mL trypsin solution containing. RapiGest SF at 0.1% concentration; (b) MALDI MS spectrum generated using a 20 μg/mL trypsin solution with no RapiGest SF. Panels (c) and (d) display a zoom in the regions between 1500-2400 m / z for the spectra in panels (a) and (b) respectively

    Journal: Journal of the American Society for Mass Spectrometry

    Article Title: Alternative Surfactants for Improved Efficiency of In Situ Tryptic Proteolysis of Fingermarks

    doi: 10.1007/s13361-015-1140-z

    Figure Lengend Snippet: MALDI MS spectra of ungroomed fingermarks digested with and without RapiGest SF. The proteolytic solution was applied by spray-coat. (a) MALDI MS spectrum generated using a 20 μg/mL trypsin solution containing. RapiGest SF at 0.1% concentration; (b) MALDI MS spectrum generated using a 20 μg/mL trypsin solution with no RapiGest SF. Panels (c) and (d) display a zoom in the regions between 1500-2400 m / z for the spectra in panels (a) and (b) respectively

    Article Snippet: In particular, there are peptide peaks between m/z 1000 and 2000 Da, present in the RapiGest SF generated peptide profile that are absent in the tryptic digest alone.

    Techniques: Mass Spectrometry, Generated, Concentration Assay

    (A‐C) Quality control and label free quantitative analysis comparison between GnHCl, RapiGest™, GnHCl and Rapigest™, and GnHCl followed by RapiGest™ using Progenesis QI software. The variation in percentage of all peptide ions (A), number of peptides (B) and proteins (C) was presented for each extraction method. (D) PCA plot of all methods, GnHCl followed by RapiGest™ samples grouped closer together. (E‐H) Significantly abundant proteins (fold change > 2 and p

    Journal: Proteomics

    Article Title: Comparison between chaotropic and detergent‐based sample preparation workflow in tendon for mass spectrometry analysis

    doi: 10.1002/pmic.201700018

    Figure Lengend Snippet: (A‐C) Quality control and label free quantitative analysis comparison between GnHCl, RapiGest™, GnHCl and Rapigest™, and GnHCl followed by RapiGest™ using Progenesis QI software. The variation in percentage of all peptide ions (A), number of peptides (B) and proteins (C) was presented for each extraction method. (D) PCA plot of all methods, GnHCl followed by RapiGest™ samples grouped closer together. (E‐H) Significantly abundant proteins (fold change > 2 and p

    Article Snippet: Another extraction technique that has recently been used in tendon proteomic studies is the surfactant RapiGest™ (Waters) , , which was shown to increase protein identification , .

    Techniques: Software

    (A) 1D SDS‐PAGE analysis of the protein profiles of GnHCl, RapiGest™, GnHCl and RapiGest™, and GnHCl followed by RapiGest™ extraction methods. (B) Protein concentration yielded with the different extraction methods. Values are mean and error bars represent SD, * p

    Journal: Proteomics

    Article Title: Comparison between chaotropic and detergent‐based sample preparation workflow in tendon for mass spectrometry analysis

    doi: 10.1002/pmic.201700018

    Figure Lengend Snippet: (A) 1D SDS‐PAGE analysis of the protein profiles of GnHCl, RapiGest™, GnHCl and RapiGest™, and GnHCl followed by RapiGest™ extraction methods. (B) Protein concentration yielded with the different extraction methods. Values are mean and error bars represent SD, * p

    Article Snippet: Another extraction technique that has recently been used in tendon proteomic studies is the surfactant RapiGest™ (Waters) , , which was shown to increase protein identification , .

    Techniques: SDS Page, Protein Concentration

    (A) Venn diagram of GnHCl, urea, and RapiGest™ extraction methods. Total number, common, and unique proteins identified following MS. All identified proteins in each method are can be found in Supporting Information Table 1. (B) Schematic workflow of follow up experiment using the chaotropic agent GnHCl, the surfactant RapiGest™, a combination of GnHCl and RapiGest™, and a combination of GnHCl followed by RapiGest™ extraction on the insoluble pellet.

    Journal: Proteomics

    Article Title: Comparison between chaotropic and detergent‐based sample preparation workflow in tendon for mass spectrometry analysis

    doi: 10.1002/pmic.201700018

    Figure Lengend Snippet: (A) Venn diagram of GnHCl, urea, and RapiGest™ extraction methods. Total number, common, and unique proteins identified following MS. All identified proteins in each method are can be found in Supporting Information Table 1. (B) Schematic workflow of follow up experiment using the chaotropic agent GnHCl, the surfactant RapiGest™, a combination of GnHCl and RapiGest™, and a combination of GnHCl followed by RapiGest™ extraction on the insoluble pellet.

    Article Snippet: Another extraction technique that has recently been used in tendon proteomic studies is the surfactant RapiGest™ (Waters) , , which was shown to increase protein identification , .

    Techniques: Mass Spectrometry

    (A) The volcano plot demonstrates all differentially abundant proteins between GnHCl and GnHCl followed by RapiGest™ (fold change > 2 and p

    Journal: Proteomics

    Article Title: Comparison between chaotropic and detergent‐based sample preparation workflow in tendon for mass spectrometry analysis

    doi: 10.1002/pmic.201700018

    Figure Lengend Snippet: (A) The volcano plot demonstrates all differentially abundant proteins between GnHCl and GnHCl followed by RapiGest™ (fold change > 2 and p

    Article Snippet: Another extraction technique that has recently been used in tendon proteomic studies is the surfactant RapiGest™ (Waters) , , which was shown to increase protein identification , .

    Techniques:

    Membrane protein identifications comparing 1% SDC, 0.15% RapiGest SF, and 60% methanol solubilization.

    Journal: Journal of proteome research

    Article Title: Extraction, Enrichment, Solubilization, and Digestion Techniques for Membrane Proteomics

    doi: 10.1021/acs.jproteome.5b01122

    Figure Lengend Snippet: Membrane protein identifications comparing 1% SDC, 0.15% RapiGest SF, and 60% methanol solubilization.

    Article Snippet: Therefore, most membrane protein solubilization techniques utilize detergents (0.1–10% w/w) to mimic the lipid membrane, , , , but the performance of detergents is variable., , , Also, the detergent must be removed prior to analysis because it can affect chromatographic separation and suppress ionization in the MS. , , , , , The acid-labile surfactant RapiGest SF (Waters) has been shown to greatly enhance membrane protein solubility and allow 100% enzyme digestion at surfactant concentrations of 0.1% and can be easily removed prior to MS analysis via acidification.

    Techniques:

    Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with Rapigest, trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: mTORC1 promotes T-bet phosphorylation to regulate Th1 differentiation

    doi: 10.4049/jimmunol.1601078

    Figure Lengend Snippet: Three of the novel T-bet phosphorylations are mTORC1 dependent A, Wild-type C57/BL6 (WT) or Rheb fl/fl CD4+ Cre (Rheb KO) CD4+ T cells were purified from spleens and lymph nodes of 6–12 week old mice and activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in Th1 polarizing culture conditions. Activated T cells were harvested, lysed with Rapigest, trypsin digested and analyzed by LC-MRM-MS. AUC on the y axis is area under the curve – measure of phosphorylated peptide abundance. Data are from one of 2 experiments with T cells from individual mice. B, CD4+ T cells were purified from spleens and lymph nodes of WT mice and activated for 48 hours as in A in the presence or absence of 500 nM Rapamycin (WT or WT Rapamycin), prepared and analyzed as in A. Data are from one of 3 experiments with T cells from individual mice. C, Schematic of T-bet with phosphorylations shown as circles with numbers. Gray circles are the phosphorylations sites. White circles show phosphorylations that are mTORC1 dependent. Data are from one of 5 experiments with T cells from individual mice.

    Article Snippet: Rapigest detergent was purchased from Waters.

    Techniques: Purification, Mouse Assay, Mass Spectrometry

    In solution digestion leads to stable results in label-free proteomics. ( a ) The distribution maximum of coefficients of variation (CV) of the selected protocols varies between 0.075 and 0.2. CV values obtained for protocol triplicates are shown as two-dimensional distribution histograms (‘violin plots’). Quantification in DDA experiments was consistent over the dynamic range, as CV values only marginally changed when filtering by peptides according to their abundance (80%, 60%, 40% or 20%). CV likelihood maxima of all protocols were below 20%, while RapidACN led to the most reproducible results (CV = 7%) (n = 3). ( b ) Stability in a quantification experiment is improved by data-independent acquisition. CV values for the same set of peptides measured with SWATH and DDA using the RapiGest protocol, as shown in a two-dimensional distribution histogram. Whereas there was a high signal variation in DDA acquisition, the variation could be largely reduced in SWATH acquisition. ( c ) In solution protocols yield the highest number of peptides suitable for label-free quantification. The number of peptides with a CV

    Journal: F1000Research

    Article Title: The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

    doi: 10.12688/f1000research.2-272.v2

    Figure Lengend Snippet: In solution digestion leads to stable results in label-free proteomics. ( a ) The distribution maximum of coefficients of variation (CV) of the selected protocols varies between 0.075 and 0.2. CV values obtained for protocol triplicates are shown as two-dimensional distribution histograms (‘violin plots’). Quantification in DDA experiments was consistent over the dynamic range, as CV values only marginally changed when filtering by peptides according to their abundance (80%, 60%, 40% or 20%). CV likelihood maxima of all protocols were below 20%, while RapidACN led to the most reproducible results (CV = 7%) (n = 3). ( b ) Stability in a quantification experiment is improved by data-independent acquisition. CV values for the same set of peptides measured with SWATH and DDA using the RapiGest protocol, as shown in a two-dimensional distribution histogram. Whereas there was a high signal variation in DDA acquisition, the variation could be largely reduced in SWATH acquisition. ( c ) In solution protocols yield the highest number of peptides suitable for label-free quantification. The number of peptides with a CV

    Article Snippet: The first protocol is based on the proprietary, acid degradable detergent RapiGest (Waters ), included in a protocol derived from Von der Haaret al. .

    Techniques:

    Protocols cover cellular compartments differently. ( a ) RapiGest and eFASP cover a unique space in the proteome. Identified proteins were visualised in a Venn diagram, excluding the in gel protocols. The RapiGest procedure yielded most unique IDs, followed by eFASP and RapidACN (n = 3). ( b ) SDS-containing protocols are best suited for the extraction of membrane proteins. For the analysis of annotated functions in each protocol, selected GO terms were expressed as percentages of identified proteins. While cytosolic proteins were not enriched in any protocol, membrane proteins were preferentially detected in the SDS-containing protocols. (n = 3, Error bars = +/- S.D.) ( c ) Filter-aided sample preparations yield a balanced representation of the proteome. The identified proteins were plotted against the percentage of proteins annotated by the GO term cytosol, in order to illustrate the similarity of extraction properties. The protocol properties required for efficient extraction of membrane and nuclear proteins is inversely correlated with the extraction efficiency for cytosolic proteins, while there is a positive correlation with ribosomal proteins.

    Journal: F1000Research

    Article Title: The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

    doi: 10.12688/f1000research.2-272.v2

    Figure Lengend Snippet: Protocols cover cellular compartments differently. ( a ) RapiGest and eFASP cover a unique space in the proteome. Identified proteins were visualised in a Venn diagram, excluding the in gel protocols. The RapiGest procedure yielded most unique IDs, followed by eFASP and RapidACN (n = 3). ( b ) SDS-containing protocols are best suited for the extraction of membrane proteins. For the analysis of annotated functions in each protocol, selected GO terms were expressed as percentages of identified proteins. While cytosolic proteins were not enriched in any protocol, membrane proteins were preferentially detected in the SDS-containing protocols. (n = 3, Error bars = +/- S.D.) ( c ) Filter-aided sample preparations yield a balanced representation of the proteome. The identified proteins were plotted against the percentage of proteins annotated by the GO term cytosol, in order to illustrate the similarity of extraction properties. The protocol properties required for efficient extraction of membrane and nuclear proteins is inversely correlated with the extraction efficiency for cytosolic proteins, while there is a positive correlation with ribosomal proteins.

    Article Snippet: The first protocol is based on the proprietary, acid degradable detergent RapiGest (Waters ), included in a protocol derived from Von der Haaret al. .

    Techniques:

    Protein identification in label-free sample preparations. ( a ) Proteolytic digestion efficiencies. Trypsin or Lys-C/trypsin (FASP) digestion efficiencies expressed as relative occurrence of spectra that could be assigned miscleaved peptides (n = 3). ( b ) Amino acid specificity of proteolytic digestion. Relative occurrence of identified peptides with C-terminal lysine or arginine, compared to the average frequency of these amino acids across all individual proteins identified (n = 3, Error bars = +/- S.D.) ( c ) Identified peptides differ per protocol, and correlate with the total peak area as recorded in a DDA experiment. 18 samples derived from the same yeast culture were processed with six protocols in triplicates, and analyzed on a TripleTOF5600 instrument. The number of identified peptides correlates with the total peak area recorded, and indicates the highest identification rate in in solution digests, followed by filter-aided , and in gel procedures. ( d ) Detection of proteins by DDA or SWATH in a label-free experiment. Samples were analyzed in triplicates both for DDA and SWATH acquisition on a TripleTOF5600 instrument, data was searched using paragon (DDA), and Spectronaut (SWATH). SWATH increased the number of detectable proteins in combination with the in solution protocols. In solution protocols RapidACN and RapiGest led to the detection of up to 1000 proteins in single injections, followed by FASP and eFASP, which gave rise to between 250 and 750 proteins, and in gel injections that yielded 300 proteins IDs. Inset: A comparison of protein IDs from the TripleTOF and QExactive platforms shows a linear correlation for the protocols investigated. Data was searched using Mascot (n = 3, Error bars = +/- S.D.).

    Journal: F1000Research

    Article Title: The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

    doi: 10.12688/f1000research.2-272.v2

    Figure Lengend Snippet: Protein identification in label-free sample preparations. ( a ) Proteolytic digestion efficiencies. Trypsin or Lys-C/trypsin (FASP) digestion efficiencies expressed as relative occurrence of spectra that could be assigned miscleaved peptides (n = 3). ( b ) Amino acid specificity of proteolytic digestion. Relative occurrence of identified peptides with C-terminal lysine or arginine, compared to the average frequency of these amino acids across all individual proteins identified (n = 3, Error bars = +/- S.D.) ( c ) Identified peptides differ per protocol, and correlate with the total peak area as recorded in a DDA experiment. 18 samples derived from the same yeast culture were processed with six protocols in triplicates, and analyzed on a TripleTOF5600 instrument. The number of identified peptides correlates with the total peak area recorded, and indicates the highest identification rate in in solution digests, followed by filter-aided , and in gel procedures. ( d ) Detection of proteins by DDA or SWATH in a label-free experiment. Samples were analyzed in triplicates both for DDA and SWATH acquisition on a TripleTOF5600 instrument, data was searched using paragon (DDA), and Spectronaut (SWATH). SWATH increased the number of detectable proteins in combination with the in solution protocols. In solution protocols RapidACN and RapiGest led to the detection of up to 1000 proteins in single injections, followed by FASP and eFASP, which gave rise to between 250 and 750 proteins, and in gel injections that yielded 300 proteins IDs. Inset: A comparison of protein IDs from the TripleTOF and QExactive platforms shows a linear correlation for the protocols investigated. Data was searched using Mascot (n = 3, Error bars = +/- S.D.).

    Article Snippet: The first protocol is based on the proprietary, acid degradable detergent RapiGest (Waters ), included in a protocol derived from Von der Haaret al. .

    Techniques: Derivative Assay

    Characteristics of label-free sample preparation methods. Left panel: Schematic overview of the different steps in an LC-MS/MS sample preparation method. Right panel: Main characteristics of the protocols compared in this study. Detailled protocols are given in the Supplementary material . Supplementary protocol 1 : In gel/SDS; 2: In gel/ABC; 3: FASP; 4: eFASP; 5: RapiGest; 6: RapidACN.

    Journal: F1000Research

    Article Title: The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

    doi: 10.12688/f1000research.2-272.v2

    Figure Lengend Snippet: Characteristics of label-free sample preparation methods. Left panel: Schematic overview of the different steps in an LC-MS/MS sample preparation method. Right panel: Main characteristics of the protocols compared in this study. Detailled protocols are given in the Supplementary material . Supplementary protocol 1 : In gel/SDS; 2: In gel/ABC; 3: FASP; 4: eFASP; 5: RapiGest; 6: RapidACN.

    Article Snippet: The first protocol is based on the proprietary, acid degradable detergent RapiGest (Waters ), included in a protocol derived from Von der Haaret al. .

    Techniques: Sample Prep, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    Bias of protein size and pI in sample preparation. ( a ) The spectrum of protein sizes is well covered for all protocols examined. The number of identified proteins was plotted against the theoretical molecular weight (MW) for each protocol investigated. Although some protocols yielded higher identifications than others, the MW range was highly reproducible for all of them when comparing against the whole yeast proteome. ( b ) Different representations of protein charges. When comparing to the distribution of theoretical protein pI values of the whole proteome, all investigated protocols showed an under-representation of proteins with a pI of 10. When expressing the total deviation as deviation score d, RapiGest, FASP and RapidACN score best. The d values were calculated as the sum of all differences in % compared to the theoretical proteome occurrence multiplied by 0.1.

    Journal: F1000Research

    Article Title: The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

    doi: 10.12688/f1000research.2-272.v2

    Figure Lengend Snippet: Bias of protein size and pI in sample preparation. ( a ) The spectrum of protein sizes is well covered for all protocols examined. The number of identified proteins was plotted against the theoretical molecular weight (MW) for each protocol investigated. Although some protocols yielded higher identifications than others, the MW range was highly reproducible for all of them when comparing against the whole yeast proteome. ( b ) Different representations of protein charges. When comparing to the distribution of theoretical protein pI values of the whole proteome, all investigated protocols showed an under-representation of proteins with a pI of 10. When expressing the total deviation as deviation score d, RapiGest, FASP and RapidACN score best. The d values were calculated as the sum of all differences in % compared to the theoretical proteome occurrence multiplied by 0.1.

    Article Snippet: The first protocol is based on the proprietary, acid degradable detergent RapiGest (Waters ), included in a protocol derived from Von der Haaret al. .

    Techniques: Sample Prep, Molecular Weight, Expressing

    Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with Rapigest, trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Proteomic Pathway Analysis Reveals Inflammation Increases Myeloid-Derived Suppressor Cell Resistance to Apoptosis *

    doi: 10.1074/mcp.M110.002980

    Figure Lengend Snippet: Proteomic analysis workflow. MDSC were harvested from BALB/c mice with 4T1 tumor, BALB/c mice with 4T1/IL-1β tumor, and TLR4 −/− mice with 4T1 tumor, lysed with Rapigest, trypsin digested and analyzed by LC-MS/MS. Relative protein abundances and identifications obtained from LC-MS/MS analysis were utilized as input lists for pathway analysis. 4T1-induced MDSC from BALB/c mice served as control samples; 4T1/IL-1β-induced MDSC from BALB/c mice and 4T1-induced MDSC from TLR4 −/− mice were experimental samples.

    Article Snippet: MDSC ( > 90% Gr1+ CD11b+ cells; 5 × 106 - 107 /mouse) were lysed at a final concentration of 0.1% Rapigest acid-cleavable detergent (Waters, Denver, CO) in 100 m m NH4 HCO3 , pH 8.4.

    Techniques: Mouse Assay, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry