Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-flow LC-MS/MS analyses - Conventional-Flow Liquid Chromatography-Mass Spectrometry for Exploratory Bottom-Up Proteomic Analyses

ABSTRACT: The major objective of our study was to find out what are the extra costs and what optimization and adjustment steps of a high-flow LC-MS system have to be undertaken to identify a comparable number of proteins as on a nanoLC-MS system.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Juraj Lenco

LAB HEAD: Jiri Stulik

PROVIDER: PXD005481 | Pride | 2019-11-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Conventional-Flow Liquid Chromatography-Mass Spectrometry for Exploratory Bottom-Up Proteomic Analyses.

Lenčo Juraj J Vajrychová Marie M Pimková Kristýna K Prokšová Magdaléna M Benková Markéta M Klimentová Jana J Tambor Vojtěch V Soukup Ondřej O

Analytical chemistry 20180404 8

Due to its sensitivity and productivity, bottom-up proteomics based on liquid chromatography-mass spectrometry (LC-MS) has become the core approach in the field. The de facto standard LC-MS platform for proteomics operates at sub-μL/min flow rates, and nanospray is required for efficiently introducing peptides into a mass spectrometer. Although this is almost a "dogma", this view is being reconsidered in light of developments in highly efficient chromatographic columns, and especially with the i ...[more]

PMID: 29582996

Similar Datasets

Capturing protein communities by structural proteomics in a thermophilic eukaryote

Project description:The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions and structure of a third of the C. thermophilum proteome within these extracts. We identified 27 distinct protein communities that include 108 interconnected complexes, which dynamically associate with each other and functionally benefit from being in close proximity in the cell. Furthermore, we investigated the structure of fatty acid synthase within these extracts by cryoEM and this revealed multiple, flexible states of the enzyme in adaptation to its association with other complexes, thus exemplifying the need for in situ studies. As the components of the captured protein communities are known – at both the protein and complex level – this study constitutes another step forward towards a molecular understanding ofsubcellular organization.

2017-07-26 | PXD006626 | Pride

Conventional and Computational Flow Cytometry Analyses Reveal Sustained Human Intrathymic T Cell Development From Birth Until Puberty.

Project description: Not available

| S-EPMC7417369 | biostudies-literature

Exploratory analysis of myocardial function after extracorporeal cardiopulmonary resuscitation vs conventional cardiopulmonary resuscitation.

Project description: Not available

| S-EPMC7060522 | biostudies-literature

Measuring Extracellular Vesicles by Conventional Flow Cytometry: Dream or Reality?

Project description: Not available

| S-EPMC7503575 | biostudies-literature

Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses.

Project description: Not available

| S-EPMC6560168 | biostudies-literature

Bubble velocimetry using the conventional and CNN-based optical flow algorithms.

Project description: Not available

| S-EPMC9279369 | biostudies-literature

Optimizing the parameters governing the fragmentation of cross-linked peptides in a tribrid mass spectrometer

Project description:We compared the five different ways of fragmentation available on a tribrid mass spectrometer and optimized their collision energies with regard to optimal sequence coverage of cross-linked peptides. We created a library of bis(sulfosuccinimidyl)suberate (BS3/DSS) cross-linked precursors, derived from the tryptic digests of three model proteins (Human Serum Albumin, creatine kinase and myoglobin). This enabled in-depth targeted analysis of the fragmentation behavior of 1065 cross-linked precursors using the five fragmentation techniques: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), and the combinations ETciD and EThcD. EThcD gave the best sequence coverage for cross-linked m/z species with high charge-density, while HCD was optimal for all others. We tested the resulting data-dependent decision tree against collision energy-optimized single methods on two samples of differing complexity (a mix of eight proteins and a highly complex ribosomal cellular fraction). For the high complexity sample the decision tree gave the highest number of identified cross-linked peptide pairs passing a 5% false discovery rate (on average ~21% more than the second best, HCD). For the medium complexity sample the higher speed of HCD proved decisive. Currently, acquisition speed plays an important role in allowing the detection of cross-linked peptides against the background of linear peptides. Enrichment of cross-linked peptides will reduce this role and favor methods that provide spectra of higher quality.

2017-04-19 | PXD006131 | Pride

Exploratory Radiomic Analysis of Conventional vs. Quantitative Brain MRI: Toward Automatic Diagnosis of Early Multiple Sclerosis.

Project description: Not available

| S-EPMC8374240 | biostudies-literature

Clinical characteristics and exploratory genomic analyses of germline BRCA1 or BRCA2 mutations in breast cancer

Project description:gBRCA1/2 mutations increase the incidence of breast cancer (BC) by interrupting the homologous recombination repair (HRR) pathway. Although gBRCA1 and gBRCA2 BC have similar clinical profiles, different molecular characteristics have been observed. In this study, we conducted comprehensive genomic analyses and compared gBRCA1/2 BC. Sanger sequencing to identify gBRCA1/2 mutations was conducted in 2,720 patients, and gBRCA1 (n=128) and gBRCA2 (n=126) mutations were analyzed. Within that population, deep target sequencing (TS) and matched whole transcriptome sequencing (WTS) results were available for 46 and 34 patients, respectively. An internal database of breast-cancer patients with wildtype gBRCA was used to compile a TS (n=195) and WTS (n=137) reference dataset. Three specific mutation sites, p.Y130X (n=14) and p.1210Afs (n=13) in gBRCA1 and p.R294X (n=22) in gBRCA2, were comparably frequent. Immunohistochemistry subtyping determined that the incidence of triple negative BC was higher among those with a gBRCA1 mutation (71.9%), and estrogen receptor (ER)-positive BC was dominant in those with a gBRCA2 mutation (76.2%). gBRCA1/2 mutations were mutually exclusive with PIK3CA somatic mutations (P<0.05), and gBRCA1 frequently co-occurred with TP53 somatic mutations (P<0.05). The median tumor mutation burden was 6.53 per megabase (MB) in gBRCA1 and 6.44 per MB in gBRCA2. The expression of AR, ESR1, and PGR was significantly upregulated with gBRCA2 mutation compared with gBRCA1 mutation. gBRCA1 and gBRCA2 BC have similar clinical characteristics, but they have different molecular subtypes, co-altered somatic mutations, and gene expression patterns. Implications: Even though gBRCA1 and gBRCA2 mutations both alter HRR pathways, our results suggest that they generate different molecular characteristics and different mechanisms of carcinogenesis.

2020-04-25 | GSE149276 | GEO

Knowledge flow and exchange in interdisciplinary primary health care teams (PHCTs): an exploratory study.

Project description: Not available

| S-EPMC3634376 | biostudies-literature