Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single amino acid variant

ABSTRACT: We performed deep proteomic profiling down to as few as 9 Panc-1 cells using sample fractionation, TMT multiplexing and carrier/reference strategy. Off line fractionation of the TMT-labeled sample pooled with TMT-labeled carrier Panc-1 whole cell proteome was achieved using alkaline reversed phase spin columns. The fractionation in conjunction with carrier/reference proteome allowed us to detect 47,414 unique peptides derived from 6261 proteins which provided a sufficient coverage to search for single amino acid variants (SAAVs)related to cancer.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Zhijing Tan

LAB HEAD: David M. Lubman

PROVIDER: PXD011471 | Pride | 2020-05-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Carrier1.dat	Other
	Carrier1.raw	Raw
	Carrier2.dat	Other
	Carrier2.raw	Raw
	Carrier3.dat	Other

Items per page:

1 - 5 of 86

Publications

Single Amino Acid Variant Discovery in Small Numbers of Cells.

Tan Zhijing Z Yi Xinpei X Carruthers Nicholas J NJ Stemmer Paul M PM Lubman David M DM

Journal of proteome research 20181121 1

We have performed deep proteomic profiling down to as few as 9 Panc-1 cells using sample fractionation, TMT multiplexing, and a carrier/reference strategy. Off line fractionation of the TMT-labeled sample pooled with TMT-labeled carrier Panc-1 whole cell proteome was achieved using alkaline reversed phase spin columns. The fractionation in conjunction with the carrier/reference (C/R) proteome allowed us to detect 47 414 unique peptides derived from 6261 proteins, which provided a sufficient cove ...[more]

PMID: 30404448

Similar Datasets

29-Plex Tandem Mass Tag Mass Spectrometry Enabling Accurate Quantification by Interference Correction

Project description:Tandem mass tag (TMT) mass spectrometry is a mainstream isobaric chemical labeling strategy for profiling proteomes. Here we present a 29-plex TMT method to combine the 11-plex and 18-plex labeling strategies. The 29-plex method was examined with a pooled sample composed of 1x, 3x and 10x E. coli peptides with 100x human background peptides, which generated two E. coli datasets (TMT11 and TMT18), displaying the distorted ratios of 1.0:1.7:4.2 and 1.0:1.8:4.9, respectively. This ratio compression from the expected 1:3:10 ratios was caused by co-isolated TMT-labeled ions (i.e., noise). Interestingly, the mixture of two TMT sets produced MS/MS spectra with unique features for the noise detection: (i) in TMT11-labeled spectra, TMT18-specific reporter ions (e.g., 135N) were shown as the noise; (ii) in TMT18-labeled spectra, the TMT11/TMT18-shared reporter ions (e.g., 131C) typically exhibited higher intensities than TMT18-specific reporter ions, due to contaminated TMT11-labeled ions in these shared channels. We further estimated the noise levels contributed by both TMT11- and TMT18-labeled peptides, and corrected reporter ion intensities in every spectrum. Finally, the anticipated 1:3:10 ratios were largely restored. This strategy was also validated using another 29-plex sample with 1:5 ratios. Thus the 29-plex method expands the TMT throughput and enhances the quantitative accuracy.

2023-03-10 | PXD033865 | Pride

Comparison of fractionation proteomics for local SWATH library building

Project description:For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells.

2017-07-04 | PXD006190 | Pride

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s diseaseGlobal quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease

Project description:Alzheimer’s disease (AD) is characterized by an early, asymptomatic phase (AsymAD) in which individuals exhibit amyloid-beta (Aβ) plaque accumulation in the absence of clinically detectable cognitive decline. Here we report an unbiased multiplex quantitative proteomic and phosphoproteomic analysis using tandem mass tag (TMT) isobaric labeling of human post-mortem cortex (n=27) across pathology-free controls, AsymAD and symptomatic AD individuals. With off-line high-pH fractionation and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on an Orbitrap Lumos mass spectrometer, we identified 11,378 protein groups across three TMT 11-plex batches. Immobilized metal affinity chromatography (IMAC) was used to enrich for phosphopeptides from the same TMT-labeled cases and 51,736 phosphopeptides were identified. Of these, 48,992 were quantified by TMT reporter ions representing 33,652 unique phosphosites. Two reference standards in each TMT 11-plex were included to assess intra- and inter-batch variance at the protein and peptide level. This comprehensive human brain proteome and phosphoproteome dataset will serve as a valuable resource for the identification of biochemical, cellular and signaling pathways altered during AD progression.

2020-09-16 | PXD020296 | Pride

An atlas of the aging mouse transcriptome and proteome reveals the features of age-related post-transcriptional dysregulation

Project description:We've collected bulk RNA-Seq and TMT-labeled proteomic data of aorta, brain, heart, kidney, liver, lung, muscle (gastrocnemius muscle), and skin of 6-, 15-, 24-, and 30-months old male C57BL/6J mice. The tissues used for transcriptomic analysis and proteomic analysis were collected from the same mice. All analyses were conducted with 4 biological replicates.

2024-09-18 | GSE225576 | GEO

Quantitative accuracy and precision in multiplexed single-cell proteomics.

Project description:Multiplexed quantitative mass spectrometry-based proteomics is shaped by numerous opposing propositions. With the emergence of multiplexed single-cell proteomics, studies increasingly present single cell measurements in conjunction with an abundant congruent carrier to improve precursor selection and enhance identifications. While these extreme carrier spikes are often >100-times more abundant than the investigated samples, undoubtedly the total ion current increases but quantitative accuracy possibly is affected. We here focus on narrowly titrated carrier spikes (i.e. <20x) and evaluate the elimination of such for comparable sensitivity at superior accuracy. We find that subtle changes in the carrier ratio can severely impact measurement variability and describe alternative multiplexing strategies to evaluate data quality. Lastly, we demonstrate elevated replicate overlap, while preserving acquisition throughput at improved quantitative accuracy with DIA-TMT and discuss optimized experimental designs for multiplexed proteomics of trace samples. This comprehensive benchmarking gives an overview of currently available techniques and guides through conceptualizing the optimal single-cell proteomics experiment.

2022-01-28 | PXD027912 | Pride

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress

Microarray analysis of the effects of a Î³-tocopherol-rich mixture of tocopherols on global gene expression in the prostates of TRAMP mice

Project description:We used whole mouse genome microarrays to the effects of Î³-TmT on global gene expression in the prostate TRAMP and age-matched C57BL/6 mice were administered either 600 mg/kg of Î³-TmT or a control vehicle via oral gavage. Twelve hours after dosing, prostate tissues were collected for RNA extraction.

2014-09-16 | E-GEOD-61416 | biostudies-arrayexpress

comprehensive SAAVs detection in PANC-1 cell line

Project description:Three different strategies were applied for SAAVs detection. We predicted deleterious SAAVs using online AssVar and confirm 3 SAAVs using SRM

2021-09-09 | PXD017449 | Pride

Microarray Coverage of Universal Human Reference RNA on microarrays with yeast controls

Project description:Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design

2006-01-05 | GSE3973 | GEO

A Peptidisc-based Survey of the Plasma Membrane Proteome of a Mammalian Cell

Project description:The low abundance and hydrophobicity of plasma membrane proteome relative to soluble proteins makes it difficult to characterize. Here, we apply the peptidisc membrane mimetic to purify the cell membrane proteome. We used HeLa cells as a reference to establish the method, and compared the plasma membrane proteomes between Pancreatic cancer cell Panc-1 and hPSC.

2023-10-24 | PXD039990 | 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