Browse
Submit Data
Databases
API
Help

Dataset Information

445 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

FeatureFinderIdentification (OpenMS) analysis of the iPRG-2015 dataset

ABSTRACT: Benchmark of FeatureFinderIdentification (FFId), a targeted feature detection algorithm for use in label-free quantification, developed in the OpenMS software framework. The dataset used for the evaluation comes from the iPRG-2015 study ("Differential abundance analysis in label-free quantitative proteomics"), created by the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF); see https://abrf.org/research-group/proteome-informatics-research-group-iprg. The samples contain yeast protein digest spiked with six digested proteins in varying, known concentrations.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Cell Culture

SUBMITTER: Hendrik Weisser

LAB HEAD: Jyoti Sharma Choudhary

PROVIDER: PXD006336 | Pride | 2017-07-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	FFId_internal_1_A.featureXML	Other
	FFId_internal_1_B.featureXML	Other
	FFId_internal_1_C.featureXML	Other
	FFId_internal_2_A.featureXML	Other
	FFId_internal_2_B.featureXML	Other

Items per page:

1 - 5 of 121

Publications

Targeted Feature Detection for Data-Dependent Shotgun Proteomics.

Weisser Hendrik H Choudhary Jyoti S JS

Journal of proteome research 20170719 8

Label-free quantification of shotgun LC-MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that direc ...[more]

PMID: 28673088

Similar Datasets

Quantitation Analysis using OpenMS of iPRG2015: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments

Project description:The 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results. The study used LC–tandem mass spectra acquired from a controlled mixture, and made the data available to anonymous volunteer participants. The participants used methods of their choice to detect differentially abundant proteins, estimate the associated fold changes, and characterize the uncertainty of the results. The study found that multiple strategies (including the use of spectral counts versus peak intensities, and various software tools) could lead to accurate results, and that the performance was primarily determined by the analysts’ expertise. This manuscript summarizes the outcome of the study, and provides representative examples of good computational and statistical practice. The data set generated as part of this study is publicly available. This project contains the analysis performed with OpenMS framework and exported to mztab. This is the first official submission of mzTab (PRIDE Complete Submission) and should used as reference by software providers as example of How to export Quantitative results into PRIDE database as Complete submission.

2018-09-10 | PXD010981 | Pride

Regional differences in the small intestinal proteome of control mice and of mice lacking lysosomal acid lipase

Project description:Background: Despite recent studies investigating the involvement of single cells in regional differences of the small intestine (SI), the metabolic contribution of the duodenum, jejunum, and ileum to the overall intestinal metabolism is still unclear. Basic procedures and main findings: Using an untargeted proteomics approach, we identified similarities and differences between the three intestinal tracts of C57BL/6J mice and found that proteins highly abundant in the mouse ileum correlated with high ileal expression of the corresponding genes in humans. Consistent with human data, we detected increasing abundance of lysosomal acid lipase (LAL) in C57BL/6J mice from the duodenum to ileum. LAL is the only enzyme known to degrade triacylglycerols and cholesteryl esters within the lysosome. Lipid accumulation in various organs along with gastrointestinal disturbances and malabsorption are typical features of patients and mice with LAL deficiency. We previously demonstrated that macrophages massively infiltrate the SI of Lal-deficient (KO) mice, especially the duodenum. To identify potential mechanisms behind the intestinal lipid accumulation and infiltration of immune cells, we used untargeted proteomics. Our results revealed a general inflammatory response and a common lipid-associated macrophage phenotype in all three intestinal segments of Lal KO mice, accompanied by higher expression of GPNMB and increased concentrations of circulating sTREM2. However, only duodenal macrophages activated a metabolic switch from lipids to other pathways such as glycolysis, TCA cycle, and oxidative phosphorylation to meet their high energy demand. Unexpectedly, these pathways were downregulated in the jejunum and ileum of Lal KO mice. Conclusion: Our results provide new insights into the process of absorption in control mice and the basis for novel markers of LAL-D and/or systemic inflammation in LAL-D.

2024-02-20 | PXD048378 | Pride

Mouse liver proteome fractionation using leptin-based cartridges.

Project description:This study is aimed at the evaluation of leptin-based cartridges fractionation for glycoprotein enrichment of mouse liver protein shotgun proteomic profile.

2021-07-30 | PXD025097 | Pride

Binding motif analysis of METTL3，WTAP in METTL3，WTAP overexpressed Human 293T cells

Project description:label the cells overexpressed Myc tagged METTL3 and Flag tagged WTAP with 4-SU, the RNA bound by METT3,WTAP can be got by Myc or Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane. discovery of the binding motif of METTL3，WTAP in METTL3，WTAP overexpressed Human 293T cells

2014-01-16 | E-GEOD-50580 | biostudies-arrayexpress

Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

Project description:Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by UV light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain completely new insights into chromatin and its regulation in the future.

2020-10-20 | PXD020290 | Pride

Proteome allocation strategies under nutrient-limiting conditions in the cyanobacterium Synechocystis

Project description:The response of the model cyanobacterium Synechocystis sp. PCC6803 towards light and carbon limitation was systematically probed. To this end, Synechocystis sp. PCC6803 was cultivated in a photo-bioreactor driven in turbidostat-mode. The turbidostat is a continuous cultivation that enabled cells to adapt to a constant environment, leading to a stable and 'optimal' proteome for the respective condition. The major dataset in this project consisted of 5 different 'concentrations' for light and CO2. Changes in the proteome were determined using using liquid chromatography/mass spectrometry and it was found that carbon and light limitation induced gradual but broad responses in gene expression. With decreasing substrate concentration (increasing limitation) a decrease in growth rate and a gradually more severe response in the proteome was visible.

2018-09-12 | PXD009582 | Pride

Low-Density Lipoprotein Receptor fuels the cellular cholesterol-mTORC1 axis required for CD8+ T cell activation

Project description:In this study, the contribution of cholesterol uptake by the low-density-lipoprotein receptor (LDLR) in the metabolic reprogramming of activated T cells was investigated at proteome level by mass-spectrometry-assisted shotgun proteomics.

2022-09-20 | PXD030365 | Pride

Identification of Altered Proteins in the Plasma of Rats with Chronic Prostatic Inflammation Induced by Estradiol Benzoate and Sex Hormones

Project description:The cause of non-bacterial chronic prostatitis is unknown, yet its prevalence accounts for more than 90% of all prostatitis cases. Whole blood, plasma, and serum have been used to identify prostate cancer biomarkers; however, few studies have performed protein profiling to identify prostatitis biomarkers. The purpose of this study was to identify protein biomarkers altered by chronic prostatitis. To perform the study, we chemically induced chronic prostate inflammation in Sprague Dawley rats using estradiol benzoate (EB), testosterone (T), and estradiol (E), then examined protein levels in their plasma. Plasma was collected on postnatal days (PNDs) 90, 100, 145, and 200; plasma proteins were profiled using liquid chromatography-tandem mass spectrometry. Chronic inflammation was observed in rat prostate induced with EB on PNDs 1, 3, and 5. Rats then were dosed with T+E during PND 90-200 via subcutaneous implants. We identified time-specific expression for several proteins (i.e., CFB, MYH9, AZGP1). Some altered proteins that were expressed in the prostate (i.e., SERPINF1, CTR9) also were identified in rat plasma in the EB+T+E group on PNDs 145 and 200. These findings suggest that the identified proteins could be used as biomarkers of chronic prostatitis. Further studies are needed to verify the results in human samples.

2021-09-10 | PXD024422 | Pride

Inducible PAX5 expression in a human B lymphoblastic leukemia cell line

Project description:Hypomorphic mutations of the transcription factor PAX5 occur in one third of B-progenitor acute lymphoblastic leukemias (B-ALLs). To identify PAX5-regulated genes in B-ALL, here we employ inducible expression of PAX5 in a human B-ALL cell line (REH) that harbors a loss-of-function mutation in PAX5. In this model, inducing PAX5 expression is associated with competitive disadvantage. Comparison of REH cell lines with Dox-inducible expression of PAX5-IRES-GFP, or control GFP alone. GFP positive cells were isolated by FACS.

2014-06-18 | E-GEOD-57480 | biostudies-arrayexpress

Proteomic profiling of glioblastoma tumour tissue

Project description:Using HiRIEF LC-MS/MS, we analysed 10 GBM tumour tissue samples ran in one TMT10 set. The set consisted of 7 primary tumours and 3 non-matched recurrent tumours. One primary tumour was highly necrotic.

2022-12-23 | PXD027341 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data