Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EuPA YPIC challenge entry - proteome data analysis

ABSTRACT: Sweet Google O’ Mine - The Importance of Online Search Engines for MS-facilitated, Database-independent Identification of Peptide-encoded Book Prefaces

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Artificial Sequences

SUBMITTER: Alexander Hogrebe

LAB HEAD: Jesper Velgaard Olsen

PROVIDER: PXD007693 | Pride | 2019-10-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20170731_LUMOS1_nLC13_RJC_YPIC_test2_all2ext_12scans.raw	Raw
	20170731_LUMOS1_nLC13_RJC_YPIC_test2_all2ext_6scans_Usens.raw	Raw
	txt.rar	Other

Items per page:

1 - 3 of 3

Similar Datasets

Candidatus Liberibacter americanus induces significant reprogramming of the transcriptome of the susceptible citrus genotype

Project description:This study evaluated the transcriptional reprogramming of a susceptible genotype (Pera sweet orange) challenged with the pathogenic bacteria Candidatus Liberibacter americanus (CaLam), using a customized 385K microarray containing about 32,000 unigene transcripts. For the microarray experiment were used symptomatic leaves from two Pera sweet orange plants inoculated with either bark or bud pieces infected with Candidatus Liberibacter americanus and two non-infected control plants.

2012-12-17 | E-GEOD-41221 | biostudies-arrayexpress

Impact of URT1-mediated uridylation on small RNA tailing in Arabidopsis

Project description:To analyse the impact of URT1-mediated uridylation on miRNA and siRNA tailing, we deep-sequenced small RNA libraries for WT and urt1 duplicate samples at the same developmental stage that was analyzed by TAIL-seq, i.e., two-week-old seedlings. Examination of miRNA and siRNA tailing in WT and urt1 samples.

2016-03-11 | E-GEOD-72456 | biostudies-arrayexpress

Plasmodium sporozoites require the protein B9 to invade hepatocytes

Project description:Here we report that the B9 protein, a member of the 6-cysteine domain protein family, is secreted from sporozoite micronemes and is required for productive invasion of hepatocytes.

2023-03-11 | PXD034830 | Pride

SIP experiment on flagellar cytoskeletons prepared using 0.2 M NaCl

Project description:To identify protein constituents of the structures at the tip of the trypanosome flagellum

2017-08-16 | PXD006761 | Pride

SIP experiment on flagellar cytoskeletons prepared using 1 M NaCl, Bound and Unbound Fractions

Project description:To identify protein constituents of the structures at the tip of the trypanosome flagellum

2017-08-16 | PXD006777 | Pride

ProAlanase is an effective alternative to trypsin for proteomics applications and disulfide bond mapping

Project description:Trypsin is the protease of choice in bottom-up proteomics. However, its application can be limited by the amino acid composition of target proteins and the pH of digestion solution. In this study we characterized ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestions are carried out at acidic pH (1.5) for relatively short (2 hr) time periods. To elucidate the potential of ProAlanase in proteomic applications, we conducted a series of investigations comprising digestion of proline-rich proteins, PTM analysis, de novo protein sequencing and disulfide bond mapping. The results demonstrated that digestion with ProAlanase improves protein sequence coverage and phosphosite localization for the proline-rich protein Notch3 intracellular domain and improves non-collagenous bone protein identification. Notably, cleavage also occurs at the C-terminus of hydroxyproline, facilitating efficient digestion of bone collagen. Finally, we demonstrate that ProAlanase is efficient in disulfide bond mapping, showing high coverage of disulfide-containing regions in monoclonal antibodies, as well as achieving nearly complete database-independent sequence reconstruction of endogenous protein by de novo sequencing.

2020-10-19 | PXD019039 | Pride

ProAlanase is an effective alternative to trypsin for proteomics applications and disulfide bond mapping_part3

Project description:Trypsin is the protease of choice in bottom-up proteomics. However, its application can be limited by the amino acid composition of target proteins and the pH of the digestion solution. In this study we characterize ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestion is carried out at acidic pH (1.5) for relatively short (2 h) time periods. To elucidate the potential of ProAlanase in proteomics applications, we conducted a series of investigations comprising comparative multi-enzymatic profiling of a human cell line proteome, histone PTM analysis, ancient bone protein identification, phosphosite mapping and de novo sequencing of a proline-rich protein and disulfide bond mapping in monoclonal antibody. The results demonstrate that ProAlanase is highly suitable for proteomics analysis of the arginine- and lysine-rich histones, enabling high sequence coverage of multiple histone family members. It also facilitates an efficient digestion of bone collagen thanks to the cleavage at the C-terminus of hydroxyproline which is highly prevalent in collagen. This allows to identify complementary proteins in ProAlanase- and trypsin-digested ancient bone samples, as well as to increase sequence coverage of non-collagenous proteins. Moreover, digestion with ProAlanase improves protein sequence coverage and phosphosite localization for the proline-rich protein Notch3 intracellular domain (N3ICD). Furthermore, we achieve a nearly complete coverage of N3ICD protein by de novo sequencing using the combination of ProAlanase and tryptic peptides. Finally, we demonstrate that ProAlanase is efficient in disulfide bond mapping, showing high coverage of disulfide-containing regions in a non-reduced monoclonal antibody.

2020-10-19 | PXD021703 | Pride

ProAlanase is an effective alternative to trypsin for proteomics applications and disulfide bond mapping_part2

2020-10-19 | PXD021191 | Pride

Development of Hypsizygus marmoreus

Project description:Hypsizygus marmoreus is one of the most popular industrialized cultivation mushrooms in East Asia, including China, Korea and Japan. It draws our attention due to its desirable, mildly sweet nutty flavor, unique texture and medicinal properties. As a result, the number of H. marmoreus cultivation factories increased gradually in different regions of the world, especially in China. H. marmoreus is the third wildly cultivated industrialized cultivated mushroom in China now. However, its development process is still not very clear. In this study, we use proteomics analysis to investigate the mechanism involved in development of Hypsizygus marmoreus.

2021-11-02 | PXD028353 | Pride

Sweet corn: low vs. high plant density

Project description:Transcriptional profiling of sweet corn response to plant density (crowding stress). Determine the extent to which hybrid and environment influences crowding stress response and identify crowding stress transcriptional response in sweet corn

2021-06-01 | GSE72434 | GEO

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