Name: Navigeren door de op massaspectrometrie gebaseerde proteomische gegevens met behulp van gratis computationele tools (Video) | JoVE Journal
Uploaded: 2025-08-19T14:40:00.000+00:00
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Description: Leer massaspectrometrie-gebaseerde proteomische data-analyse met gratis tools zoals DIA-NN en MSFragger. Deze methode helpt biologen bij het valideren van bevindingen in kankeronderzoek.

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</ol>

<table><tbody><tr><td>.NET SDK v. 9.0.203</td><td>Microsoft</td><td></td><td>https://dotnet.microsoft.com/en-us/download</td></tr><tr><td>DIA-NN v. 2.1.0</td><td></td><td></td><td>https://github.com/vdemichev/DiaNN/releases/tag/2.0&nbsp;</td></tr><tr><td>FragPipe v. 22.0</td><td></td><td></td><td>https://github.com/Nesvilab/FragPipe/releases</td></tr><tr><td>MSFileReader v. 3.1&nbsp;</td><td>Thermo Fisher</td><td></td><td>https://github.com/thermofisherlsms/MSFileReader/blob/main/MSFileReader_x64.exe</td></tr><tr><td>R 4.5.0</td><td></td><td></td><td>https://cran.rstudio.com/bin/windows/base/R-4.5.0-win.exe</td></tr><tr><td>Rstudio v. 2024.12.1+563</td><td></td><td></td><td>https://posit.co/download/rstudio-desktop/</td></tr></tbody></table>

navigeren door de op massaspectrometrie gebaseerde proteomische gegevens met behulp van gratis computationele tools

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Navigeren door de op massaspectrometrie gebaseerde proteomische gegevens met behulp van gratis computationele tools

Mass spectrometry (MS)-based proteomics data, including Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA), are widely used in ...

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Source:Tia Rizakos1, Jennifer Geddes-McAlister11Molecular and Cellular Biology Department, University of Guelph.This video demonstrates peptide purification through the STAGE Tip procedure. A miniature column containing resin beads bonded to long hydrocarbon chains facilitates hydrophobic interaction-based purification. Upon loading a pre-digested peptide sample into the column, the peptide fragments bind to the resin beads, allowing impurities to pass through. An elution buffer that disrupts...

A STAGE Tip Procedure for Desalting and Purification of Peptides

Hier presenteren we protocollen voor affiniteitszuivering van eiwitcomplexen en hun scheiding door blauwe natieve PAGE, gevolgd door proteïne correlatie profilering middels label vrije kwantitatieve massaspectrometrie. Deze methode is nuttig voor interactomen in verschillende proteïnecomplexen lossen.

Het oplossen van Affiniteit gezuiverde eiwit complexen door Blue inheemse PAGE en Protein Correlatie Profiling

We presenteren een protocol om te kwantificeren nauwkeurig eiwitten met isobaar etikettering, uitgebreide fractionering, bioinformatica tools en kwaliteitscontrole stappen in combinatie met vloeibare chromatografie geïnterfacet met een hoge resolutie massaspectrometer.

Diepe Proteoom profilering door isobaar Labeling, uitgebreide vloeistofchromatografie, massaspectrometrie en Software-bijgewoonde kwantificering

Een gedetailleerd protocol wordt beschreven voor de scheiding, identificatie en karakterisering van proteoforms in EiwitSteekproeven met behulp van capillaire zone elektroforese-electrospray ionisatie-tandem massaspectrometrie (CZE-ESI-MS/MS). Het protocol kan worden gebruikt voor de hoge-resolutie karakterisatie van proteoforms in simple EiwitSteekproeven en de grootschalige identificatie van proteoforms in complexe Proteoom monsters.

Grootschalige topdown Proteomics met behulp van capillaire Zone elektroforese Tandem massaspectrometrie

OpenProt is een vrij toegankelijke databank die wordt afgedwongen door een polycistronic model van eukaryotische genomen. Hier presenteren we een protocol voor het gebruik van OpenProt databases wanneer ondervragen massaspectrometrie datasets. Met behulp van OpenProt zorgt database voor analyse van proteomic experimenten voor de ontdekking van de roman en eerder niet detecteerbaar eiwitten.

Massa spectrometrie gebaseerde Proteomics Analyses met behulp van de OpenProt Database te onthullen nieuwe eiwitten vertaald uit niet-canonieke Open lezing Frames

Een veelzijdig cryoslicing BN-MS protocol met behulp van een microtoom wordt gepresenteerd voor hoge-resolutie complexome profilering.

Hoge-resolutie Complexome profilering door Cryoslicing BN-MS analyse

Beschreven is een proteomica-workflow voor het identificeren van eiwit interactie partners uit een nucleaire subcellulaire fractie met behulp van immunoaffinity verrijking van een gegeven proteïne van belang en label-vrije massaspectrometrie. De workflow omvat subcellulaire fractionering, immunoprecipitatie, filter aided monstervoorbereiding, offline opruimen, massaspectrometrie, en een downstream bioinformatica pijpleiding.

Label-vrije Immunoprecipitation massaspectrometrie workflow voor grootschalige nucleaire interactome profilering

Het beschreven protocol biedt een geoptimaliseerde kwantitatieve proteomics-analyse van weefselmonsters met behulp van twee benaderingen: labelgebaseerde en labelvrije kwantificering. Labelgebaseerde benaderingen hebben het voordeel van een nauwkeurigere kwantificering van eiwitten, terwijl een labelvrije aanpak kosteneffectiever is en wordt gebruikt om honderden monsters van een cohort te analyseren.

Uitgebreide workflow van op massaspectrometrie gebaseerde Shotgun Proteomics van weefselmonsters

Hier stellen we een op massaspectrometrie gebaseerde proteomische methode op met behulp van geïsoleerde interessegebieden in formaline-gefixeerde, in paraffine ingebedde weefselsecties. Dit protocol wordt gebruikt om proteoom te analyseren van specifieke weefselgebieden in gearchiveerde, in formaline gefixeerde, in paraffine ingebedde weefselsecties.

Een gestroomlijnde aanpak voor proteomics op basis van massaspectrometrie met behulp van geselecteerde weefselregio's

Deze video toont de voorbereiding van een ultra-dunne matrix / analyt laag voor het analyseren van peptiden en eiwitten door Matrix-assisted laser desorptie ionisatie massaspectrometrie (MALDI-MS).

MALDI Monstervoorbereiding: de Ultra Thin Layer methode

Leer massaspectrometrie-gebaseerde proteomische data-analyse met gratis tools zoals DIA-NN en MSFragger. Deze methode helpt biologen bij het valideren van bevindingen in kankeronderzoek.

Navigeren door de op massaspectrometrie gebaseerde proteomische gegevens met behulp van gratis computationele tools

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