Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of TMT6plex MS3 IT vs OT

ABSTRACT: This dataset is associated with a manuscript where the SPS MS3 method was used for quantifying peptides and a comparison was made between using the ion trap or Orbitrap for the MS3 analysis

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Sonja Hess

PROVIDER: MSV000079696 | MassIVE | Tue May 03 09:54:00 BST 2016

SECONDARY ACCESSION(S): PXD004093

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap-High-Energy Collision Induced Dissociation MS(3) Scan.

Liu Jane M JM Sweredoski Michael J MJ Hess Sonja S

Analytical chemistry 20160713 15

The use of tandem mass tags (TMT) as an isobaric labeling strategy is a powerful method for quantitative proteomics, yet its accuracy has traditionally suffered from interference. This interference can be largely overcome by selecting MS(2) fragment precursor ions for high-energy collision induced dissociation (HCD) MS(3) analysis in an Orbitrap scan. While this approach minimizes the interference effect, sensitivity suffers due to the high AGC targets and long acquisition times associated with ...[more]

PMID: 27377715

Similar Datasets

TKO6: A Peptide Standard to Assess Interference for Unit-Resolved Isobaric Labeling Platforms

Project description:Protein abundance profiling using isobaric labeling is a well-established quantitative mass spectrometry technique. However, ratio distortion resulting from co-isolated and co-fragmented ions - commonly referred to as interference - remains a caveat of this technique. Tribrid mass spectrometers, such as the Orbitrap Fusion and the Orbitrap Fusion Lumos with a triple mass analyzer configuration, facilitate methods (namely SPS-MS3) that can help alleviate interference. Yet, few standards are available to measure interference. Here we introduce the TKO6 standard that assesses ion interference and is designed specifically for data acquired at low (unit) mass resolution. We use TKO6 to compare the degree of interference in MS2 versus MS3-based quantitation methods, data acquisition methods of different lengths, and ion trap-based TMT reporter ion analysis (IT-MS3). We show that the TKO6 standard is a valuable tool for assessing data quality and is particularly useful for benchmarking ion trap-based SPS-MS3 analyses.

2019-03-07 | PXD011653 | Pride

TMT characterisation: iPSC vs hESC

Project description:Detailed comparison of human pluripotent stem cells, to determine how hESC and iPSC differ in their protein expression profiles. The data was acquired in a TMT 10-plex SPS-MS3. 4 replicates of hESC compared to 4 replicates of HipSci human iPSCs.

2021-11-03 | PXD014502 | Pride

Real-Time Search Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics

Project description:In the young field of single-cell proteomics (scMS), there is a great need for improved global proteome characterization, both in terms of proteins quantified per cell and quantitative performance thereof. The recently introduced real-time search (RTS) on the Orbitrap Eclipse Tribrid mass spectrometer in combination with SPS-MS3 acquisition has been shown to be beneficial for the measurement of samples that are multiplexed using isobaric tags. Multiplexed single-cell proteomics requires high ion injection times and high-resolution spectra to quantify the single-cell signal, however the carrier channel facilitates peptide identification and thus offers the opportunity for fast on-the-fly precursor filtering before committing to the time intensive quantification scan. Here, we compared classical MS2 acquisition against RTS-SPS-MS3, both using the Orbitrap Eclipse Tribrid MS with the FAIMS Pro ion mobility interface and we present a new acquisition strategy termed RETICLE (RTS Enhanced Quant of Single Cell Spectra) that makes use of fast real-time searched linear ion trap scans to preselect MS1 peptide precursors for quantitative MS2 Orbitrap acquisition. Here we show that classical MS2 acquisition is outperformed by both RTS-SPS-MS3 through increased quantitative accuracy at similar proteome coverage, and RETICLE through higher proteome coverage, with the latter enabling the quantification of over 1000 proteins per cell at a MS2 injection time of 750ms using a 2h gradient.

2022-03-14 | PXD029320 | Pride

Methodologies comparison of porcine lung tissue

Project description:Mechanistic study of H2S interference on swine, we used TMT-based comparative proteomics of lung tissues from control and hydrogen sulfide (H2S) breathing swines as a test case for evaluation of MS2, SPS MS3 and RTS-MS3 acquisition methods in both Orbitrap Fusion and Orbitrap Eclipse.

2023-06-02 | PXD020392 | Pride

Carnobacterium jeotgali MS3

Project description:Carnobacterium jeotgali MS3 Genome sequencing and assembly

| PRJNA235041 | ENA

Carnobacterium jeotgali MS3

Project description:Carnobacterium jeotgali MS3 Genome sequencing and assembly

| PRJNA237991 | ENA

Dickeya zeae strain:MS3

Project description:Dickeya zeae strain:MS3 Genome sequencing

| PRJNA1095728 | ENA

Evaluating linear ion trap incorporation for MS3-based multiplexed single-cell proteomics

Project description:The project aims to evaluate the use of a linear ion trap to increase the sensitivity of multiplexed single-cell proteomics. Using diluted mouse peptide samples from C10 and Raw, we compared the proteome coverages, data missingness, and quantification performance between linear ion trap and Orbitrap acquisition modes for both MS2 and MS3 based analysis. The optimized RTS-LIT-MS3 method was further applied to the study of macrophage activation at single-cell resolution. Samples were labeled with 16-plex TMT. Data was searched with FragPipe.

2022-08-22 | MSV000090178 | MassIVE

I/L-discrimination by MS3 of dimethylated peptides

Project description:A novel mass spectrometric method for discriminating isoleucine and leucine by MS3. The dimethylation of peptide N-termini leads to intense a1 ions in CID and MS3 fragmentation of the isoleucine/leucine a1-ion leads to spectra with fragments that can discriminate between the two isomers. The method was applied to two antibodies in combination with a set of protease treatments using trypsin, thermolysin, chymotrypsin and pepsin to generate peptides exposing N-terminal I/L residues.

2018-07-24 | PXD009295 | Pride

Morus alba cultivar:MS3

Project description:Morus alba cultivar:MS3 Raw sequence reads

| PRJNA282698 | ENA