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

1051 48 15149 3 48248 document 15149 SUPPLEMENTARY_TABLE1.xlsx application/vnd.openxmlformats-officedocument.spreadsheetml.sheet 058d62f0513ff2632200b1edf14bfcb1 MD5 1530777 2021-07-26 15:05:52 https://researchdata.bath.ac.uk/1051/1/SUPPLEMENTARY_TABLE1.xlsx 1051 1 1 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet other 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." en public cc_by

SUPPLEMENTARY_TABLE1.xlsx

data 15150 3 48250 document 15150 SUPPLEMENTARY_TABLE2.xlsx application/vnd.openxmlformats-officedocument.spreadsheetml.sheet e97bc65bd985b410a2ecedf5f4af69f5 MD5 11698 2021-07-26 15:05:55 https://researchdata.bath.ac.uk/1051/2/SUPPLEMENTARY_TABLE2.xlsx 1051 2 2 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet other Microsoft Excel document containing mitochondrial membrane protein dataset desribed in manuscript; "Development of methodology to investigate the surface SMALPome of mammalian cells." en public cc_by

SUPPLEMENTARY_TABLE2.xlsx

data 15151 3 48252 document 15151 SUPPLEMENTARY_TABLE3.xlsx application/vnd.openxmlformats-officedocument.spreadsheetml.sheet ab66cfd50748c3360db5032585a599f5 MD5 10933 2021-07-26 15:06:01 https://researchdata.bath.ac.uk/1051/3/SUPPLEMENTARY_TABLE3.xlsx 1051 3 3 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet other Microsoft Excel document containing Glycosylphosphatidylinositol (GPI) anchour protein dataset desribed in manuscript; "Development of methodology to investigate the surface SMALPome of mammalian cells." en public cc_by

SUPPLEMENTARY_TABLE3.xlsx

data 15153 3 48267 document 15153 Doctoral_Data_Management_Plan_Kerrie_Morrison.docx application/vnd.openxmlformats-officedocument.wordprocessingml.document 5f5ae08d1c59a8d674358fe7a3a45c70 MD5 446948 2021-07-26 15:48:03 https://researchdata.bath.ac.uk/1051/4/Doctoral_Data_Management_Plan_Kerrie_Morrison.docx 1051 4 4 application/vnd.openxmlformats-officedocument.wordprocessingml.document other en staffonly

Doctoral_Data_Management_Plan_Kerrie_Morrison.docx

dmp 15154 1 48272 document 15154 indexcodes.txt text/plain 002280d7fb4d440daea7d10f9c16eafd MD5 2371 2021-07-26 15:51:39 https://researchdata.bath.ac.uk/1051/5/indexcodes.txt 1051 5 5 text/plain other Generate index codes conversion from other to indexcodes en public

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/15153 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/15153 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/15153 archive 9042 disk0/00/00/10/51 2021-12-15 09:34:27 2024-07-18 12:32:02 2021-12-15 09:34:27 data_collection show Morrison Kerrie K.A.Morrison@bath.ac.uk 0000-0001-7130-1183 University of Bath TRUE Whitley Paul P.R.Whitley@bath.ac.uk 0000-0001-9796-8488 University of Bath FALSE Koumanov Francoise F.Koumanov@bath.ac.uk 0000-0002-9029-3390 University of Bath FALSE Supervisor Edler Karen K.Edler@bath.ac.uk 0000-0001-5822-0127 University of Bath Dataset for "Development of Methodology to Investigate the Surface SMALPome of Mammalian Cells" BY0040 BY0100 dept_chem dept_bio MS proteomics, SMA 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. 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". 2021-11-18 University of Bath public RightsHolder University of Bath Engineering and Physical Sciences Research Council https://doi.org/10.13039/501100000266 EP/L016354/1 EPSRC Centre for Doctoral Training in Sustainable Chemical Technologies Science and Technology Facilities Council https://doi.org/10.13039/501100000271 SA-54 ISIS Studentship Agreement Medical Research Council https://doi.org/10.13039/501100000265 MR/P002927/1 Role of Rab3 in Peripheral Tissue Insulin Resistance cent_sus_tech 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. 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). 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. en 1 10.15125/BATH-01051 https://doi.org/10.3389/fmolb.2021.780033 pub open Dataset