Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

2 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 1006

Immunoaffinity profiling of mitochondrial ubiquitin substrates modulated of Parkin and USP30

ABSTRACT: Data from Massive, ID: MSV000078977. File: 20140408_OBJ03492_Ubiscan_USP30oe_bioreplicate_2ndSTelute_CCCP_inj01.mzml.

INSTRUMENT(S): Instrument

ORGANISM(S): Homo_sapiens_viruses, Human

DISEASE(S): Not Available

SUBMITTER: Kirkpatrick DS, et al.

PROVIDER: GPM32320005486 | GPMDB |

REPOSITORIES: GPMDB

ACCESS DATA

Json Xml

Similar Datasets

Proteomics data of Escherichia phage vB_EcoS-EE09 isolated from wastewater treatment plant effluent and its infected and non-infected host E. coli DSM613

Project description:This dataset was created to (i) compare the protein expression of E. coli DSM613 cells infected and uninfected with phage vB_EcoS-EE09 and (ii) detect structural proteins of phage vB_EcoS-EE09. Thus, this set provides proteomic data of three setups: 1. Uninfected E. coli DSM613 (file names [file ID]: 04_22A [F40]; 13_ecolicontrol_01 [F13]; 14_ecolicontrol_02 [F14]) 2. E. coli DSM613 infected with phage vB_EcoS-EE09 (file names [file ID]: 02_13A [F39]; 27_ecoliinfected_01 [F27]; 28_ecoliinfected_02 [F28]) 3. Cell-free phage lysate of phage vB_EcoS-EE09 (sample name: 01_EE09)

2023-11-13 | PXD046455 | Pride

iTRAQ MS of mouse LbetaT2 cells transfected with Galphas siRNA vs. scrambled siRNA

Project description:Twenty million LbetaT2 cells were transfected with either control or Galphas siRNA, then were seeded in 100-mm cell culture plates in DMEM + 10% FBS. Two days later, cells were washed twice with pre-warmed PBS. Conditioned media was harvested another 24 h later, and centrifuged at 20,000 g for 10 min at 4°C to remove cell debris. To enrich secreted proteins in the conditioned media, conditioned media samples were centrifuged using Amicon centrifugal filters with a 3kDa cutoff (Millipore, Billerica, MA). A total of 8 concentrated conditioned media samples were independently prepared: 4 samples from control siRNA-treated cells, and 4 samples from Galphas siRNA-treated cells. Samples were stored at –70°C until they were sent to the Mount Sinai Proteomics Core Facility.HPLC-isobaric tags for relative and absolute quantitation mass-spectrometry (iTRAQ MS) - Data analysis ProteinPilot 3.0 (AB Sciex) was used to search the MS/MS spectra for protein identification and quantitation with its searching algorithm Paragon 3.0.0.0 (*Reference). The protein database used for searching was Uniprot mouse fasta file (release-2010_11). The search parameters include quantitation for iTRAQ 8-plex (peptide-labeled), MMTS for cysteine alkylation, trypsin for enzyme digestion, biological modifications for ID focus, and taxonomy set for Mus musculus. The detected protein threshold was set to 1.3 (95% confidence). Additionally, we converted our AB Sciex mass spectral data (TOF/TOF data) into an mzML format, using the AB Sciex MS Data Converter (beta version 1.3) tool. Finally, we used the command line tool group2xml, which is included with ProteinPilot Software, to convert the .group search engine result file to an XML file.

2016-09-27 | PXD000063 | Pride

Project description:SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis

| PRJNA744329 | ENA

A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array]

Project description:These are the tiling array data for the experiments describing LADs on murine chromosomes 5, 12, and 15 by Dam-ID, as determined by LMNB and EMD Dam tagging and detection experiments Supplemental Bed file contains GADA algorithm calls for genomic regions of chromosomes 5, 12 and 15 (-1= no lad, high confidence, 0=indeterminate, 1=LAD, high confidence)

2012-02-14 | GSE35777 | GEO

Insilico TOF top-down proteomics datasets generated using FTMS simulator (Spectroswiss)

Project description:This dataset consists of in silico generated TOF top-down proteomics spectra created using the FTMS simulator software (Spectroswiss). The simulated datasets are designed to evaluate FDR estimation in spectral deconvolution. Protein sequences were used to generate MS datasets with varying resolution, noise, and charge characteristics. The dataset includes deconvolved TSV files and corresponding input mzML insilico file.

2026-03-09 | PXD063631 | Pride

Aird: A computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time

Project description:We describe "Aird", an opensource and computation-oriented format with controllable precision, flexible indexing strategies, and high compression rate. Aird provides a novel compressor called Zlib-Diff-PforDelta (ZDPD) for m/z data. Compared with Zlib only, m/z data size is about 55% lower in Aird on average. With the high-speed decoding and encoding performance brought by the Single Instruction Multiple Data(SIMD) technology used in the ZDPD, Aird merely takes 33% decoding time compared with Zlib. We used the open dataset HYE, which contains 48 raw files from SCIEX TripleTOF 5600 and TripleTOF6600. The total file size is 206GB as the vendor format. The total size increases to 854GB after converting to mzML with 32-bit encoding precision. While it takes only 189GB when using Aird. Aird uses JavaScript Object Notation (JSON) for metadata storage. Aird-SDK is written in Java and AirdPro is a GUI client for vendor file converting which is written in C#. They are freely available at https://github.com/CSi-Studio/Aird-SDK and https://github.com/CSi-Studio/AirdPro.

2021-04-12 | PXD025142 | Pride

Urine proteomics profiling of the COVID-19

Project description:Urine proteomics profiling from the mild and severe COVID-19 patients<ul><li>Dataset imported into MassIVE from <a href="https://www.iprox.org/page/project.html?id=IPX0002166000">https://www.iprox.org/page/project.html?id=IPX0002166000</a> on 05/30/20</li></ul>

2020-05-30 | MSV000085516 | MassIVE

Proteomic profiling reveals difference of X and Y chromosome-bearing sperm in indigenous boars

Project description:The summary file contains summary information for all theraw files processed with a single MaxQuant run. Thesummaryinformation consists of some MaxQuantparameters, information of the raw file contents, andstatistics on the peak detection. Based on this file a quickoverview can be gathered on the quality of the data in theraw file.

| PXD067977 |

Comparative proteomic profiling reveals the roles of proteins during spermatozoa capacitation in sheep

Project description:The summary file contains summary information for all the raw files processed with a single MaxQuant run. The summary information consists of some MaxQuant parameters, information of the raw file contents, and statistics on the peak detection. Based on this file a quick overview can be gathered on the quality of the data in the raw file.

2020-12-12 | PXD023101 |

Blank analysis datasets for plantMASST

Project description:Blank analysis datasets for plantMASST MassIVE data MSV000099792, MSV000099788, MSV000099790, MSV000099793, MSV000099794, MSV000087872, MSV000092992, MSV000092820. Please see their corresponding MassIVE ID metadata for LCMS methods.

2025-11-10 | MSV000099831 | MassIVE

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