Dataset for "Development of Methodology to Investigate the Surface SMALPome of Mammalian Cells"

The purpose behind obtaining this data was to determine whether there were any differences between biotinylated surface membrane proteins that were extracted using styrene maleic acid (SMA), compared to detergent buffer (SDS/Sodium deoxycholate/NP-40). Here, Excel spreadsheets which contain raw datasets from mass-spectroscopy proteomics are present. Subsequent datasets are also included, following filters described in "Development of methodology to investigate the surface SMALPome of mammalian cells".

Keywords:
MS proteomics, SMA
Subjects:
Biomolecules and biochemistry

Cite this dataset as:
Morrison, K., Whitley, P., Koumanov, F., 2021. Dataset for "Development of Methodology to Investigate the Surface SMALPome of Mammalian Cells". Bath: University of Bath Research Data Archive. Available from: https://doi.org/10.15125/BATH-01051.

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Data

SUPPLEMENTARY_TABLE1.xlsx
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet (1MB)
Creative Commons: Attribution 4.0

Microsoft Excel document containing raw datasets. Also includes subsequent datasets from filters desribed in manuscript; "Development of methodology to investigate the surface SMALPome of mammalian cells."

SUPPLEMENTARY_TABLE2.xlsx
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet (11kB)
Creative Commons: Attribution 4.0

Microsoft Excel document containing mitochondrial membrane protein dataset desribed in manuscript; "Development of methodology to investigate the surface SMALPome of mammalian cells."

SUPPLEMENTARY_TABLE3.xlsx
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet (10kB)
Creative Commons: Attribution 4.0

Microsoft Excel document containing Glycosylphosphatidylinositol (GPI) anchour protein dataset desribed in manuscript; "Development of methodology to investigate the surface SMALPome of mammalian cells."

Creators

Paul Whitley
University of Bath

Contributors

Karen Edler
Supervisor
University of Bath

University of Bath
Rights Holder

Documentation

Data collection method:

Samples were generated as described in "Development of methodology to investigate the surface SMALPome of mammalian cells." In summary, 3T3-L1 mouse fibroblasts were surface biotinylated prior to extraction with either styrene maleic acid (SMA) or detergent buffer control (SDS/Sodium deoxycholate/NP-40). Purification of biotinylated surface membrane proteins using NeutrAvidin beads was conducted, prior to three different wash protocols. Samples underwent nano-LC MS/MS with further proteomic analysis to determine differences between proteins extracted using SMA and detergent control. The raw data files were processed and quantified using Proteome Discoverer software v2.1 (Thermo Scientific) and searched against the UniProt Mouse database (downloaded February 2020; 83561 sequences) using the SEQUEST HT algorithm. The outputs from the Proteome Discoverer were filtered to identify transmembrane proteins and proteins that have a signal sequence. Firstly, any non-mouse contaminants were removed (i.e. contaminants = TRUE) from the data sets. Next, proteins with ≤ 1 unique peptide were removed from the data sets. The filtered data sets were compared with mouse proteins (86521 proteins) in the Uniprot database.

Data processing and preparation activities:

Uniprot lists for mouse protein searches; To identify integral membrane proteins: Organism [OS], Mus musculus (mouse) AND Keyword [KW] Transmembrane helix (18359 proteins, downloaded December 2020). To identify proteins with a signal sequence but not a transmembrane domain: Organism [OS] mus musculus (mouse) AND PTM Processing>molecule processing.signal peptide, NOT Keyword [KW] transmembrane helix (6683 proteins, downloaded April 2021). To identify GPI anchor proteins associated with lipid rafts: keyword:"GPI-anchor [KW-0336]" AND organism:"Mus musculus (Mouse) [10090]" (226 proteins, downloaded July 2021). To identify mitochondrial transmembrane proteins: keyword:"Transmembrane [KW-0812]" keyword:"Mitochondrion [KW-0496]" AND organism:"Mus musculus (Mouse) [10090]" (810 proteins, downloaded June 2021).

Technical details and requirements:

Surface biotinylation following the protocol from the Pierce™ Cell Surface Protein Isolation Kit (#89881). Analysis of peptides by nano-LC MSMS using an Ultimate 3000 nano-LC system in line with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) controlled by Xcalibur 3.0 software (Thermo Scientific) and operated in data-dependent acquisition mode.

Additional information:

Supplementary table 1: Contains the raw datasets and subsequent filters, legends are supplied for each tab to describe the dataset. Supplementary table 2: Contains datasets referring to mitochondrial membrane protein comparisons. Legends are supplied to further describe the dataset. Supplementary table 3: Contains datasets referring to Glycosylphosphatidylinositol (GPI) anchour protein comparisons. Legends are supplied to further describe the dataset.

Funders

Engineering and Physical Sciences Research Council (EPSRC)
https://doi.org/10.13039/501100000266

EPSRC Doctoral Training Centre in Sustainable Chemical Technologies
EP/L016354/1

Science and Technology Facilities Council (STFC)
https://doi.org/10.13039/501100000271

Grant
#SA-54

Medical Research Council (MRC)
https://doi.org/10.13039/501100000265

Grant
MR/P0002927/1

Publication details

Publication date: 18 November 2021
by: University of Bath

Version: 1

DOI: https://doi.org/10.15125/BATH-01051

URL for this record: https://researchdata.bath.ac.uk/id/eprint/1051

Related papers and books

Morrison, K. A., Heesom, K. J., Edler, K. J., Doutch, J., Price, G. J., Koumanov, F. and Whitley, P., 2021. Development of Methodology to Investigate the Surface SMALPome of Mammalian Cells. Frontiers in Molecular Biosciences, 8. Available from: https://doi.org/10.3389/fmolb.2021.780033.

Contact information

Please contact the Research Data Service in the first instance for all matters concerning this item.

Contact person: Kerrie Morrison

Departments:

Faculty of Science
Biology & Biochemistry
Chemistry

Research Centres & Institutes
Centre for Sustainable Chemical Technologies