Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics.

Journal of Proteome Research
Abla TannousPeter Lobel

Abstract

Knowledge of intracellular location can provide important insights into the function of proteins and their respective organelles, and there is interest in combining classical subcellular fractionation with quantitative mass spectrometry to create global cellular maps. To evaluate mass spectrometric approaches specifically for this application, we analyzed rat liver differential centrifugation and Nycodenz density gradient subcellular fractions by tandem mass tag (TMT) isobaric labeling with reporter ion measurement at the MS2 and MS3 level and with two different label-free peak integration approaches, MS1 and data independent acquisition (DIA). TMT-MS2 provided the greatest proteome coverage, but ratio compression from contaminating background ions resulted in a narrower accurate dynamic range compared to TMT-MS3, MS1, and DIA, which were similar. Using a protein clustering approach to evaluate data quality by assignment of reference proteins to their correct compartments, all methods performed well, with isobaric labeling approaches providing the highest quality localization. Finally, TMT-MS2 gave the lowest percentage of missing quantifiable data when analyzing orthogonal fractionation methods containing overlapping proteomes...Continue Reading

References

Aug 1, 1978·The Journal of Cell Biology·R WattiauxF Dubois
Sep 24, 2004·Molecular & Cellular Proteomics : MCP·Philip L RossDarryl J Pappin
Apr 18, 2006·Cell·Leonard J FosterMatthias Mann
Jan 22, 2011·Molecular & Cellular Proteomics : MCP·Maria Cecilia Della VallePeter Lobel
Jun 19, 2013·Journal of Proteome Research·Mikhail M SavitskiMarcus Bantscheff
Aug 21, 2013·Biochimica Et Biophysica Acta·Dominik A MeggerBarbara Sitek
Oct 23, 2014·Journal of Proteome Research·Navin Rauniyar, John R Yates
Jan 7, 2015·Molecular & Cellular Proteomics : MCP·Nathalie SelevsekRuedi Aebersold
Dec 22, 2015·Nucleic Acids Research·Andrew YatesPaul Flicek
Jan 6, 2016·Molecular & Cellular Proteomics : MCP·Bo ZhangRoman A Zubarev
Jan 13, 2016·Nature Communications·Andy ChristoforouKathryn S Lilley
Jun 10, 2016·ELife·Daniel N ItzhakGeorg Hh Borner
Aug 30, 2016·Nature Methods·Fridtjof Lund-JohansenJan Stuchly
Oct 28, 2016·Cell Systems·Pierre M Jean BeltranIleana M Cristea
Dec 8, 2016·Molecular & Cellular Proteomics : MCP·Michel JadotPeter Lobel
Apr 19, 2017·Journal of Proteome Research·Christopher S HughesGregg B Morin
May 5, 2017·Nature Protocols·Claire M MulveyKathryn S Lilley
Dec 1, 2017·Journal of Proteome Research·Christian D KelstrupJesper V Olsen
Mar 15, 2018·Nature Communications·Alexander HogrebeJesper V Olsen
Apr 11, 2018·Journal of Proteome Research·Jeremy D O'ConnellSteven P Gygi
Dec 28, 2016·F1000Research·Lisa M BreckelsLaurent Gatto
Nov 26, 2018·Current Opinion in Chemical Biology·Thao NguyenMartin Wühr
Dec 15, 2018·Current Opinion in Chemical Biology·Dalila BensaddekAngus I Lamond
Jan 5, 2019·Chembiochem : a European Journal of Chemical Biology·Nishant PappireddiMartin Wühr
Jan 5, 2019·Molecular Cell·Lukas Minus OrreJanne Lehtiö
Jan 20, 2019·Nature Communications·Aikaterini GeladakiKathryn S Lilley
Oct 11, 2019·Journal of Proteome Research·Takeshi MasudaYasushi Ishihama

❮ Previous
Next ❯

Citations

Apr 30, 2020·Molecular & Cellular Proteomics : MCP·Georg H H Borner
Nov 1, 2020·Journal of Mass Spectrometry : JMS·Domenico Taverna, Marco Gaspari
Jan 17, 2021·Molecular & Cellular Proteomics : MCP·Georg H H Borner
Sep 10, 2021·Expert Review of Proteomics·Lindsay Pino, Birgit Schilling
Oct 13, 2021·ChemPlusChem·Ziqi Lyu, Joseph C Genereux

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.