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. 2022 Feb 2;3(1):101177. doi: 10.1016/j.xpro.2022.101177
REAGENT or RESOURCE SOURCE IDENTIFIER
Chemicals, peptides, and recombinant proteins
Acetone (HPLC grade) Merck SF2SF62425
Ethanol absolute Merck K51871183 942
Quick Start Bradford 1× Dye Reagent Bio-Rad 5000205
Acetonitrile (ACN; MS grade) Fisher Scientific A/0620/21
Bovine Serum Albumin HiMedia TC194-25G
Calcium chloride Fisher Scientific BP510-500
Formic acid (FA; MS grade) Fisher Scientific 147930250
Iodoacetamide Sigma-Aldrich 1149-25G
Isopropanol (MS grade) Fisher Scientific Q13827
Magnesium Chloride Fischer Scientific BP214-500
Methanol (MS grade) Fisher Scientific A456-4
M.S. grade water Pierce 51140
Phosphate Buffer Saline HiMedia TL1006-500ML
Sodium Chloride Merck DF6D661300
TCEP Sigma-Aldrich 646547
Tris Base Merck 648310
Trypsin (MS grade) Pierce 90058
Urea Merck MB1D691237
Biological samples
Clinical samples from COVID-19 patients Bankar et al. (2021) For the characteristics see Table S1 from Bankar et al. (2021);
Mendeley Data: https://doi.org/10.17632/rnfn3vhg63.1
Software and algorithms
MaxQuant Tyanova et al. (2016) MaxQuant v1.6.6.0
Metaboanalyst Xia et al. (2015) Metaboanalyst software V4
Reactome Fabregat et al. (2018) Reactome Version 73
Metascape Zhou et al. (2019) Metascape Version 3.5
STRING Szklarczyk et al. (2019) STRING Version 11
Skyline MacLean et al. (2018) Skyline Version 20.2.1.286
Deposited data
LFQ raw files and search output files for proteomics data sets Bankar et al. (2021) ProteomeXchange Consortium via the PRIDE partner repository: "PRIDE: PXD020580" and "PRIDE: PXD023016" https://www.ebi.ac.uk/pride/archive/projects/PXD023016
https://www.ebi.ac.uk/pride/archive/projects/PXD020580
Targeted proteomics data Bankar et al. (2021) Panorama Public: “https://panoramaweb.org/COVID_Swab_MRM.url”.
Additional supplemental items Bankar et al. (2021) Tables S1, S8 and S10 from Bankar et al. (2021); Mendeley Data: https://doi.org/10.17632/rnfn3vhg63.1.
Additional supplemental items This paper Table S4; Mendeley Data: DOI: https://doi.org/10.17632/ykx6jrpsm3.1 (https://data.mendeley.com/datasets/ykx6jrpsm3/1)
Other
Microtubes 1.5 mL Axygen, A corning brand MCT-150-C
BD™ Universal Viral Transport Becton, Dickinson and Company 220239
PK20 EMPORE OCTADECYL C18 47MM Merck 66883-U
Acclaim™ PepMap™ 100 C18 HPLC Columns Thermo Scientific™ (P/N 164564)
PepMap TM RSLC C18 2 μm,100 Å, 75 μm∗50 cm Thermo Scientific™ (P/N ES803A)
Hypersil Gold C18 column Thermo Fisher Scientific 25002-102130
Micropipettes Gilson F167380
C18 material for in-house C18 tips Merck Millipore ZTC18M008
Zirconia/Silica beads BioSpec products 11079110z
Pierce™ LTQ Velos ESI Positive Ion Calibration Solution Thermo Scientific™ 88323
Microplate reader (spectrophotometer) Thermo Fisher Scientific MultiSkan Go
pH meter Eutech CyberScan pH 510
Digital Shaking Drybath Thermo Fisher Scientific 88880028
Orbitrap Fusion mass spectrometer Thermo Fisher Scientific FSN 10452
Nano LC Thermo Fisher Scientific EASY-nLC1200
TSQ Altis mass spectrometer Thermo Fisher Scientific TSQ02-10002
uHPLC - Vanquish Thermo Fisher Scientific VQF01-20001
Vacuum concentrator Thermo Fisher Scientific Savant ISS 110