JBEI - A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins

JBEI - 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: 6460 Triple Quadrupole LC/MS
  • 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, 3:30 PM
Flag FileDownloadCreatedProteinsPeptidesPrecursorsTransitionsReplicates
Pathways-CalCurve-Sugars-Panorama_2014-02-27_20-15-34.sky.zip (22 MB)2018-06-114096896891,36527
Phospholipid Anabolism.zip (475 KB)2018-06-11142626769
Tyrosine Biosynthesis.zip (684 KB)2018-06-111632329610
Serine, Glycine Biosynthesis.zip (232 KB)2018-06-11488244
Panthothenate-CoA Biosynthesis.zip (175 KB)2018-06-1181414423
Lysine, Threonine, Methionine Biosynthesis.zip (1 MB)2018-06-1119383811417
Purine & Pyrmidine Biosynthesis.zip (1 MB)2018-06-1134555516526
Pentose Phosphate Pathway.zip (579 KB)2018-06-11815154511
NAD Phosphorylation & Dephosphorylation.zip (108 KB)2018-06-11366182
Mixed Acid Fermentation.zip (1 MB)2018-06-111832329623
Iron cluster assembly.zip (422 KB)2018-06-11713133910
Glutathione Biosynthesis.zip (198 KB)2018-06-11366184
Leucine, Valine, Isoleucine Biosynthesis.zip (696 KB)2018-06-111528288411
Methylerythritol Phosphate (MEP) Pathway.zip (599 KB)2018-06-1171414427
Glycerold & glycerolphosphodiester degredation.zip (177 KB)2018-06-11488244
Folate Anabolism.zip (414 KB)2018-06-1181616479
Tricarboxylic Acid Cycle.zip (1 MB)2018-06-111122226628
Fatty Acid Biosynthesis.zip (1 MB)2018-06-11132222638
Aspartate & Asparagine Biosynthesis.zip (417 KB)2018-06-1171414427
Acetyl-CoA Biosynthesis from Pyruvate.zip (233 KB)2018-06-11366185
Acetate formation.zip (235 KB)2018-06-11488245
NAD I Biosynthesis and Salvage Cycle.zip (240 KB)2018-06-1191515454
Serine Protease.zip (1 MB)2018-06-111521216327
Lipid Anabolism.zip (1 MB)2018-06-1134626218519
Glycolysis I.zip (1 MB)2018-06-111530309025
Limit of Detection Data_2014-02-27_16-44-26.sky.zip (3 MB)2018-06-114136136101,21915
Qcat9-Ind.sky (80 KB)2018-06-11112222662
Qcat8-Ind.sky (147 KB)2018-06-112441411271
Qcat7-Ind.sky (193 KB)2018-06-113055551652
Qcat6-Ind.sky (152 KB)2018-06-112445451343
Qcat5-Ind.sky (157 KB)2018-06-112343431291
Qcat4-Ind.sky (158 KB)2018-06-112345451341
Qcat3-Ind.sky (199 KB)2018-06-113258581731
Qcat2-Ind.sky (161 KB)2018-06-112651511501
Qcat18-Ind.sky (171 KB)2018-06-112748481422
Qcat17-Ind.sky (165 KB)2018-06-112445451351
Qcat16-Ind.sky (170 KB)2018-06-112548481441
Qcat15-Ind.sky (156 KB)2018-06-112344441321
Qcat14-Ind.sky (184 KB)2018-06-112548481633
Qcat13-Ind.sky (164 KB)2018-06-112546461373
Qcat12-Ind.sky (159 KB)2018-06-112444441361
Qcat11-Ind.sky (161 KB)2018-06-112444441392
Qcat10-Ind.sky (108 KB)2018-06-11153030903
Qcat1-Ind.sky (132 KB)2018-06-112141411221
Tyrosine-pathway-data_2014-02-28_09-56-52.sky.zip (2 MB)2018-06-111629288416