Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS_Trapped ion mobility spectrometry (TIMS) and parallel accumulation - serial fragmentation (PASEF) enable in-depth lipidomics from minimal sample amounts_Vasilopoulou et al.

ABSTRACT: In this study, we develop a high-sensitivity lipidomics workflow based on nanoflow liquid chromatography and trapped ion mobility spectrometry. Taking advantage of the PASEF principle, we fragmented on average fifteen precursors in each 100 ms TIMS scans, while maintaining the full mobility resolution of co-eluting isomers. The very high acquisition speed of about 100 Hz allowed us to obtain MS/MS spectra of the vast majority of detected isotope patterns for automated lipid identification. Analyzing 1 uL of human plasma, 100ug of mouse liver and 5e5 HeLa cells PASEF almost doubled the number of identified lipids and reduced the analysis time by a factor of three without loss of coverage. Our single-extraction workflow surpasses the plasma lipid coverage of extensive multi-step protocols in common lipid classes and achieves attomol sensitivity. Building on the high precision and accuracy of TIMS collisional cross section measurements (median CV 0.2%), we compiled 1,856 lipid CCS values from human plasma, mouse liver and human cancer cells.

INSTRUMENT(S): tims TOF Pro Bruker, Bruker Daltonics instrument model

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Catherine Vasilopoulou

PROVIDER: MSV000083858 | GNPS | Sat May 25 01:03:00 BST 2019

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF

Project description:Data-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry (MS)-based proteomics, because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation – serial fragmentation (dia-PASEF) on a Bruker trapped ion mobility separated (TIMS) quadrupole time-of-flight (TOF) mass spectrometer. This requires alignment of the ion mobility separation with the downstream mass selective quadrupole, leading to a more complex scheme for dia-PASEF window placement compared to DIA. To achieve high data completeness and deep proteome coverage, here we employ variable isolation windows that are placed optimally depending on precursor density in the m/z and ion mobility plane. This Automatic Isolation Design procedure is implemented in the freely available py_diAID package. In combination with in-depth project-specific proteomics libraries and the Evosep LC system, we reproducibly identified over 7,700 proteins in a human cancer cell line in 44 minutes with quadruplicate single-shot injections at high sensitivity. Even at a throughput of 100 samples per day (11 minutes LC gradients), we consistently quantified more than 6,000 proteins in mammalian cell lysates by injecting four replicates. We found that optimal dia-PASEF window placement facilitates in-depth phosphoproteomics with very high sensitivity, quantifying more than 35,000 phosphosites in a human cancer cell line stimulated with an epidermal growth factor (EGF) in triplicate 21 minutes runs. This covers a substantial part of the regulated phosphoproteome with high sensitivity, opening up for extensive systems-biological studies.

2022-08-11 | PXD034128 | Pride

Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-based Quantitation in Proteomic LC/MS/MS

Project description:Two-dimensional separation by nano-LC and trapped ion mobility spectrometry (TIMS) prior to Q-TOF tandem mass spectrometry significantly improves the accuracy of isobaric tag-based quantitation in proteome analysis without the need for additional measurement time for TIMS insertion. The obtained peak capacity of up to 3,300 per hour in LC/TIMS reduced the co-isolation of precursor ions at the quadrupole analyzer, resulting in more accurate ratios of reporter ions derived from isobaric tags in product ion spectra obtained at the TOF analyzer. We also found that TIMS with a narrow quadrupole isolation window could reduce the ratio compression effect at least as effectively as the synchronous precursor selection method using MS3 scans without compromising sensitivity or coverage. Our results suggest that the short-gradient LC/TIMS/Q/TOF system is an excellent platform for high-throughput proteomics studies.

2020-05-22 | PXD018650 | JPOST Repository

Optimizing single cell proteomics on a trapped ion mobility spectrometry for label-free experiments

Project description:Although single cell RNA-seq has had a tremendous impact on biological research, a corresponding technology for unbiased mass spectrometric analysis of single cells has only recently become available. Significant technological breakthroughs including miniaturized sample handling have enabled proteome profiling of single cells. Further, a trapped ion mobility spectrometry (TIMS) in combination with parallel accumulation-serial fragmentation operated with data-dependant acquisition mode has allowed improved proteome coverage from low-input samples. It has been demonstrated that modulating ion flux in TIMS affects overall performance of proteome profiling. However, the effect of TIMS settings for analyzing low-input samples has been less investigated. Thus, we sought to optimize conditions of TIMS in regards of ion accumulation/ramp times and ion mobility range for low-input samples. We observed that ion accumulation times of 180 ms and monitoring a narrower ion mobility range from 0.7 to 1.3 Vs cm-2 resulted in a substantial gain in the depth of proteome coverage and in detecting proteins with low abundance. We applied these optimized conditions for proteome profiling of sorted human primary T cells, which yielded an average of 365, 804, 1,116, and 1,651 proteins from single, five, ten, and forty T cells, respectively. Notably, we demonstrated that the depth of proteome coverage from low number of cells was sufficient to delineate several essential metabolic pathways and T cell receptor signaling pathway. Finally, we showed the feasibility of detecting post-translational modifications including phosphorylation and acetylation from single cells. We believe that these parameters could be applied to label-free analysis of single cells obtained from clinically relevant samples.

2024-08-02 | PXD039066 | Pride

A Novel Factor Associating with Hepatic Insulin Sensitivity in Humans with Nonalcoholic Fatty Liver Disease

Project description:We comprehensively searched for the factors that may attribute to hepatic insulin sensitivity in the patients with NAFLD. Forty-three NAFLD patients were assessed for putative biomarkers in blood and urine, body composition, tissue lipid content, tissue insulin sensitivity by hyperinsulinemic-euglycemic clamp, hepatic histology and gene expressions using liver biopsies, and life styles. In results, the higher levels of plasma adiponectin, muscle insulin sensitivity, and adipose tissue insulin sensitivity positively, but the higher levels of HbA1c, ALT, and log converted high-sensitive CRP negatively correlated with hepatic insulin sensitivity. Interestingly, whole liver volume and hepatic lean volume corrected by body surface area (cm3/m2) showed significant negative correlation with hepatic insulin sensitivity, specifically in patients with T2DM.

2019-07-18 | GSE134438 | GEO

Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with novel MS2PIP timsTOF fragmentation prediction model

Project description:Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, we trained a novel timsTOF-specific peak intensity MS2PIP model for tryptic and non-tryptic peptides and implemented it in MS2Rescore (v3) together with the CCS predictor from ionmob. The optimized method, Thunder-DDA-PASEF, semi-selectively fragments singly and multiply charged HLAIps based on their IMS and m/z. Moreover, the method employs the high sensitivity mode and extended IMS resolution with fewer MS/MS frames (300 ms TIMS ramp, 3 MS/MS frames), doubling the coverage of immunopeptidomics analyses, compared to the proteomics-tailored DDA-PASEF (100 ms TIMS ramp, 10 MS/MS frames). Additionally, rescoring boosted the HLAIps identification by 41.7% to 33%. This enabled in-depth profiling of HLAIps from diverse human cell lines and human plasma. Finally, profiling JY and Raji cells transfected to express the SARS-CoV-2 spike protein resulted in 16 spike HLAIps, thirteen of which had been reported to elicit immune responses in human patients.

2024-03-18 | PXD040385 | JPOST Repository

Ion Mobility-Assisted Free Radical Initiated Peptide Sequencing v2

Project description:Free radical-initiated peptide sequencing (FRIPS) is a tandem mass spectrometry technique (MS/MS) that enables radical-based dissociation on instruments only capable of collisional activation. In FRIPS, peptides are chemically-derivatized with a compound that undergoes homolytic cleavage and generates radicals upon collisional activation. These radicals then propagate through the peptide backbone enabling the sequencing of peptide ions. This MS/MS technique has shown promise in sequencing post-translationally modified peptides, but it is typically performed in an MS3 workflow and single-step MS/MS approaches result in the generation of both collisional- and radical-driven dissociation products and highly complex spectra. Recently, our group developed a method to dissociate peptide ions prior to ion mobility analysis within a trapped-ion mobility spectrometry (TIMS) device. In this work, we examine if this CIDtims technique is capable of initiating the homolytic cleavage of the FRIPS precursor. We then examine if the resultant ion mobility separation results in additional assignments of product ions and improved sequence coverage. We demonstrate that activation within the TIMS device does indeed promote robust radical initiation and fragmentation and that the generated product ions are mobility separated enabling facile assignment and increased sequence coverage.

2024-10-15 | MSV000096102 | MassIVE

Effect of anti-miR-33 treatment on gene expression in non-human primate liver

Project description:In this study the effect of anti-miR-33 treatment on plasma and liver lipid profiles was examined in non-human primates. A significant increase in plasma HDL-C, and a significant decrease in plasma triglyceride levels were observed. African green monkeys on a Normal chow diet were treated with anti-miR-33 or control anti-miR for 4 weeks and were then switched to a High Carb/Med. Cholesterol diet and treated with anti-miR-33 or control anti-miR for 8 more weeks (n=6/group). Gene expression profiling was performed on liver biopsies obtained at -5 weeks (baseline), 4 weeks and 12 weeks.

2011-08-26 | E-GEOD-31177 | biostudies-arrayexpress

Ion mobility fractionation coupled to PASEF for enhanced proteome coverage

Project description:Data provided report the use of trapped ion mobility spectrometry (TIMS) to fractionate ions in the gas phase based on their ion mobility (V⋅s/cm2) followed by parallel accumulation serial fragmentation (PASEF) in a quadrupole time-of-flight instrument. TIMS fractionation coupled to DDA-PASEF allowed for the detection of approximately 7,000 proteins and over 70,000 peptides per overall run from 200ng of human (HeLa) cell lysate per injection using a commercial UPLC column with a 90-minute gradient. This project also explored the utility of TIMS fractionation to generate a DDA library for downstream DIA analysis using shorter LC gradients (20 minutes) as well as lower sample input. Using a 20min gradient, we identified 4,092 and 6,654 proteins on average per run, respectively, from 10ng and 200ng of human (HeLa) cell lysate input based on a TIMS-fractionated library consisting of 82,214 peptides derived from 7,615 proteins.

2022-08-12 | PXD033129 | Pride

Effect of anti-miR-33 treatment on gene expression in non-human primate liver

2011-08-27 | GSE31177 | GEO

Modulation of atherogenic lipidome

Project description:Objective: Although relationships between smoking and cardiovascular diseases (CVD), and CVD and lipids are established, direct impact of cigarette smoke (CS) on lipidomes remains elusive. We investigated the effect of 6 month smoke exposure on a well-established mouse model for human atherogenesis, Apoe mouse plasma, liver, and aorta molecular lipid profiles and liver transcriptome. // Methods: Plasma, liver, and aorta samples from Apoe mice exposed to CS or fresh air for 6 months were extracted for lipids using robotic-assisted method and analyzed by mass spectrometry. Gene expression of samples from the same livers was obtained on microarrays. Development of atherosclerosis in aorta was further assessed by plaque size measurement in the aortic arch and lipoprotein measurements in plasma and in the plaque. // Results: CS increased most lipid classes and molecular lipid species in tissues evaluated. In plasma, free cholesterol, ceramides, cerebrosides, and majority of phospholipids were increased in CS-exposed mice. In liver, CS elevated several lipid species including free and esterified cholesterol, triacylglycerols, phospholipids, sphingomyelins, and ceramides. In aorta, more than 2-fold higher cholesteryl ester (CE), lysophosphatidylcholine, and glucosyl/galactosylceramide levels were recorded in mice exposed to CS compared to mice exposed to fresh air. Moreover, CS exposure induced a significant decrease in several plasma CE and phosphatidylcholine species that contained polyunsaturated fatty acids. Genes involved in amino acid and lipid metabolism showed perturbed transcription profiles in liver. // Conclusion: These data reveal molecular details accompanying the increase in plaque size, sign of atherogenesis in Apoe mice, which is accelerated by CS exposure.

2013-10-03 | E-MTAB-1195 | biostudies-arrayexpress

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