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Fractionated Human/E. coli Benchmark Data Set

ABSTRACT: This benchmark data set is composed of two groups of fractionated samples. The first group contained a mixture of E. coli and human digest, and the second group contained a similar mixture except that the amount of E. coli was twice the amount as the first group.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Escherichia Coli

SUBMITTER: Robert Millikin

LAB HEAD: Lloyd M. Smith

PROVIDER: PXD016470 | Pride | 2020-04-06

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	09-04-18_EcoliSpikeInSingleShot1x.raw	Raw
	09-04-18_EcoliSpikeInSingleShot2x.raw	Raw
	09-07-18_EcoliSpikeIn_1xF1R1.raw	Raw
	09-07-18_EcoliSpikeIn_1xF1R2.raw	Raw
	09-07-18_EcoliSpikeIn_1xF1R3.raw	Raw

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Publications

A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics.

Millikin Robert J RJ Shortreed Michael R MR Scalf Mark M Smith Lloyd M LM

Journal of proteome research 20200414 5

Statistical significance tests are a common feature in quantitative proteomics workflows. The Student's <i>t</i>-test is widely used to compute the statistical significance of a protein's change between two groups of samples. However, the <i>t</i>-test's null hypothesis asserts that the difference in means between two groups is exactly zero, often marking small but uninteresting fold-changes as statistically significant. Compensations to address this issue are widely used in quantitative proteom ...[more]

PMID: 32243168

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In-depth and reproducibly quantitation of benchmark dataset consiting of 20 files

Project description:We prepared a benchmark dataset where the various levels of spikeed-in E. Coli proteome that true fold change (i.e. 1 fold, 1.5 fold, 2 fold, 2.5 fold and 3 fold) and true identities of positives/negatives (i.e. E.Coli proteins are true positives while Human proteins are true negatives) are known. To best mimic the proteomics application in comparison of multiple replicates, each fold change

2017-04-20 | PXD005590 | Pride

29-Plex Tandem Mass Tag Mass Spectrometry Enabling Accurate Quantification by Interference Correction

Project description:Tandem mass tag (TMT) mass spectrometry is a mainstream isobaric chemical labeling strategy for profiling proteomes. Here we present a 29-plex TMT method to combine the 11-plex and 18-plex labeling strategies. The 29-plex method was examined with a pooled sample composed of 1x, 3x and 10x E. coli peptides with 100x human background peptides, which generated two E. coli datasets (TMT11 and TMT18), displaying the distorted ratios of 1.0:1.7:4.2 and 1.0:1.8:4.9, respectively. This ratio compression from the expected 1:3:10 ratios was caused by co-isolated TMT-labeled ions (i.e., noise). Interestingly, the mixture of two TMT sets produced MS/MS spectra with unique features for the noise detection: (i) in TMT11-labeled spectra, TMT18-specific reporter ions (e.g., 135N) were shown as the noise; (ii) in TMT18-labeled spectra, the TMT11/TMT18-shared reporter ions (e.g., 131C) typically exhibited higher intensities than TMT18-specific reporter ions, due to contaminated TMT11-labeled ions in these shared channels. We further estimated the noise levels contributed by both TMT11- and TMT18-labeled peptides, and corrected reporter ion intensities in every spectrum. Finally, the anticipated 1:3:10 ratios were largely restored. This strategy was also validated using another 29-plex sample with 1:5 ratios. Thus the 29-plex method expands the TMT throughput and enhances the quantitative accuracy.

2023-03-10 | PXD033865 | Pride

ChipFilter: Microfluidic Based Comprehensive Sample Preparation Methodology for Metaproteomics

Project description:Here, we show that a ChipFilter microfluidic device coupled to LC-MS/MS can successfully be used for identification of microbial proteins. Using cultures of E. coli, B. subtilis and S. cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow higher number of proteins and peptides identification than standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amount of 16 of these species.

2024-05-24 | PXD039581 | Pride

A multi-species spike-in sample set for performance evaluation of label-free proteomics quantification

Project description:When evaluating the quantitative performance of label-free proteomics method(s), samples with known compositions are necessary to define key parameters such as reproducibility, missing data levels, accuracy, precision, as well as sensitivity/specificity for biomarker discovery. Here, we provide a carefully-designed multi-species spike-in sample set for such purposes, which was prepared by spiking small, variable amounts of E. Coli (for mimicking significant protein changes, i.e., true positives) and yeast (for balancing the variable levels of E. coli proteins) proteins into a large, constant background of human proteins (representing unchanged proteins). The sample set encompasses a total of 25 LC-MS sample runs (5 E.coli-level groups, 5 LC-MS replicate runs in each group). The proportion of human proteins is 60% across all samples, and each group contains the following percentage of E. coli and yeast proteins : A: 5%/35%, B: 7.5%/32.5%, C: 10%/30%, D: 15%/25%, E: 20%/20%. These files were used to comprehensively evaluate the quantitative performances by ultra-high-resolution (UHR)-IonStar and SWATH-MS in Result 3.2 of “Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification (DOI: 10.1021/acs.analchem.0c05002)”.

2022-01-06 | PXD030780 | Pride

Quantitative Proteomics Benchmark Dataset to evaluate label-free quantitative methods- LC/Orbitrap Fusion MS analysis of E coli proteomes spiked-in Human proteins at 5 different levels (N=20)

Project description:To unbiasedly evaluate the quantitative performance of different quantitative methods, and compare different popular proteomics data processing workflows, we prepared a benchmark dataset where the various levels of spikeed-in E. Coli proteome that true fold change (i.e. 1 fold, 1.5 fold, 2 fold, 2.5 fold and 3 fold) and true identities of positives/negatives (i.e. E.Coli proteins are true positives while Human proteins are true negatives) are known. To best mimic the proteomics application in comparison of multiple replicates, each fold change group contains 4 replicates, so there are 20 LC-MS/MS analysis in this benchmark dataset. To our knowledge, this spike-in benchmark dataset is largest-scale ever that encompasses 5 different spike level, >500 true positive proteins, and >3000 true negative proteins (2peptide criteria, 1% protein FDR), with a wide concentration dynamic range. The dataset is ideal to test quantitative accuracy, precision, false-positive biomarker discovery and missing data level.

2018-05-16 | PXD003881 | Pride

Proteomes of uropathogenic Escherichia coli growing in human urine and in J82 urinary bladder cell.

Project description:Uropathogenic Escherichia coli (UPEC) are the most common cause of urinary tract infection (UTI). UPEC normally reside in the intestine, and during establishment of UTI, it undergoes metabolic adaptations, first to urine and then upon tissue invasion to the bladder cell interior. In order to understand these adaptations, we used quantitative proteomic profiling to characterize protein expression of UPEC strain UTI89 growing in human urine and when inside J82 bladder cells. In order to facilitate detection of UPEC proteins over the excess amount of eukaryotic proteins in bladder cells, we developed a method where proteins from UTI89 grown in MOPS and urine was spiked-in to enhance detection of bacterial proteins. More than 2000 E. coli proteins were detected. During growth in urine, proteins associated with iron acquisition and several amino acid uptake and biosynthesis systems, in particular arginine metabolism, were significantly upregulated. During growth in J82 cells, proteins related to iron uptake and arginine metabolisms were upregulated together with proteins involved in sulphur compound turnover. Results suggested that UPEC experience a richer environment in bladder cells compared to urine. There was no direct correlation between upregulated proteins and proteins reported to be essential for infections, showing that upregulation during growth does not signify that the proteins are essential for growth under a condition.

2022-06-09 | PXD032049 | Pride

Hartwig Medical Foundation Benchmark Set

Project description:Hartwig Medical Foundation Benchmark Set

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Temporal response of mouse peritoneal cells to a non-pathogenic E. coli infection

Project description:Analysis of early and late changes in the mouse peritoneal cells in response to E. coli induced sepis. Result provide an insight into the molecular function and pathways expressed at these different time points. The mice were divided in two groups; the first group of mice were not treated with E. coli and was referred to as the naive group. Each mouse of the second group was injected with 2 X108 cells of a non- pathogenic isolate of E. coli suspended in a phosphate buffered saline (PBS) solution. After 1h, 2h and 18h of E. coli administration, peritoneal lavage fluid was obtained from two mice each for E. coli treated group at 1 and 2h and three mice of both groups (control and E. coli treated) at 18h. A common naive group of 2 mice harvested at 2h served as a control for both 1h and 2h.

2012-12-30 | E-GEOD-34114 | biostudies-arrayexpress

Evaluation of the MPA Portable software performance on analyzing benchmark datasets

Project description:Within the scope of a technical note we tested our MetaProteomeAnalyzer Portable software workflow on experimental data sets from samples with known composition. For generating a benchmarking data set, the bacterial strains (5BCT) Bacillus subtilis, Escherichia coli, Pseudomonas fluorescens, Micrococcus luteus and Desulfovibrio vulgaris were mixed with a protein ratio of 1:1:1:1:1.

2012-12-13 | PXD007681 | Pride

Variation in the Genomic islands of porcine enteropathogenic E. coli strains of serogroup O45 revealed by CGH and PCR.

Project description:Background: Members of E. coli serogroup O45 are porcine enteropathogenic E. coli (PEPEC) strains which cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most of O45 PEPEC strains possess the locus of enterocyte effacement (LEE), encoding the virulence factors for A/E lesions, and often possess the paa gene, which is thought to contribute to the early stages of PEPEC virulence. Methodology: Nine O45 PEPEC strains and a rabbit enteropathogenic (REPEC) strain, known to produce A/E lesions, were characterized using an E. coli O157-E. coli K12 whole genome microarray and a virulence gene-specific microarray, and by PCR experiments. Results: Based on their virulence genes profiles, the 10 strains were characterized as atypical EPEC. The differences in their genomes pointed to two distinct evolutionary groups of O45 PEPEC, Group I and Group II, and to the contribution these genetic differences have on virulence in pigs. Group I contained the REPEC strain and four O45 PEPEC strains known to induce severe A/E lesions in challenged pigs whereas Group II was composed of five other O45 PEPEC strains which induced less severe or no A/E lesions in challenged pigs. Significant differences between Groups I and II were found in the presence or absence of 50 O-Islands (OIs) or S-loops and 13 K-islands (KIs) or K-loops, including the virulence-associated islands OI#1 (S-loop#1), OI#47 (S-loop#71), OI#57 (S-loop#85), OI#71 (S-loop#108), OI#115, OI#122, and OI#154 (S-loop#253). 10 samples, with two microarrays per sample. Each microarray includes duplicates of every spot.

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