Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Orbitrap mass spectrometry and high-field asymmetric waveform ion mobility spectrometry (FAIMS) enable the in-depth analysis of human serum proteoforms

ABSTRACT: After molecular weight-based fractionation, we supplemented the traditional liquid chromatography tandem mass spectrometry (LC-MS2) data acquisition with high-field asymmetric waveform ion mobility spectrometry (FAIMS), which served as an additional separation dimension to further simplify serum proteoforms mixtures.

INSTRUMENT(S): Orbitrap Eclipse

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

SUBMITTER: Luca Fornelli

PROVIDER: MSV000091309 | MassIVE | Thu Feb 16 20:03:00 GMT 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Orbitrap Mass Spectrometry and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Enable the in-Depth Analysis of Human Serum Proteoforms.

Kline Jake T JT Belford Michael W MW Boeser Cornelia L CL Huguet Romain R Fellers Ryan T RT Greer Joseph B JB Greer Sylvester M SM Horn David M DM Durbin Kenneth R KR Dunyach Jean-Jacques JJ Ahsan Nagib N Fornelli Luca L

Journal of proteome research 20230929 11

Blood serum and plasma are arguably the most commonly analyzed clinical samples, with dozens of proteins serving as validated biomarkers for various human diseases. Top-down proteomics may provide additional insights into disease etiopathogenesis since this approach focuses on protein forms, or proteoforms, originally circulating in blood, potentially providing access to information about relevant post-translational modifications, truncations, single amino acid substitutions, and many other sour ...[more]

PMID: 37774690

Similar Datasets

Orbitrap mass spectrometry and high-field asymmetric waveform ion mobility spectrometry (FAIMS) enable the indepth analysis of human serum proteoforms

Project description:In this study, we describe a straightforward protocol for intact proteoform sample preparation based on depletion of albumin and immunoglobulins followed by simplified fractionation of remaining serum proteins via polyacrylamide gel electrophoresis. After molecular weight-based fractionation, we supplemented the traditional liquid chromatography tandem mass spectrometry data acquisition with high field asymmetric waveform ion mobility spectrometry (FAIMS), which served as an additional separation dimension to further simplify serum proteoforms mixtures

2023-08-02 | MSV000092574 | MassIVE

pFAIMS: An optimized workflow for quantitative multiplexed phosphorylation analysis using high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS)

Project description:Protein phosphorylation is vital for the regulation of cellular signaling. Isobaric tag-based proteomic techniques, such as tandem mass tags (TMT), can measure the relative phosphorylation states of peptides in a multiplexed format. However, the overall low stoichiometry of protein phosphorylation constrains the analytical depth of phosphopeptide analysis by mass spectrometry, thereby requiring robust and sensitive workflows. Here we evaluate and optimize high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS) coupled to Orbitrap Tribrid mass spectrometers for the analysis of TMT10plex-labeled phosphopeptides. We determined that using FAIMS-SPS-MS3 with three compensation voltages (CV) in a single method minimizes inter-CV overlap and maximizes peptide coverage (e.g., CV=-40V/-60V/-80V) and that consecutive analyses using CID-MSA and HCD fragmentation at the MS2 stage increases the depth of phosphorylation analysis.

2020-01-10 | PXD014593 | Pride

IMPROVED N- AND O-GLYCOPEPTIDE IDENTIFICATION USING HIGH-FIELD ASYMMETRIC WAVEFORM ION MOBILITY SPECTROMETRY (FAIMS)

Project description:Mass spectrometry is the premier tool for identifying and quantifying site-specific protein glycosylation globally. Analysis of intact glycopeptides often requires an enrichment step, after which the samples remain highly complex and exhibit a broad dynamic range of abundance. Here, we evaluated the analytical benefits of high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to nano-liquid chromatography mass spectrometry (nLC-MS) for analyses of intact glycopeptide devoid of any enrichment step. We compared the effects of compensation voltage on the transmission of N- and O-glycopeptides derived from heterogeneous protein mixtures using two FAIMS devices. We comprehensively demonstrate the performance characteristics of the FAIMS device for glycopeptide analysis and recommend optimal electrode temperature and compensation voltage (CV) settings for N- and O-glycopeptide analysis. Under optimal CV settings, FAIMS-assisted gas-phase fractionation in conjunction with chromatographic reverse phase separation resulted in a 31% increase in the detection of both N- and O-glycopeptide compared to control experiments without FAIMS. Overall, our results demonstrate that FAIMS provides an alternative means to access glycopeptides without any enrichment providing an unbiased global glycoproteome landscape. In addition, our work provides the framework to verify ‘difficult-to-identify’ glycopeptide features.

2023-10-24 | PXD038673 | Pride

Accurate quantitative proteomic analyses using metabolic labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS)

Project description:Stable isotope labeling by amino acids in cell culture (SILAC) is routinely used to profile changes in protein and peptide abundance across different experimental paradigms. As with other quantitative proteomic approaches, the detection of peptide isotopomers can be limited by the presence of interference ions that ultimately affect the quality of quantitative measurements. Here, we evaluate high field asymmetric waveform ion mobility spectrometry (FAIMS) to improve the accuracy and dynamic range of quantitative proteomic analyses using SILAC. We compared quantitative measurements for tryptic digests of isotopically labeled protein extracts mixed in different ratios using LC-MS/MS with and without FAIMS. To further reduce sample complexity, we also examined the improvement in quantitative measurements when combining strong cation exchange (SCX) fractionation prior to LC-MS/MS analyses. Using the same amount of sample consumed, analyses performed using FAIMS provided more than 30% and 200% increase in the number of quantifiable peptides compared LC-MS/MS performed with and without SCX fractionation, respectively. Furthermore, FAIMS reduced the occurrence of interfering isobaric ions and improved the accuracy of quantitative measurements. We leveraged the application of FAIMS in phosphoproteomic analyses to profile dynamic changes in protein phosphorylation in HEK293 cells subjected to heat shock for periods up to 20 min. In addition to the enhanced phosphoproteomic coverage, FAIMS also provided the ability to separate phosphopeptide isomers that often co-elute and can be misassigned in conventional LC-MS/MS experiments.

2019-05-28 | PXD012924 | Pride

High Field Asymmetric Waveform Ion Mobility Spectrometry in Non-targeted Bottom-up Proteomics of Dried Blood Spot

Project description:Dried Blood Spots samples are a rich source of proteins and have therefore great potential for proteomics biomarker discovery studies. Only a few articles have used DBS samples for non-targeted bottom-up protein analysis, probably due to the complexity of the DBS samples. Gas-phase separation by ion mobility spectrometry such as Field Asymmetric Waveform Ion Mobility (FAIMS) could be useful in analysis of DBS samples as FAIMS has previously shown to be advantageous for bottom-up protein analysis of complex samples. The aim of this project was therefore to evaluate FAIMS in non-targeted analysis of Dried Blood Spots.

2018-05-03 | PXD007926 | Pride

Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size-exclusion Chromatography for Proteome-wide Crosslinking Mass Spectrometry_CLMS dataset

Project description:Ion mobility spectrometry shows great promise to tackle analytically challenging research questions by adding another separation dimension to liquid chromatography-mass spectrometry. The understanding of how analyte properties influence ion mobility has increased through recent studies but no clear rationale for the design of customized experimental settings has emerged. Here, we leverage machine learning to deepen our understanding of field asymmetric-waveform ion-mobility spectrometry (FAIMS) for the analysis of crosslinked peptides. Knowing that predominantly m/z, then size and charge state of an analyte influences the separation, we found ideal compensation voltages correlating with size-exclusion chromatography (SEC) fraction number. The effect of this relationship on analytical depth can be substantial as exploiting it allowed us to almost double unique residue pair detections in a proteome-wide crosslinking experiment. Other applications involving liquid- and gas-phase separation may also benefit from considering such parameter dependencies.

2022-12-16 | PXD022360 | JPOST Repository

Capillary Zone Electrophoresis-High Field Asymmetric Ion Mobility Spectrometry-Tandem Mass Spectrometry for Top-down Characterization of Histone Proteoforms

Project description:Characterization of histone proteoforms with various post-translational modifications (PTMs) is critical for a better understanding of functions of histone proteoforms in epigenetic control of gene expression. Mass spectrometry (MS)-based top-down proteomics (TDP) is a valuable approach for delineating histone proteoforms because it can provide us with a bird's-eye view of histone proteoforms carrying diverse combinations of PTMs. Here, we present the first example of coupling capillary zone electrophoresis (CZE), ion mobility spectrometry (IMS), and MS for online multi-dimensional separations of histone proteoforms. Our CZE-high-field asymmetric waveform IMS (FAIMS)-MS/MS platform identified 366 histone proteoforms from a commercial calf histone sample using a low microgram amount of histone sample as the starting material. CZE-FAIMS-MS/MS improved the number of histone proteoform identifications by about 3 folds compared to CZE-MS/MS alone (without FAIMS). The results indicate that CZE-FAIMS-MS/MS could be a useful tool for comprehensive characterization of histone proteoforms with high sensitivity.

2023-12-07 | PXD041357 | Pride

Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size-exclusion Chromatography for Proteome-wide Crosslinking Mass Spectrometry_protein ID dataset

2022-12-16 | PXD022341 | JPOST Repository

Evaluation and Optimization of High-Field Asymmetric Waveform Ion Mobility Spectrometry for Multiplexed Quantitative Site-specific N-glycoproteomics

Project description:The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has shown to improve the scope of bottom-up proteomics. The benefits of FAIMS for quantitative N-glycoproteomics have not been investigated yet. In this work, we optimized FAIMS settings for N-glycopeptide identification, with or without the tandem mass tag (TMT) label. The optimized FAIMS approach significantly increased the identification of site-specific N-glycopeptides derived from the purified IgM protein or human lymphoma cells. We explored in detail the changes in FAIMS mobility caused by N-glycopeptides with different characteristics, including TMT labeling, charge state, glycan type, peptide sequence, glycan size and precursor m/z. Importantly, FAIMS also improved multiplexed N-glycopeptide quantification, both with the standard MS2 acquisition method and with our recently developed Glyco-SPS-MS3 method. The combination of FAIMS and Glyco-SPS-MS3 provided the highest quantitative accuracy and precision. Our results demonstrate the advantages of FAIMS for improved mass-spectrometry-based qualitative and quantitative N-glycoproteomics.

2021-05-05 | PXD023951 | Pride

Coupling high-field asymmetric ion mobility spectrometry with capillary electrophoresis-electrospray ionization-tandem mass spectrometry improves protein identifications in bottom-up proteomic analysis of low nanogram samples

Project description:In this work, we pioneered the assessment of coupling high-field asymmetric waveform ion mobility spectrometry (FAIMS) with ultra-sensitive capillary electrophoresis hyphenated with tandem mass spectrometry (CE-MS/MS) to achieve deeper proteome coverage of low nanogram amounts of digested cell lysates. An internal stepping strategy using three or four compensation voltages (CVs) per analytical run with varied cycle times was tested to determine optimal FAIMS settings and MS parameters for the CE-FAIMS-MS/MS method. The optimized method applied to bottom-up proteomic analysis of 1 ng HeLa protein digest standard identified 1,314±30 proteins, 4,829±200 peptide groups, and 7,577±163 peptide spectrum matches (PSMs) corresponding to a 16%, 25%, and 22% increase, respectively, over CE-MS/MS alone, without FAIMS. Furthermore, the percentage of acquired MS/MS spectra that resulted in PSMs increased nearly 2-fold with CE-FAIMS-MS/MS. Our results also identified from 1 ng HeLa protein digest without any prior enrichment, 76±9 phosphopeptides, 18% of which were multiphosphorylated. These results represent a 46% increase in phosphopeptide identifications over the control experiments without FAIMS yielding 2.5-fold more multiphosphorylated peptides.

2023-05-10 | PXD034255 | 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