Browse
Submit Data
Databases
API
Help

Dataset Information

286 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Trimodal chromatography enables facile peptide fractionation

ABSTRACT: We evaluated the utility of a trimodal stationary phase (Trinity P1) in offline peptide fractionation, and found it performed similarly to ion exchange or high pH reversed phase based techniques. It is orthogonal to low pH reversed phase and uses MS compatible mobile phase solvents.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture, Cell Culture

SUBMITTER: Peng Yu

LAB HEAD: Bernhard Kuster

PROVIDER: PXD006188 | Pride | 2017-08-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	01703_A01_P018141_S00_N01_R1.raw	Raw
	01703_A02_P018141_S00_N16_R1.raw	Raw
	01703_A03_P018141_S00_N17_R1.raw	Raw
	01703_A04_P018141_S00_N25_R1.raw	Raw
	01703_A05_P018141_S00_N33_R1.raw	Raw

Items per page:

1 - 5 of 447

Publications

Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis.

Yu Peng P Petzoldt Svenja S Wilhelm Mathias M Zolg Daniel Paul DP Zheng Runsheng R Sun Xuefei X Liu Xiaodong X Schneider Günter G Huhmer Andreas A Kuster Bernhard B

Analytical chemistry 20170818 17

Offline two-dimensional chromatography is a common means to achieve deep proteome coverage. To reduce sample complexity and dynamic range and to utilize mass spectrometer (MS) time efficiently, high chromatographic resolution of and good orthogonality between the two dimensions are needed. Ion exchange and high pH reversed phase chromatography are often used for this purpose. However, the former requires desalting to be MS-compatible, and the latter requires fraction pooling to create orthogonal ...[more]

PMID: 28759994

Similar Datasets

HeLa proteome of 12,250 protein-coding genes

Project description:We developed an optimized multi-shot proteomics workflow based on high-resolution offline high pH reversed-phase peptide separation of high peptide loads collecting many fractions that were in turn analyzed by short online chromatographic separations and fast peptide sequencing using orbitrap tandem mass spectrometry.

2017-06-12 | PXD004452 | Pride

Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

Project description:The faster sequencing speed available on the latest Q Exactive HF mass spectrometer is investigated and evaluated by four different acquisition methods and benchmarked across three generations of Q Exactive instruments. Also the instrument capabilities for offline high pH reversed-phase peptide fractionation and single-shot phosphoproteomics are evaluated.

2014-10-31 | PXD001305 | Pride

Comprehensive evaluation of different TiO2-based phosphopeptide enrichment and fractionation methods for phosphoproteomics

Project description:We performed a comprehensive evaluation of four different TiO2-based phosphopeptide enrichment methods using different non-phosphopeptide excluders. Then, two phosphopeptide fractionation methods, including the ammonia-based and the TEA based high pH reversed-phase fractionation, are also evaluated.

2022-06-02 | PXD034264 |

The P1 Transcription Factor Binding to the Genome

Project description:To determine which of the genes differentially expressed between P1-rr and P1-ww pericarps were immediate (direct) targets of P1, we conducted chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) using P1 polyclonal antibodies (alphaP1344) that recognize the non-conserved C-terminal region of P1 (Falcone Ferreyra et al., 2010), on pericarp chromatin. Comparison of pericarp chromatin inmunoprecipitated material P-rr_14DAP (P1 expressed) vs P-ww_14DAP (P1 not expressed) to determine P1 direct targets

2012-09-14 | E-GEOD-38587 | biostudies-arrayexpress

The Whi2p-Psr1p/Psr2p complex regulates interference competition and expansion of cells with competitive advantage in multicellular yeast colonies - Proteomics of P1, P1-whi2 and P1-psr1psr2 colonies.

Project description:The associated files are mass spec raw data from Orbitrap Fusion. Proteins originated from colonies of Saccharomyces cerevisiae P1, P1-whi2 and P1-psr1psr2 strains.

2020-06-04 | PXD016670 | Pride

Effects of abolishing Whi2 on the proteome and nitrogen catabolite repression-sensitive protein production - Proteomics of P1 and P1-whi2 strains in SCCSH and SCME liquid media.

Project description:The associated files are mass spec data of proteins from liquid cultures of Saccharomyces cerevisiae P1 and P1-whi2 strains.

2021-11-29 | PXD028004 | Pride

HeLa proteome of 12,250 protein-coding genes

| MSV000081563 | MassIVE

Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (fractionation data)

Project description:Circulating miRNAs are an emerging class of biomarkers correlating their specific expression patterns to disease states. A considerable proportion of hematopoietically-derived miRNAs are present in plasma with the ability to confound the signature of true circulating miRNA species. We use microarray analysis to catalogue a list of 313 haemotopoetic miRNAs and analyze expression profiles of cell-free miRNAs in individual plasma fractions after calibrating for cellular miRNA signals. Comprehensive global maps of bona fide circulating miRNA species are presented, and inter-individual variability and gender-specific expression is explored in populations of healthy individuals. Healthy Caucasian individuals were used to segregate blood into 8 subfractions: white blood cells (WBC)/buffy coat, leukocytes, red blood cells (red blood cells (RBC)), cloudy supernatant (CS), supernatant 1 (S1), supernatant 2 (S2), pellet 1 (P1) and pellet 2 (P2) through differential centrifugation to understand the proportion of cellular miRNAs in each category.

2011-06-17 | E-GEOD-27230 | biostudies-arrayexpress

Pre-fractionation extends, but creates a bias in the detectable HLA class Ι ligandome

Project description:HLA class Ι molecules on the cell surface enable CD8+ T lymphocytes to recognize cellular alterations in the form of antigens, including mutations, protein copy number alterations, aberrant post-translational modifications or pathogen proteins. At any given moment, tens of thousands of different self and foreign HLA class Ι peptide ligands may be presented on the cell surface by MHC class Ι complexes. Analysis of the HLA ligandome thrusts therefore unique challenges due to their enormous biochemical diversity and inherently wide range of abundances. Despite advances in enrichment, separation, MS instrumentation and fragmentation, it is still not achievable to cover the HLA class Ι ligandome in sufficient depth to support routine identification of e.g. viral pathogens or immuno-therapeutically important tumor neo-antigens. In this study, we evaluate two pre-fractionation techniques, high pH reversed phase and strong cation exchange for complementary analysis of HLA class Ι peptide ligands, benchmarking them against analyses circumventing pre-fractionation. We observe that pre-fractionation substantially extends the detectable HLA class Ι ligandome, but also creates an identification bias. We advocate a rational choice between no-fractionation, high pH reversed phase or strong cation exchange pre-fractionation for deeper HLA class Ι ligandome analysis depending on the targeted HLA locus, allele or peptide ligand modification

2019-02-25 | PXD011257 | Pride

Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques.

Project description:Circulating antibodies provide valuable information about an individual’s immune status and constitute a significant portion of the human plasma proteome. Proteomic analysis of plasma is challenged by the large dynamic concentration range of plasma proteins, including antibodies. Peptide fractionation prior to data-independent (shotgun) proteomics has the potential to overcome this obstacle and enable increased coverage of plasma proteins. In this work, we evaluated the detection of tryptic immunoglobulin variable region peptides using multidimensional chromatography (high-pH preparative LC) or gas-phase ion mobility spectrometry (FAIMS). Typical digests of eight serum samples were obtained by (a) direct LC-MS (without prior fractionation, 1D), (b) LC-FAIMS-MS, and (c) high-pH reversed-phase fractionation into 24 fractions and subsequent measurement of each fraction. As de novo search is an essential step in antibody variable region peptide identification, all MS/MS spectra were acquired in high resolution Orbitrap mode.

2024-08-09 | PXD046072 | 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