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Nonspecific cleavages arising from reconstitution of trypsin under mildly acidic conditions. PLoS One 2020; 15:e0236740. [PMID: 32722706 PMCID: PMC7386593 DOI: 10.1371/journal.pone.0236740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/13/2020] [Indexed: 11/19/2022] Open
Abstract
Tryptic digestion of proteins followed by liquid chromatography with tandem mass spectrometry analysis is an extensively used approach in proteomics research and biopharmaceutical product characterization, owing to the high level of cleavage fidelity produced with this technique. However, nonspecific trypsin cleavages have been frequently reported and shown to be related to a number of digestion conditions and predigestion sample treatments. In this work, we reveal that, for a number of commercial trypsins, reconstitution and storage conditions can have a significant impact on the occurrence of trypsin nonspecific cleavages. We analyzed the tryptic digestion of a variety of biotherapeutics, using trypsins reconstituted under different conditions. The results indicate that, for many commercial trypsins, commonly recommended reconstitution/storage conditions (mildly acidic, e.g., 50 mM acetic acid, 1 mM HCl) can actually promote nonspecific trypsin activities, which are time dependent and can be as high as 20% in total relative abundance. In contrast, using water for reconstitution and storage can effectively limit nonspecific cleavages to 1%. Interestingly, the performances of different commercial trypsins were found to be quite distinct in their levels of nonspecific cleavages and responses to the two reconstitution conditions. Our findings demonstrate the importance of choosing the appropriate trypsin for tryptic digestion and the necessity of assessing the impact of trypsin reconstitution and storage on nonspecific cleavages. We advocate for manufacturers of commercial trypsins to reevaluate manufacturing processes and reconstitution/storage conditions to provide good cleavage specificity.
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Kuang Y, Liu L, Wang Z, Chen Y. A photocleavable and mass spectrometric DNA-peptide probe enables fast and specific enzyme-free detection of microRNA. Talanta 2020; 211:120726. [PMID: 32070590 DOI: 10.1016/j.talanta.2020.120726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 11/17/2022]
Abstract
MiRNAs are known to be involved in a series of diseases, including breast cancer, and they have the potential to serve as diagnostic/prognostic markers and therapeutic targets. A prerequisite for miRNAs to be applied in clinical practice is the quantitative profiling of their expression. However, the majority of current assays used in miRNA detection are highly enzyme-dependent. In this study, a novel enzyme-free assay was developed that relies on stacking hybridization and a photocleavable DNA-PL-peptide probe, which contains a reporter peptide (AVLGVDPFR), a photocleavable o-nitrobenzyl derivative linker and a detection DNA sequence that is complementary to a part of the target miRNA (e.g., miR-21, miR-125a or miR-200c). Stacking hybridization enabled the DNA-PL-peptide probe to capture DNA in a contiguous tandem arrangement to generate a long DNA single strand complementary to the target miRNA. Then, photolysis was initiated to rapidly release the reporter peptide, and the reporter peptide was ultimately monitored by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this experiment, the parameters linked with photorelease, binding, conjugation and hybridization were characterized. The results showed that the assay time was significantly shortened, and the detection specificity was improved. After validation of the assay, the target miRNA level was determined in human breast cells and tissue samples. The results demonstrated that photocleavable materials coupled with mass spectrometric detection have great potential in clinical practice.
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Affiliation(s)
- Yuqiong Kuang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China; Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zhongcheng Wang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China; China State Key Laboratory of Reproductive Medicine, Nanjing, 210029, China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Nanjing, 211166, China.
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Heissel S, Frederiksen SJ, Bunkenborg J, Højrup P. Enhanced trypsin on a budget: Stabilization, purification and high-temperature application of inexpensive commercial trypsin for proteomics applications. PLoS One 2019; 14:e0218374. [PMID: 31246970 PMCID: PMC6597055 DOI: 10.1371/journal.pone.0218374] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/02/2019] [Indexed: 01/22/2023] Open
Abstract
Trypsin is by far the most commonly used protease in proteomics. Even though the amount of protease used in each experiment is very small, digestion of large amounts of protein prior to enrichment can be rather costly. The price of commercial trypsin is highly dependent on the quality of the enzyme, which is determined by its purity, activity, and chemical modifications. In this study we evaluated several strategies for improving the quality of crude trypsin by reductive methylation and affinity purification. We present a protocol applicable to most proteomics laboratories for obtaining a highly stable and pure trypsin preparation using reductive methylation and purification by benzamidine-sepharose. The entire workflow can be performed within a day and yields ~4 mg per batch but is completely scalable. The methylated product was benchmarked against sequencing grade trypsin from Promega and they were found to be comparable for one hour digestions at elevated temperatures, where residual chymotryptic activity was found to be negligible.
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Affiliation(s)
- Søren Heissel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Sigurd J. Frederiksen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | | | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- * E-mail:
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Ueno HM, Kato T, Ohnishi H, Kawamoto N, Kato Z, Kaneko H, Kondo N, Nakano T. T-cell epitope-containing hypoallergenic β-lactoglobulin for oral immunotherapy in milk allergy. Pediatr Allergy Immunol 2016; 27:818-824. [PMID: 27540712 DOI: 10.1111/pai.12642] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/16/2016] [Indexed: 11/29/2022]
Abstract
BACKGROUND Optimally hydrolyzed β-Lactoglobulin (βLg) is a promising milk oral immunotherapy (OIT) candidate with respect to showing reduced B-cell reactivity but retaining the T-cell epitope. To demonstrate that an edible hypoallergenic βLg hydrolysate containing the T-cell epitope is suitable for OIT. We tested how chymotrypsin affected the retention of the T-cell epitope of βLg when preparing βLg hydrolysates using food-grade trypsin. METHODS We investigated the effect of chymotrypsin activity on the formation of the T-cell epitope-containing peptide of βLg (βLg102-124 ) and prepared an edible βLg hydrolysate containing βLg102-124 using screened food-grade trypsins. B-cell reactivity was determined using immunoassays in which ELISA was performed with anti-βLg rabbit IgG and Western blotting was performed with a milk-specific IgE antiserum. RESULTS In βLg hydrolysis performed by varying the activity of trypsin and chymotrypsin, chymotrypsin activity inhibited the formation of βLg102-124 with an increase in hydrolysis time in a dose-dependent manner. βLg102-124 was generated by two of five food-grade trypsins used at a ratio of 1:50 (w/w, enzyme/substrate) for 20 h at 40°C. The edible βLg hydrolysate retained βLg102-124 and showed a reduction in molecular weight distribution and antigenicity against IgG and IgE. CONCLUSIONS Chymotrypsin activity inhibited the formation of βLg102-124 in the trypsin hydrolysate of βLg. This βLg trypsin hydrolysate is a novel candidate for peptide-based OIT in cow's milk allergy for safely inducing desensitization.
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Affiliation(s)
- Hiroshi M Ueno
- Research and Development Department, Bean Stalk Snow Co., Ltd., Kawagoe, Japan
| | - Teruhiko Kato
- Research and Development Department, Bean Stalk Snow Co., Ltd., Kawagoe, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Norio Kawamoto
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Zenichiro Kato
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hideo Kaneko
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Naomi Kondo
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Taku Nakano
- Research and Development Department, Bean Stalk Snow Co., Ltd., Kawagoe, Japan
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Wu F, Zhao M, Zhang Y, Su N, Xiong Z, Xu P. Recombinant acetylated trypsin demonstrates superior stability and higher activity than commercial products in quantitative proteomics studies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1059-1066. [PMID: 27003043 DOI: 10.1002/rcm.7535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/31/2016] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE Trypsin is an important digestive enzyme in peptide sample preparation for proteomics. It digests proteins at the C-terminal of Arg or Lys residues. The majority of commercial products are obtained from animal sources. In a previous study, we reported the production process for recombinant trypsin (r-trypsin) and acetylated trypsin (r-Ac-trypsin). In this paper, we want to evaluate whether the r-trypsin and r-Ac-trypsin are suitable for proteomics research. METHODS The trypsins used in this research were first normalized to the same concentration and used for further evaluation. The stability and buffer compatibility (2M urea, 0.1% SDS and 10% acetonitrile) were compared and visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The digestion efficiency and specificity were compared based on a simple protein substrate, human serum albumin (HSA) and a complex proteomic sample, yeast lysate. The acquisition of proteomics data was achieved by ultra-high performance liquid chromatography (UPLC) connected to an LTQ Orbitrap Velos mass spectrometer. RESULTS r-Ac-trypsin demonstrated similar tolerance to 2 M urea and 10% acetonitrile but weaker 0.1% SDS tolerance than commercial trypsins. Based on simple protein sample HSA, the activity and specificity of r-Ac-trypsin were similar to that of commercial trypsins. However, it demonstrated superior activity and specificity on complicated samples like yeast lysate. More interestingly, the newly developed r-Ac-trypsin was more resistant to autolysis, which enabled more complete digestion of proteomic samples. CONCLUSIONS The r-Ac-trypsin described here is a recombinant product. In addition it showed similar or superior properties such as stability activity and specificity to commercial products. It can be used in peptide sample preparation in proteomics studies.
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Affiliation(s)
- Feilin Wu
- Life Science College, Southwest Forestry University, Kunming, 650224, P.R. China
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Mingzhi Zhao
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Yao Zhang
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
- Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Na Su
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Zhi Xiong
- Life Science College, Southwest Forestry University, Kunming, 650224, P.R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, P.R. China
- Anhui Medical University, Hefei, 230032, Anhui, P.R. China
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Rašković B, Vatić S, Anđelković B, Blagojević V, Polović N. Optimizing storage conditions to prevent cold denaturation of trypsin for sequencing and to prolong its shelf life. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fang P, Liu M, Xue Y, Yao J, Zhang Y, Shen H, Yang P. Controlling nonspecific trypsin cleavages in LC-MS/MS-based shotgun proteomics using optimized experimental conditions. Analyst 2015; 140:7613-21. [PMID: 26418741 DOI: 10.1039/c5an01505g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The highlight of this study is the efficient control of nonspecific trypsin cleavages in shotgun proteomics and N-glycoproteomics using optimized experimental conditions, which greatly increased the specificity of trypsin.
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Affiliation(s)
- Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Mingqi Liu
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Yu Xue
- Department of Chemistry
- Fudan University
- Shanghai
- P. R. China
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Yang Zhang
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Huali Shen
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
- Department of Systems Biology for Medicine and School of Basic Medical Sciences
| | - Pengyuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
- Department of Chemistry
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Lv Y, Zhang J, Wu H, Zhao S, Song Y, Wang S, Wang B, Lv G, Ma X. A protease inhibition strategy based on acceleration of autolysis. Chem Commun (Camb) 2015; 51:5959-62. [DOI: 10.1039/c5cc01448d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An iconoclastic protease inhibition strategy based on autolysis acceleration: proteases are concentrated and induced to self-digest by a polymer via electrostatic interaction. Such a catalytic cycle results in high inhibition efficiency.
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Affiliation(s)
- Yan Lv
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Jianbin Zhang
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Hao Wu
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Shan Zhao
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Yizhe Song
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Shujun Wang
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Bing Wang
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Guojun Lv
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Xiaojun Ma
- Laboratory of Biomedical Materials Engineering
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
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Bayramoglu G, Ozalp VC, Altintas B, Arica MY. Preparation and characterization of mixed-mode magnetic adsorbent with p-amino-benzamidine ligand: Operated in a magnetically stabilized fluidized bed reactor for purification of trypsin from bovine pancreas. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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10
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Kubienová L, Kopečný D, Tylichová M, Briozzo P, Skopalová J, Šebela M, Navrátil M, Tâche R, Luhová L, Barroso JB, Petřivalský M. Structural and functional characterization of a plant S-nitrosoglutathione reductase from Solanum lycopersicum. Biochimie 2012; 95:889-902. [PMID: 23274177 DOI: 10.1016/j.biochi.2012.12.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/10/2012] [Indexed: 12/25/2022]
Abstract
S-nitrosoglutathione reductase (GSNOR), also known as S-(hydroxymethyl)glutathione (HMGSH) dehydrogenase, belongs to the large alcohol dehydrogenase superfamily, namely to the class III ADHs. GSNOR catalyses the oxidation of HMGSH to S-formylglutathione using a catalytic zinc and NAD(+) as a coenzyme. The enzyme also catalyses the NADH-dependent reduction of S-nitrosoglutathione (GSNO). In plants, GSNO has been suggested to serve as a nitric oxide (NO) reservoir locally or possibly as NO donor in distant cells and tissues. NO and NO-related molecules such as S-nitrosothiols (S-NOs) play a central role in the regulation of normal plant physiological processes and host defence. The enzyme thus participates in the cellular homeostasis of S-NOs and in the metabolism of reactive nitrogen species. Although GSNOR has recently been characterized from several organisms, this study represents the first detailed biochemical and structural characterization of a plant GSNOR, that from tomato (Solanum lycopersicum). SlGSNOR gene expression is higher in roots and stems compared to leaves of young plants. It is highly expressed in the pistil and stamens and in fruits during ripening. The enzyme is a dimer and preferentially catalyses reduction of GSNO while glutathione and S-methylglutathione behave as non-competitive inhibitors. Using NAD(+), the enzyme oxidizes HMGSH and other alcohols such as cinnamylalcohol, geraniol and ω-hydroxyfatty acids. The crystal structures of the apoenzyme, of the enzyme in complex with NAD(+) and in complex with NADH, solved up to 1.9 Å resolution, represent the first structures of a plant GSNOR. They confirm that the binding of the coenzyme is associated with the active site zinc movement and changes in its coordination. In comparison to the well characterized human GSNOR, plant GSNORs exhibit a difference in the composition of the anion-binding pocket, which negatively influences the affinity for the carboxyl group of ω-hydroxyfatty acids.
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Affiliation(s)
- Lucie Kubienová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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Strakova E, Bobek J, Zikova A, Rehulka P, Benada O, Rehulkova H, Kofronova O, Vohradsky J. Systems insight into the spore germination of Streptomyces coelicolor. J Proteome Res 2012. [PMID: 23181467 DOI: 10.1021/pr300980v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An example of bacterium, which undergoes a complex development, is the genus of Streptomyces whose importance lies in their wide capacity to produce secondary metabolites, including antibiotics. In this work, a proteomic approach was applied to the systems study of germination as a transition from dormancy to the metabolically active stage. The protein expression levels were examined throughout the germination time course, the kinetics of the accumulated and newly synthesized proteins were clustered, and proteins detected in each group were identified. Altogether, 104 2DE gel images at 13 time points, from dormant state until 5.5 h of growth, were analyzed. The mass spectrometry identified proteins were separated into functional groups and their potential roles during germination were further assessed. The results showed that the full competence of spores to effectively undergo active metabolism is derived from the sporulation step, which facilitates the rapid initiation of global protein expression during the first 10 min of cultivation. Within the first hour, the majority of proteins were synthesized. From this stage, the full capability of regulatory mechanisms to respond to environmental cues is presumed. The obtained results might also provide a data source for further investigations of the process of germination.
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Affiliation(s)
- Eva Strakova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Bioinformatics, Vídeňská 1083, 142 20 Prague 4, Czech Republic
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Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics. J Proteomics 2012; 75:1454-62. [DOI: 10.1016/j.jprot.2011.11.016] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 11/04/2011] [Accepted: 11/14/2011] [Indexed: 11/20/2022]
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