T.S. Batth et al. Metab. Eng. 2014 - A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins

T.S. Batth et al. Metab. Eng. 2014 - A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins
targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins

  • Organism: Escherichia coli
  • Instrument: Agilent 1290-6460
  • SpikeIn: No
Abstract
Transformation of engineered Escherichia coli into a robust microbial factory is contingent on precise control of metabolism. Yet, the throughput of omics technologies used to characterize cell components has lagged far behind our ability to engineer novel strains. To expand the utility of quantitative proteomics for metabolic engineering, we validated and optimized targeted proteomics methods for over 400 proteins from more than 20 major pathways in E. coli metabolism. Complementing these methods, we constructed a series of synthetic genes to produce concatenated peptides (QconCAT) for absolute quantification of the proteins and made them available through the Addgene plasmid repository (www.addgene.org). To facilitate high sample throughput, we developed a fast, analytical- flow chromatography method using a 5.5-min gradient (10 min total run time). Overall this toolkit provides an invaluable resource for metabolic engineering by increasing sample throughput, minimizing development time and providing peptide standards for absolute quantification of E. coli proteins.
Created on 6/11/18 10:03 AM
Flag FileDownloadCreatedProteinsPeptidesPrecursorsTransitionsReplicates
Qcat9-Ind.sky (80 KB)2014-03-20112222662
Qcat8-Ind.sky (147 KB)2014-03-202441411271
Qcat7-Ind.sky (193 KB)2014-03-203055551652
Qcat6-Ind.sky (152 KB)2014-03-202445451343
Qcat5-Ind.sky (157 KB)2014-03-202343431291
Qcat4-Ind.sky (158 KB)2014-03-202345451341
Qcat3-Ind.sky (199 KB)2014-03-203258581731
Qcat2-Ind.sky (161 KB)2014-03-202651511501
Qcat18-Ind.sky (171 KB)2014-03-202748481422
Qcat17-Ind.sky (165 KB)2014-03-202445451351
Qcat16-Ind.sky (170 KB)2014-03-202548481441
Qcat15-Ind.sky (156 KB)2014-03-202344441321
Qcat14-Ind.sky (184 KB)2014-03-202548481633
Qcat13-Ind.sky (164 KB)2014-03-202546461373
Qcat12-Ind.sky (159 KB)2014-03-202444441361
Qcat11-Ind.sky (161 KB)2014-03-202444441392
Qcat10-Ind.sky (108 KB)2014-03-20153030903
Qcat1-Ind.sky (132 KB)2014-03-202141411221
Tyrosine-pathway-data_2014-02-28_09-56-52.sky.zip (2 MB)2014-02-281629288416
Pathways-CalCurve-Sugars-Panorama_2014-02-27_20-15-34.sky.zip (22 MB)2014-02-274096896891,36527
Limit of Detection Data_2014-02-27_16-44-26.sky.zip (3 MB)2014-02-274136136101,21915
NAD I Biosynthesis and Salvage Cycle.zip (240 KB)2013-05-2391515454
Phospholipid Anabolism.zip (475 KB)2013-05-22142626769
Tyrosine Biosynthesis.zip (684 KB)2013-05-211632329610
Tricarboxylic Acid Cycle.zip (1 MB)2013-05-211122226628
Serine Protease.zip (1 MB)2013-05-211521216327
Serine, Glycine Biosynthesis.zip (232 KB)2013-05-21488244
Purine & Pyrmidine Biosynthesis.zip (1 MB)2013-05-2134555516526
Pentose Phosphate Pathway.zip (579 KB)2013-05-21815154511
NAD Phosphorylation & Dephosphorylation.zip (108 KB)2013-05-21366182
Panthothenate-CoA Biosynthesis.zip (175 KB)2013-05-2181414423
Mixed Acid Fermentation.zip (1 MB)2013-05-211832329623
Lysine, Threonine, Methionine Biosynthesis.zip (1 MB)2013-05-2119383811417
Lipid Anabolism.zip (1 MB)2013-05-2134626218519
Leucine, Valine, Isoleucine Biosynthesis.zip (696 KB)2013-05-211528288411
Methylerythritol Phosphate (MEP) Pathway.zip (599 KB)2013-05-2171414427
Iron cluster assembly.zip (422 KB)2013-05-21713133910
Glycolysis I.zip (1 MB)2013-05-211530309025
Glycerold & glycerolphosphodiester degredation.zip (177 KB)2013-05-21488244
Glutathione Biosynthesis.zip (198 KB)2013-05-21366184
Folate Anabolism.zip (414 KB)2013-05-2181616479
Fatty Acid Biosynthesis.zip (1 MB)2013-05-21132222638
Aspartate & Asparagine Biosynthesis.zip (417 KB)2013-05-2171414427
Acetyl-CoA Biosynthesis from Pyruvate.zip (233 KB)2013-05-21366185
Acetate formation.zip (235 KB)2013-05-21488245