Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GpGrouper: A Peptide Grouping and Quantification Algorithm

ABSTRACT: Validation of gpGrouper peptide grouping and quantitation algorithm.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Anna Malovannaya

PROVIDER: MSV000081870 | MassIVE | Sun Dec 31 10:26:00 GMT 2017

SECONDARY ACCESSION(S): PXD008560

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

In situ synthesis of peptide microarrays - shadow mask design [3]

Project description:In this paper several computer programs were used to simulate in situ synthesis of peptides using shadow masks and BOC synthesis. The peptides were designed to be random, or pseudo-random, but fulfill requirements of immunosignaturing. This file contains data from actual 330,000 peptide arrays that used the first iteration of the peptide generation algorithm. Monoclonal antibodies were bound to the microarrays and the total number of peptides that distinguished each monoclonal was measured. This provides a baseline against which to compare purely random sequences.

2014-01-16 | GSE50571 | GEO

In situ synthesis of peptide microarrays - shadow mask design [3]

2014-01-16 | E-GEOD-50571 | biostudies-arrayexpress

AGA algorithm

Project description:Aminoglycosides resistance mechanisms inference algorithm

| PRJEB29576 | ENA

In situ synthesis of peptide microarrays - shadow mask design [1]

Project description:A computer program was used to create random amino acid sequences based on and restricted by physical shadow masks which will be used for lithography-based synthesis of peptides. The output from this algorithm was used to create peptides that were synthesized by Sigma Aldrich, and printed onto glass slides. The arrays contained 384 peptides printed in duplicate for each of 4 different mask designs. 52 different monoclonal antibodies were incubated on these microarrays and analyzed for their propensity to bind the peptides created from each mask set. The diversity of binding served as a proxy for the 'randomness' of these peptides, and provided information about how many masks are needed to truly generate random sequence peptides. two replicates of each peptide was printed on 1 Mask peptide microarray. A minimum of Two microarrays were tested for each sample. Image was qualified using in-house metrics for quality assurance.

2014-01-16 | E-GEOD-49217 | biostudies-arrayexpress

Histone protein and peptide reactivity within patients with systemic lupus erythematosus (SLE) from the ABCoN cohort

Project description:The aim of the study was to test the hypothesis that IFN high SLE patient sera is more reactive to whole histone proteins and post-translationally modified histone peptides than IFN low patient sera. We diluted patient sera 1:250 and incubated dilutions on a nitrocellulose-platform array printed with whole protein and peptide histone antigens. In this study, serum from 30 patients subsetted into high and low interferon signature categories were profiled for IgG autoantibody reactivity to whole histone proteins, unmodified and post-translationally modified histone peptides. IFN high patient sera was found using the significance analysis of microarrays (SAM) algorithm to be significantly more reactive with whole histone and modified histone peptide antigens.

2011-12-02 | E-GEOD-34070 | biostudies-arrayexpress

The Null-Test for Peptide Identification Algorithm in Shotgun Proteomics

Project description:The present research proposed generally evaluating strategy named Null-Test for peptide identification algorithm in Shotgun proteomics. The Null-Test method based on random matching can be utilized to check whether the algorithm has a tendency to make a mistake or be over-fitting, thus can validate the reliability of the identification algorithm.

2016-05-25 | MSV000079774 | MassIVE

Stadard peptide mixture plus HeLa

Project description:To test our peak detection and label-free quantitation algorithm, practical applications of AB3D for LC-MS data sets were evaluated using a standard peptide mixture consisting of bovine serum albumin (BSA) peptides with different concentrations, peptides derived from four standard proteins (data set 1), and complex peptide samples derived from HeLa cells and BSA (data set 2).

2014-12-04 | PXD001259 | Pride

Autoimmune peptide antigen reactivity in normal B6 mice Pepperchip 2.0

2015-02-28 | GSE65277 | GEO

Autoimmune peptide antigen reactivity in BXD2 mice with spontaneous systemic autoimmune disease

Project description:The aim of the study was to determine autoimmune BXD2 mouse sera reactivity to linear peptide epitopes from the Immune Epitope Database. Pooled sera from six 8-10 month old BXD2 mice was diluted at 1:1000 and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens.

2015-02-28 | GSE65276 | GEO

Autoimmune peptide antigen reactivity in normal B6 mice Pepperchip 2.0

Project description:The aim of the array was to determine the B6 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old B6 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens Pooled sera from three 6-9 month old B6 mice was profiled for IgG or IgM-specific analysis of autoantibody reactivity to peptide auto-epitopes printed in duplicate on a PepperPrint Chip.

2015-02-28 | E-GEOD-65277 | biostudies-arrayexpress

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