configuring and calibrating the tims software interface for proteomic analysis

histon proteomische analyse en karakterisering van posttranslationele modificatie

In eukaryotic cells, DNA is packaged as chromatin into functional units called nucleosomes. These units are composed of an octamer of four core histones (two each of H2A, H2B, H3, and H4)1,2,3,4. Histones are amongst the most abundant and highly conserved proteins in eukaryotes, which are largely responsible for gene regulation5. Histone posttranslational modifications (PTMs) play a large role in the regulation of chromatin dynamics and rigger various biological processes such as DNA transcription, replication, and repair6. PTMs occur primarily on the accessible surface of the N-terminal regions of histones that are in contact with DNA3,7. However, tail and core modifications influence chromatin structure, altering inter-nucleosome interactions and recruiting specific proteins3,8.
A current challenge during liquid chromatography-mass spectrometry (LC-MS)-based proteomics is the potential co-elution of analytes of interest. In the case of data-dependent analyses (DDA), this translates into the potential loss of several precursor ions during the MS/MS acquisition process9. Time-of-flight (ToF) instruments acquire spectra at very high frequency9,10 (up to tens of kHz)11; this makes them capable of rapidly scanning the total precursor ions within a complex sample (MS1), thus promising optimal sensitivity and MS/MS sequencing rates (up to 100 Hz)9 and making them ideal for biological sample analysis10. Nevertheless, the sensitivity available at these high scan rates is limited by the MS/MS rate9. The addition of trapped ion mobility spectrometry (TIMS) in combination with an orthogonal quadrupole time-of-flight (qToF) mass spectrometer was used to mitigate these limitations. In TIMS, all precursor ions are accumulated in tandem and eluted as a function of their mobility, rather than selecting single precursor masses with a quadrupole9. Parallel accumulation-serial fragmentation (PASEF) allows for hundreds of MS/MS events per second without any loss of sensitivity9.
The principal aim of this work was to show the recent developments of DDA using parallel accumulation in the mobility trap followed by sequential fragmentation and collision-induced dissociation (CID). Histone PTMs were confidently assigned based on their retention times (RTs), mobilities, and fragmentation patterns.

Auteur in de schijnwerpers: verbeterde identificatie van histon PTM-isomeren door middel van LC-TIMS-ToF MS/MS en PASEF

Screening op histonmodificatie met behulp van vloeistofchromatografie, Trapped Ion Mobility Spectrometry en Time-Of-Flight Mass Spectrometry

A method is proposed using histone extraction protocol with 95%efficiency. Together with LC-TIMS-ToF MS/MS, in a short time, it is possible to obtain a screening for those PTMs present in the histone. And above all, the possibility of separating isomers.The separation of isomeric peptides though possible using tandem mass spectrometry alone is often difficult. By incorporating TIMS, we introduce an extra dimension of separation, simplifying many positional isomer identifications. In addition, passive technology increases the sensitivity of these experiments, further improving our ability to analyze epigenetic variations.With the increased ability to identify PTM positions, there comes the ability to further determine the correlation between various environmental or biological factors, and their effects on the epigenome. Methods that improve and facilitate analysis of histones can be applied to several research areas, including medical and environmental chemistry. The dynamics of protein confirmation in native or damaged states will be established from the implementation of TIMS MS/MS with HDX.Through LC-TIMS-ToF MS/MS and Nano LC-TIMS-ToF MS/MS, the differences in PTM existing in various biological sample will be charted.

Configureren en kalibreren van de TIMS-software-interface voor proteomische analyse

Open de TIMS-besturingssoftware. Klik op het tabblad Instrument en schakel over naar Bedienen. Controleer de TIMS-parameters en controleer vervolgens de MS-instellingen, waaronder Scan Begin, Scan End, Ion Polarity en Scan Mode.Controleer nogmaals de TIMS-instellingen, waaronder de Mode, Mobility Start, Mobility End, Ramp Time, Accumulation Time, Duty Cycle, Ramp Rate, MS Rate, MS Averaging en Auto-Calibration. Wijzig vervolgens de scanmodus in MS voor kalibratiedoeleinden. Nadat u ervoor hebt gezorgd dat het instrument in de bedrijfsmodus staat, activeert u op het tabblad Bron de Hamilton 500 Microliter-spuit met stemmix.Ga naar het tabblad Kalibratie. Klik op de Massa om op te laden en kies onder de Kalibratiemodus de Kwadratische modus. Regel de zoom tot plus of min 0.01% Klik vervolgens op Kalibreren.En wanneer een score van 100% is bereikt, klikt u op Accepteren. Ga vervolgens naar het tabblad Mobiliteit en selecteer onder Kalibratiemodus de optie Lineaire modus. Stel het detectiebereik in op plus of min 5% en breedte op 0,1 Dalton.Klik vervolgens op Kalibreren en bij ontvangst van een score van meer dan 98.5% klikt u op Accepteren.

Research

JoVE Journal

Chemistry

Configuring and Calibrating the TIMS Software Interface for Proteomic Analysis

Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry

Histone proteins are highly abundant and conserved among eukaryotes and play a large role in gene regulation as a result of structures known as ...

LC-TIMS-PASEF-ToF MS/MS Method for Proteolytic Histone Peptide Analysis

LC-TIMS-PASEF-ToF MS/MS-methode voor proteolytische histonpeptide-analyse