Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evaluating the carrier proteome effect on a TIMSTOF mass analyzer

ABSTRACT: We have simulated a carrier proteome effect using a two-proteome quantitative TMTPro 9-plex labeled sample series to evaluate the effects of extreme carrier channels on TIMSTOF quantification.

INSTRUMENT(S): timsTOF fleX

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Benjamin C Orsburn

PROVIDER: MSV000089066 | MassIVE | Tue Mar 15 12:36:00 GMT 2022

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Evaluation of the carrier proteome effect on a TIMSTOF Flex mass analyzer

Project description:Evaluation of the carrier proteome effects on a TIMSTOF mass analyzer

2022-05-06 | MSV000089428 | MassIVE

A deeper look at carrier proteome effects for single-cell proteomics

Project description:We probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. Guidelines for optimized mass spectrometry acquisition parameters and best practices for fold-change or protein copy number-based comparisons are provided.

2022-02-24 | PXD027742 | Pride

Bio-carrier metagenome

Project description:Bio-carrier metagenome Metagenome

| PRJNA448658 | ENA

Single Cell Proteomics and the Carrier Proteome Effect

Project description:Single cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method that utilizes isobaric labels to quantify multiplexed single cell proteomes. While this technique has generated great excitement, the technologies underlying SCoPE-MS - isobaric labels and mass spectrometry - comprise technical limitations with the potential to unfavorably impact data quality and biological interpretation. These limitations are due to the carrier proteome, a sample added at 25-500x single cell proteomes to enable peptide identifications. Here, we perform SCoPE-MS experiments with increasing amounts of carrier proteome and evaluate quantitative accuracy as it relates to mass analyzer dynamic range, multiplexing level, and number of ions sampled. We demonstrate that an increase in carrier proteome level requires a concomitant increase in the number of ions sampled to maintain quantitative accuracy – we term this the carrier proteome effect. Based on our findings, we provide guidance on experimental design, data collection, and data analysis to limit the impact of the carrier proteome effect within SCoPE-MS measurements.

2020-12-16 | PXD016573 | Pride

Single cell proteomics and epiproteomics of cancer cells treated with a histone deacetylate inhibitor

Project description:NCI-H-358 cancer cells were treated with the histone deacetylase inhibitor mocetinostat or DMSO mock control. SIngle cells were isolated by FACs and were multiplexed using every other channel (c-Channels of the TMTPro reagent) a carrier channel of 75 control and 75 treated cells labeled with 135n were used for each experiment. Single cells were pseudo-randomized so that each following injection had an alternate mixture of control or treated cells as each label. Analysis was performed using an EvoSep system coupled to a TIMSTOF SCP. Cells were analyzed using 30SPD, 60SPD, 100SPD, 200SPD, 300SPD and 500SPD. After blank and carrier lanes, 7 cells were analyzed in each LCMS injection, allowing 210 cells, 420 cells, 700 cells, 1400 cells, 2100 cells and 3500 cells to be analyzed in a 24 hour day, respectively. Bruker .d files were converted to MGF and the reporter mass region was recalibrated to compensate for mass error. The resulting files were analyzed in Proteome Discoverer 2.4 and SCP-Viz.

2023-11-20 | MSV000093434 | MassIVE

Evaluating Genetic Ancestry and Self-Reported Ethnicity in the Context of Carrier Screening

Project description:Evaluating Genetic Ancestry and Self-Reported Ethnicity in the Context of Carrier Screening

| PRJNA417534 | ENA

Evaluating Genetic Ancestry and Self-Reported Ethnicity in the Context of Carrier Screening

Project description:Evaluating Genetic Ancestry and Self-Reported Ethnicity in the Context of Carrier Screening

| PRJNA417535 | ENA

Offset mass carrier proteome improves quantification of multiplexed single cell proteomics

Project description:Multiplexed single cell proteomics by mass spectrometry (scpMS) approaches currently offer the highest throughput as measured by cells analyzed per day. These methods employ isobaric labels and typically a carrier proteome - a sample added at 20-500x the single cell level that improves peptide sampling and identification. Peptides from the carrier and single cell proteomes exist within the same precursor isotopic cluster and are co-isolated for identification and quantification. This represents a challenge as high levels of carrier proteome limit the sampling of peptide ions from single cell samples and can potentially lead to decreased accuracy of quantitative measurements. Here, we address this limitation by introducing a triggered by offset mass acquisition method for scpMS (toma-scpMS) that utilizes a carrier proteome labeled with non-isobaric tags that have the same chemical composition but different mass as the labels used for quantitative multiplexing. Within toma-scpMS the carrier proteome and single cell proteome are separated at the precursor level, enabling separate isolation, fragmentation, and quantitation of the single cell samples. To enable this workflow we implemented a custom data acquisition scheme within inSeqAPI, an instrument application programming interface program, that performed real-time identification of carrier proteome peptides and subsequent triggering of offset single cell quantification scans. We demonstrate that toma-scpMS is more robust to high-levels of carrier proteome and offers superior quantitative accuracy as compared to traditional multiplexed scpMS approaches when similar carrier proteome levels are employed.

2024-08-16 | MSV000095629 | MassIVE

A carrier-based quantitative proteomics method applied to biomarker discovery in pericardial fluid

Project description:Data-dependent liquid chromatography tandem mass spectrometry (LC-MS/MS) is challenged by the large concentration range of proteins in plasma and related fluids. We adapted the SCoPE method from single-cell proteomics to pericardial fluid, where a myocardial tissue carrier was used to aid protein quantification. The carrier proteome and patient samples were labeled with distinct isobaric labels, which allowed separate quantification. Undepleted pericardial fluid from patients with type 2 diabetes mellitus and/or heart failure undergoing heart surgery was analyzed with either a traditional LC-MS/MS method or with the carrier proteome. In total, 1398 proteins were quantified with a carrier, compared to 265 without, and a higher proportion of these proteins were of myocardial origin. The number of differentially expressed proteins also increased nearly four-fold. For patients with both heart failure and type 2 diabetes mellitus, pathway analysis of upregulated proteins demonstrated enrichment of immune activation, blood coagulation, and stress pathways. Overall, our work demonstrates the applicability of a carrier for enhanced protein quantification in challenging biological matrices such as pericardial fluid, with potential applications for biomarker discovery.

2024-07-31 | PXD053450 | Pride

timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Cancer cohort dataset)

Project description:Mass spectrometry (MS) has emerged as a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide range of plasma protein concentrations along with technical and biological variabilities, continue to present significant challenges for deep and reproducible protein quantitation across large patient cohorts. Here we demonstrate the qualitative and quantitative performance gain of the timsTOF HT over the timsTOF Pro 2 mass spectrometer in the analysis of neat (unfractionated) and Proteograph™ (PG)-processed plasma across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV<20%) with timsTOF HT compared to timsTOF Pro 2. In an exploratory study of 20 late-stage cancer and 20 control sampleswe observed a ~50% increase in total and statistically significant plasma peptide precursors (q<0.05) with timsTOF HT compared to Pro 2. Our data demonstrated the superior performance of timsTOF HT in identifying and quantifying differences between biologically diverse samples, which can improve disease biomarker discovery in large cohort studies. Moreover, researchers can leverage datasets from this study to optimize their LCMS workflows for plasma protein profiling and biomarker discovery. See the details in a paper, entitled "timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery".

2024-01-16 | PXD047839 | 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