Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

De novo peptide sequencing tools benchmark

ABSTRACT: Our study is a large-scale evaluation of de novo peptide sequencing tools using both publicly and proprietary heterogeneous datasets spanning multiple species, mass spectrometers, post-translational modifications, and a wide range of use cases. This dataset contains a publicly available subset of this dataset. The dataset includes raw MS/MS spectra in their original vendor formats as well as in mzML and Mascot Generic Format (MGF). Additionally, peptide spectral hits (PSMs) identified through a database search and rescoring workflow, along with the dataset-specific protein databases used for annotation, are provided.

INSTRUMENT(S): LTQ Orbitrap, Orbitrap Fusion ETD, LTQ Orbitrap Velos, Q Exactive HF-X, TripleTOF 5600+, Orbitrap Astral, Orbitrap Fusion, Orbitrap Exploris 480, timsTOF Pro, Orbitrap Fusion Lumos, 6550 iFunnel Q-TOF LC/MS, Q Exactive HF, Q Exactive

ORGANISM(S): Bacillus Subtilis (ncbitaxon:1423) Candidatus Thiodiazotropha Endoloripes (ncbitaxon:1818881) Salmonella Enterica (ncbitaxon:28901) Escherichia Coli (ncbitaxon:562) Vigna Mungo (ncbitaxon:3915) Solanum Lycopersicum (ncbitaxon:4081) Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) Mus Musculus (ncbitaxon:10090) Methanosarcina Mazei (ncbitaxon:2209) Apis Mellifera (ncbitaxon:7460)

SUBMITTER: Wout Bittremieux

PROVIDER: MSV000096182 | MassIVE | Wed Oct 23 15:40:00 BST 2024

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Defining genetic variation in widely used congenic and backcrossed mouse models reveals varied regulation of genes important for immune responses [ChIP-seq]

Project description:In our study, we developed an alternative next-generation sequencing dataset processing strategy to identify genetic variation in backcross mouse models. We used this approach to define SJL genetic content in B6.SJL-CD45.1 mice from different vendor sources.

2019-06-24 | GSE129576 | GEO

Defining genetic variation in widely used congenic and backcrossed mouse models reveals varied regulation of genes important for immune responses [RNA-seq]

2019-06-24 | GSE129575 | GEO

MASH Explorer: A Universal Software Environment for Top-Down Proteomics

Project description:MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database searching algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.

2021-09-09 | PXD020615 | Pride

Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts.

Project description:High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. We found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. Up to 45% of peaks in publicly available HITS-CLIP libraries are attributable to this artifact, and the majority of libraries have detectable levels of mispriming. We also found that standard techniques for validating miRNA-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks. Here, we present a modification to the HITS-CLIP protocol that effectively eliminates this artifact. Argonaute HITS-CLIP on the MCF-7 breast cancer cell line treated with 17Î²-estradiol for 0, 6 or 24 hours using a nested reverse transcriptions pimer and protected or unprotected reverse PCR primers for library amplification.

2016-02-19 | E-GEOD-78059 | biostudies-arrayexpress

Large-scale analysis of the human transcriptome - Novartis dataset

Project description:High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations. Keywords: other. This dataset is part of the TransQST collection.

2002-12-06 | E-GEOD-96 | biostudies-arrayexpress

Transcription profiling of 91 human and mouse samples across a diverse array of tissues, organs, and cell lines to provide a preliminary, but substantial, description of the normal mammalian transcriptome.

2007-12-19 | E-GEOD-97 | biostudies-arrayexpress

PIA - iPRG2008 Benchmark Dataset

Project description:This dataset is no actual new study but the iPRG2008 benchmark dataset used in the PIA manuscript.

2015-05-08 | PXD000793 | Pride

Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts.

2016-02-19 | GSE78059 | GEO

Reanalysis of dataset PXD005780: “Relating human gut metagenome and metaproteome”

Project description:This project contains raw data, intermediate files and results is a re-analysis of the publicly available dataset from the PRIDE dataset PXD005780. The RAW files were processed using ThermoRawFileParser, SearchGUI and PeptideShaker through standard settings (see ‘Data Processing Protocol’). This reanalysis work is part of the MetaPUF (MetaProteomics with Unknown Function) project, which is a collaboration between EMBL-EBI and the University of Luxembourg. The dataset was selected with the following conditions: 1. It has been made publicly available in PRIDE and focuses on metaproteomics of the human gut; 2. The corresponding metagenomics assemblies were also available from ENA (European Nucleotide Archive) or MGnify. The processed peptide reports for each sample are available to view at the contig level on the MGnify website. In total, the reanalysis identified 15,417 unique proteins from 15 samples.

2022-05-04 | PXD032303 | Pride

Reanalysis of dataset PXD003791: “MuSt multiomics - Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes”

Project description:This project contains raw data, intermediate files and results is a re-analysis of the publicly available dataset from the PRIDE dataset PXD003791. The RAW files were processed using ThermoRawFileParser, SearchGUI and PeptideShaker through standard settings (see ‘Data Processing Protocol’). This reanalysis work is part of the MetaPUF (MetaProteomics with Unknown Function) project, which is a collaboration between EMBL-EBI and the University of Luxembourg. The dataset was selected with the following conditions: 1. It has been made publicly available in PRIDE and focuses on metaproteomics of the human gut; 2. The corresponding metagenomics assemblies were also available from ENA (European Nucleotide Archive) or MGnify. The processed peptide reports for each sample are available to view at the contig level on the MGnify website. In total, the reanalysis identified 59,613 unique proteins from 36 samples.

2022-06-17 | PXD034617 | 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