MetaMass, a Tool for Meta-analysis of Subcellular Proteomics Data

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2016 Aug 30

PMID 27571551

Citations 19

Authors

Fridtjof Lund-Johansen

Daniel De la Rosa Carrillo

Adi Mehta

Krzysztof Sikorski

Marit Inngjerdingen

Tomas Kalina

Kjetil Roysland

Gustavo Antonio de Souza

Andrew R M Bradbury

Quentin Lecrevisse

Jan Stuchly

Affiliations

Soon will be listed here.

Abstract

We report a tool for the analysis of subcellular proteomics data, called MetaMass, based on the use of standardized lists of subcellular markers. We analyzed data from 11 studies using MetaMass, mapping the subcellular location of 5,970 proteins. Our analysis revealed large variations in the performance of subcellular fractionation protocols as well as systematic biases in protein annotation databases. The Excel and R versions of MetaMass should enhance transparency and reproducibility in subcellular proteomics.

Citing Articles

Altered relaxation and Mitochondria-Endoplasmic Reticulum Contacts Precede Major (Mal)adaptations in Aging Skeletal Muscle and are Prevented by Exercise.

Allen R, Kronemberger A, Shi Q, Pope M, Cuadra-Munoz E, Son W bioRxiv. 2025; .

PMID: 39975407 PMC: 11838400. DOI: 10.1101/2025.01.14.633043.

Machine learning approaches for spatial omics data analysis in digital pathology: tools and applications in genitourinary oncology.

Kim H, Kim J, Yeon S, You S Front Oncol. 2024; 14:1465098.

PMID: 39678498 PMC: 11638011. DOI: 10.3389/fonc.2024.1465098.

Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology.

Bhushan V, Nita-Lazar A J Proteome Res. 2024; 23(8):2700-2722.

PMID: 38451675 PMC: 11296931. DOI: 10.1021/acs.jproteome.3c00839.

Deep and fast label-free Dynamic Organellar Mapping.

Schessner J, Albrecht V, Davies A, Sinitcyn P, Borner G Nat Commun. 2023; 14(1):5252.

PMID: 37644046 PMC: 10465578. DOI: 10.1038/s41467-023-41000-7.

SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry.

Arslan T, Pan Y, Mermelekas G, Vesterlund M, Orre L, Lehtio J Nat Protoc. 2022; 17(8):1832-1867.

PMID: 35732783 DOI: 10.1038/s41596-022-00699-2.

References

Christoforou A, Mulvey C, Breckels L, Geladaki A, Hurrell T, Hayward P . A draft map of the mouse pluripotent stem cell spatial proteome. Nat Commun. 2016; 7:8992. PMC: 4729960. DOI: 10.1038/ncomms9992. View

Rodriguez-Pineiro A, van Der Post S, Johansson M, Thomsson K, Nesvizhskii A, Hansson G . Proteomic study of the mucin granulae in an intestinal goblet cell model. J Proteome Res. 2012; 11(3):1879-90. PMC: 3292267. DOI: 10.1021/pr2010988. View

de Souto M, Jaskowiak P, Costa I . Impact of missing data imputation methods on gene expression clustering and classification. BMC Bioinformatics. 2015; 16:64. PMC: 4350881. DOI: 10.1186/s12859-015-0494-3. View

Larance M, Lamond A . Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol. 2015; 16(5):269-80. DOI: 10.1038/nrm3970. View

de Hoon M, Imoto S, Nolan J, Miyano S . Open source clustering software. Bioinformatics. 2004; 20(9):1453-4. DOI: 10.1093/bioinformatics/bth078. View

Ramsby M, Makowski G . Differential detergent fractionation of eukaryotic cells. Cold Spring Harb Protoc. 2011; 2011(3):prot5592. DOI: 10.1101/pdb.prot5592. View

Bileck A, Kreutz D, Muqaku B, Slany A, Gerner C . Comprehensive assessment of proteins regulated by dexamethasone reveals novel effects in primary human peripheral blood mononuclear cells. J Proteome Res. 2014; 13(12):5989-6000. DOI: 10.1021/pr5008625. View

Choi S, Srivas R, Fu K, Hood B, Dost B, Gibson G . Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. J Proteome Res. 2012; 11(10):4983-91. PMC: 3495236. DOI: 10.1021/pr3005524. View

Boisvert F, Ahmad Y, Gierlinski M, Charriere F, Lamont D, Scott M . A quantitative spatial proteomics analysis of proteome turnover in human cells. Mol Cell Proteomics. 2011; 11(3):M111.011429. PMC: 3316722. DOI: 10.1074/mcp.M111.011429. View

10.

Carvalho A, Ribeiro H, Voabil P, Penque D, Jensen O, Molina H . Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress. Mol Cell Proteomics. 2014; 13(12):3294-307. PMC: 4256484. DOI: 10.1074/mcp.M113.034363. View

11.

Thakar K, Karaca S, Port S, Urlaub H, Kehlenbach R . Identification of CRM1-dependent Nuclear Export Cargos Using Quantitative Mass Spectrometry. Mol Cell Proteomics. 2012; 12(3):664-78. PMC: 3591659. DOI: 10.1074/mcp.M112.024877. View

12.

Gatto L, Breckels L, Burger T, Nightingale D, Groen A, Campbell C . A foundation for reliable spatial proteomics data analysis. Mol Cell Proteomics. 2014; 13(8):1937-52. PMC: 4125728. DOI: 10.1074/mcp.M113.036350. View

13.

Adam S, Marr R, Gerace L . Nuclear protein import in permeabilized mammalian cells requires soluble cytoplasmic factors. J Cell Biol. 1990; 111(3):807-16. PMC: 2116268. DOI: 10.1083/jcb.111.3.807. View

14.

Pinto G, Alhaiek A, Amadi S, Qattan A, Crawford M, Radulovic M . Systematic nucleo-cytoplasmic trafficking of proteins following exposure of MCF7 breast cancer cells to estradiol. J Proteome Res. 2014; 13(2):1112-27. PMC: 4261610. DOI: 10.1021/pr4012359. View

15.

Drissi R, Dubois M, Boisvert F . Proteomics methods for subcellular proteome analysis. FEBS J. 2013; 280(22):5626-34. DOI: 10.1111/febs.12502. View

16.

Larance M, Kirkwood K, Xirodimas D, Lundberg E, Uhlen M, Lamond A . Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway. Mol Cell Proteomics. 2011; 11(3):M111.014407. PMC: 3316733. DOI: 10.1074/mcp.M111.014407. View

17.

Andreyev A, Shen Z, Guan Z, Ryan A, Fahy E, Subramaniam S . Application of proteomic marker ensembles to subcellular organelle identification. Mol Cell Proteomics. 2009; 9(2):388-402. PMC: 2830848. DOI: 10.1074/mcp.M900432-MCP200. View

18.

Mulvey C, Tudzarova S, Crawford M, Williams G, Stoeber K, Godovac-Zimmermann J . Subcellular proteomics reveals a role for nucleo-cytoplasmic trafficking at the DNA replication origin activation checkpoint. J Proteome Res. 2013; 12(3):1436-53. PMC: 4261602. DOI: 10.1021/pr3010919. View