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Standard dataset of UPS1 spiked into yeast at various concentrations

ABSTRACT: A standard proteolytic digest of a human protein mixture, prepared at 1.5-fold to 3-fold protein concentration changes, and diluted into a constant background of yeast proteins. Similar to other datasets used for ground truth in quantitative studies, with the exception of being more granular, and much larger in terms of replicates, to enable more rigorous and accurate testing of quantitative algorithms.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Michael Hoopmann

LAB HEAD: Robert L. Moritz

PROVIDER: PXD006447 | Pride | 2018-09-24

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	112015-Standard-A-01-ipro.pep.xml	Pepxml
	112015-Standard-A-01.raw	Raw
	112015-Standard-A-02-ipro.pep.xml	Pepxml
	112015-Standard-A-02.raw	Raw
	112015-Standard-A-03-ipro.pep.xml	Pepxml

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Publications

Robust determination of differential abundance in shotgun proteomics using nonparametric statistics.

Slama Patrick P Hoopmann Michael R MR Moritz Robert L RL Geman Donald D

Molecular omics 20181201 6

Label-free shotgun mass spectrometry enables the detection of significant changes in protein abundance between different conditions. Due to often limited cohort sizes or replication, large ratios of potential protein markers to number of samples, as well as multiple null measurements pose important technical challenges to conventional parametric models. From a statistical perspective, a scenario similar to that of unlabeled proteomics is encountered in genomics when looking for differentially ex ...[more]

PMID: 30259924

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Standard dataset of UPS1 spiked into yeast at various concentrations

Project description:A standard proteolytic digest of a human protein mixture, prepared at 1.5-fold to 3-fold protein concentration changes, and diluted into a constant background of yeast proteins. Similar to other datasets used for ground truth in quantitative studies, with the exception of being more granular, and much larger in terms of replicates, to enable more rigorous and accurate testing of quantitative algorithms.

2019-02-28 | MSV000083496 | MassIVE

Arabidopsis thaliana spiked UPS1 standard protein mixtures

Project description:This project aims at providing a quantitative dataset from LC-MS/MS injections of a calibrated UPS1 mixture spiked in an Arabidopsis thaliana background.

2022-07-31 | PXD027800 | Pride

Comparative analysis of mRNA degradation and protein degradation in prostate tissues indicates high stability of proteins

Project description:To benchmark the PIN algorithm that quantifies the extent of protein degradation in samples, we generated a set of “ground truth” samples, in which the levels of proteome degradation were known and independently validated by western blotting. Protein extracts of HeLa Kyoto cells were treated with the low specificity protease Proteinase K at different protease concentrations.

2019-06-12 | PXD013622 | Pride

Molecular mechanism of mitochondrial phosphatidate transfer by Ups1.

Project description:Cardiolipin, an essential mitochondrial physiological regulator, is synthesized from phosphatidic acid (PA) in the inner mitochondrial membrane (IMM). PA is synthesized in the endoplasmic reticulum and transferred to the IMM via the outer mitochondrial membrane (OMM) under mediation by the Ups1/Mdm35 protein family. Despite the availability of numerous crystal structures, the detailed mechanism underlying PA transfer between mitochondrial membranes remains unclear. Here, a model of Ups1/Mdm35-membrane interaction is established using combined crystallographic data, all-atom molecular dynamics simulations, extensive structural comparisons, and biophysical assays. The α2-loop, L2-loop, and α3 helix of Ups1 mediate membrane interactions. Moreover, non-complexed Ups1 on membranes is found to be a key transition state for PA transfer. The membrane-bound non-complexed Ups1/ membrane-bound Ups1 ratio, which can be regulated by environmental pH, is inversely correlated with the PA transfer activity of Ups1/Mdm35. These results demonstrate a new model of the fine conformational changes of Ups1/Mdm35 during PA transfer.

| S-EPMC7447767 | biostudies-literature

yeast-UPS1 standard LC-MS/MS dataset

Project description:Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years due to the technical improvement of mass spectrometers, and now allow to extensively characterize complex protein mixtures. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, which appear as an attractive way to analyze differential protein expression in complex biological samples. Classical label-free quantitative workflows are based either on spectral counting of MS/MS sequencing scans for each protein, or on the extraction of peptide ion peak area values in the LC-MS map composed of all the survey MS scans acquired during the chromatographic gradient. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we provide a dual proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate, that was used to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). This dataset can also be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods

2015-12-01 | PXD001819 | Pride

Hydrothermal Vent Campylobacteria Proteome in Response to N2O

Project description:A culture of the hydrothermal vent bacterium Nitrosophilus labii HRV44T was grown with N2O to investigate molecular mechanisms of N2O-based respiration. Limited sample sizes were collected at 0 hours (before N2O addition to the culture headspace) and at 3, 6, and 24 hours after N2O addition.

2024-10-06 | PXD053214 | Pride

The landscape of accessible chromatin in mammalian pre-implantation embryos (ChIP -Seq)

Project description:In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Mouse 2-cell embryos were obtained from crosses of C57BL/6N x PWK for ChIP-seq samples.

2016-06-15 | E-GEOD-79935 | biostudies-arrayexpress

irrigation water pre-enrichment spiked with ten fold dilutions of STEC EDL 933 O157:H7

Project description:irrigation water pre-enrichment spiked with ten fold dilutions of STEC EDL 933 O157:H7 Metagenome

| PRJNA639799 | ENA

Deep sequencing of synthetic RNA (complex molecular spike-in set)

Project description:A highly complex set of 264 molecular spikes, based on 11 unique spike sequences spanning different lengths (570 to 3070 nts) and GC contents (40-60%) was designed. In order to be able to precisely evaluate quantification over different expression levels, transcript lengths and GC contents, barcodes of 7 nucleotides in 2-fold abundance steps were cloned into each spike sequence (12 steps in duplicates; 24 barcodes per sequence) creating a standard curve for each spike sequence. To determine the molecular abundance of each of the 264 molecular spike-ins (i.e., the ‘ground truth’), we performed an exhaustive sequencing across the spike barcodes and spUMIs and determined the total complexity in the pool to be 76 million unique molecules

2022-02-16 | E-MTAB-11448 | biostudies-arrayexpress

Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex.

Project description:Ups1 forms a complex with Mdm35 and is critical for the transport of phosphatidic acid (PA) from the mitochondrial outer membrane to the inner membrane. We report the crystal structure of the Ups1-Mdm35-PA complex and the functional characterization of Ups1-Mdm35 in PA binding and transfer. Ups1 features a barrel-like structure consisting of an antiparallel β-sheet and three α-helices. Mdm35 adopts a three-helical clamp-like structure to wrap around Ups1 to form a stable complex. The β-sheet and α-helices of Ups1 form a long tunnel-like pocket to accommodate the substrate PA, and a short helix α2 acts as a lid to cover the pocket. The hydrophobic residues lining the pocket and helix α2 are critical for PA binding and transfer. In addition, a hydrophilic patch on the surface of Ups1 near the PA phosphate-binding site also plays an important role in the function of Ups1-Mdm35. Our study reveals the molecular basis of the function of Ups1-Mdm35 and sheds new light on the mechanism of intramitochondrial phospholipid transport by the MSF1/PRELI family proteins.

| S-EPMC4515121 | biostudies-literature

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