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14 protocols using trifluoroacetic acid

1

Mass Spectrometry Sample Preparation

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All chemicals were of the highest purity obtainable. Water, formic acid, trifluoroacetic acid (TFA), acetonitrile (ACN), and methanol were purchased from Biosolve B. V. (Valkenswaard, the Netherlands). Ammonium bicarbonate, ethanol (EtOH), α-cyano-4-hydroxycinnamic acid, aniline (ANI), sinapinic acid (SA), and 1,1,1,3,3,3-hexafluoro-2-propanol reagents for Toluidine blue staining were purchased from Sigma-Aldrich (Saint-Quentin Fallavier, France). Trypsin was purchased from Promega (Charbonnieres, France).
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2

N-Glycan Release and Characterization

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Ammonium bicarbonate, sodium chloride, acetonitrile
(MeCN), trifluoroacetic acid (TFA), and ethanol (EtOH) were purchased
from Biosolve B.V. (Valkenswaard, The Netherlands). Water was filtered
using the Milli-Q water purification system of Merck Millipore (Molsheim,
France). Sodium dodecyl sulfate (SDS), 2-mercaptoethanol (2-BME),
2,5-dihydroxybenzoic acid (DHB), fetuin originated from fetal bovine
serum, and branched octylphenoxy poly(ethoxy)ethanol (IGEPAL CA-630)
were provided by Sigma-Aldrich (St. Louis). A mixture of maltodextrins
was obtained from Avebe (Veendam, The Netherlands). The complex N-glycans
NA2 (No. 24) and NA2F (No. 33) and the high-mannose
structures Man6 (No. 11) and Man8 (No. 27) (Table 1) were provided by Ludger (Oxfordshire, U.K.).
Peptidyl N-glycosidase F (PNGase F) was bought from
Asparia Glycomics (San Sebastian, Spain).
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3

Mass Spectrometry Sample Preparation

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All chemicals were of the highest obtainable purity. Water, formic acid (FA), trifluoroacetic acid (TFA), acetonitrile (ACN), and methanol (MeOH) were purchased from Biosolve B.V. (Valkenswaard, the Netherlands), alpha-cyano-4-hydroxycinnamic acid (HCCA), 2.5-dihydroxybenzoïc (2,5-DHB), sinapinic acid (SA), lysozyme C and cytochrome C, ammonium bicarbonate (AB), dithiothreitol (DTT) and iodoacetamide (IAA) from Sigma-Aldrich (Saint-Quentin Fallavier, France), bradykinin (BK) from PolyPeptide Group (Strasbourg, France), Phosphatidyl Choline 15:0/15:0 lipid species (PC) from Avanti Polar Lipid (Alabaster, Alabama, USA), carmine from George T. GURR LTD (London, England) and Congo red from Microcolor (Boulogne, Seine, France). Trypsin (sequencing grade modified trypsin, porcine) was purchased from Promega (Charbonnieres, France).
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4

Solid-Phase Peptide Synthesis Reagents

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1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (HATU), 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium fluorophosphate (HBTU) and N-Fmoc-protected amino acids were obtained from Iris Biotech GmbH. Piperidine, diisopropylcarbodiimide (DIC), N-hydroxybenzotriazole (HOBt), MPAA (97%, MPAA), 3-mercaptopropionic acid (MPA), tris(2-carboxyethyl)phosphine hydrochloride (≥98%, TCEP·HCl), thiophenol, triisopropylsilane (TIS), guanidine hydrochloride (≥99%, Gn·HCl), hydrochloric acid (reagent grade, 37%), and sodium hydroxide (pellets, 97%) as well as other reagents were purchased from Sigma Aldrich, Acros Organics or Merck and were of the purest grade available. Peptide synthesis grade N,N-dimethylformamide (DMF), dichloromethane, diethyl ether, acetonitrile, heptane, LC-MS-grade acetonitrile (0.1% TFA), LC-MS grade water (0.1% TFA), N,N-diisopropylethylamine (DIEA), acetic anhydride (Ac2O), and trifluoroacetic acid (TFA) were purchased from Biosolve and Fisher-Chemical. NovaSyn TGR solid support was purchased from Sigma Aldrich. Bis(2-sulfenylethyl)amino trityl 1% divinylbenzene cross-linked polystyrene solid support (SEA PS) was produced on demand by Roowin. Solvents and reagents were used as received.
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5

Peptide Synthesis and Cell Labeling

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All chemicals were purchased from Sigma unless
otherwise stated. Amino acids and HCTU were purchased from Novabiochem.
Tentagel HL RAM resin was purchased from Iris Biotech GmbH. Piperidine,
trifluoroacetic acid, acetic anhydride, and all other solvents were
purchased from Biosolve. Oxyma pure was purchased from Carl Roth GmbH.
Dextran 70 was supplied by Pharmacosmos. CellTracker Red and Green,
lipofectamine 3000, and 2 kDa MWCO dialysis membrane were purchased
from Thermo Fisher. Confocal chambered coverslips (μ-Slide 8
Well) were purchased from Ibidi. All cell culture supplies were purchased
from Starstedt. Carbon/Formvar grids for transmission electron microscopy
were purchased from Agar Scientific.
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6

Analytical Chemistry Reagent Procurement

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High-purity chemicals from various suppliers were purchased for the different experiments and used as received without any further modifications. Acetonitrile (ACN) HPLC grade, Ethanol HPLC grade, Methanol LC-MS grade, and Isopropyl alcohol LC-MS were purchased from CARLO ERBA Reagents SAS (Val de Reuil, France). Water UHPLC-MS was supplied by Fisher Scientific (Illkirch, France). Trifluoroacetic acid and Formic Acid (FA) were obtained from Biosolve B.V. (Valkenswaard, the Netherlands). Additionally, alpha-Cyano-4-hydroxycinnamic acid (4-HCCA), Aniline (ANI), and Glycerol were sourced from Sigma Aldrich (Saint-Quentin-Fallavier, France).
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7

Proteomic Analysis of Glioma Cell Lines

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Water (H2O), formic acid (FA), acetonitrile (ACN), and trifluoroacetic acid (TFA) were obtained from Biosolve B. V. (Valkenswaard, Netherlands). DL-dithiothreitol (DTT), Hydrochloric acid (HCl), and Triton X-114 were purchased from Sigma-Aldrich (Saint-Quentin Fallavier, France). Trypsin was purchased from Promega (Charbonnieres, France). Tris was purchased from Interchim (Montluçon, France). EZ-Link Sulfo-NHS-SS-Biotin, Streptavidin UltraLink Resin (Pierce), Sodium chloride (NaCl), Dulbecco’s Modified Eagle’s Medium (DMEM), DMEM high glucose GlutaMAX™ Supplement, heat-inactivated fetal bovine serum (FBS), Trypsin, phosphate buffer saline (PBS), penicillin and streptomycin were purchased from Thermo Fisher Scientific (Massachusetts, USA). U-87 MG (ATCC® HTB-14™) cell lines were purchased from ATTC (Manassas, Virginia, USA). Immortalized Human Astrocytes (Ref: P10251-IM) and astrocyte medium were obtained from Innoprot (Derio, Spain). Human NCH82 stage IV glioma cells were obtained from Dr Regnier-Vigouroux.
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8

Solid-Phase Peptide Synthesis Reagents

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Dimethylformamide (DMF), piperidine, acetic anhydride, pyridine, trifluoroacetic acid (TFA) and acetonitrile (MeCN) were purchased from Biosolve. N,N-diisopropylethylamine (DIPEA), and Oxyma were obtained from Carl Roth. Dichloromethane (DCM) and diethyl ether were supplied by Honeywell. Tentagel HL-RAM was obtained from Rapp Polymere. All amino acids were supplied by NovaBioChem. All other chemicals were purchased from Sigma Aldrich. Ultrapure water was obtained from a MILLI-Q™ purification system. All buffers were made at pH 7.4 unless otherwise stated.
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9

Plasma Sample Preparation for UPLC-MS Analysis

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All solvents used were of UPLC grade. Acetonitrile
and dimethyl sulfoxide (DMSO) were supplied by Scharlau (Barcelona,
Spain). Methanol was from Lab-Scan (Gliwice, Poland). Ammonium formate,
formic acid and trifluoroacetic acid (TFA) were purchased from BioSolve
(Valkenswaard, Netherlands), and HPLC-grade water was obtained from
an EASYpure II (Barnstead, Dubuque, IA) water purification system.
Blank K3EDTA C57BL/6N mouse plasma was collected for generating
plasma calibrators and quality controls (QC).
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10

Alginate-Chitosan Hydrogel for Drug Delivery

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Sodium alginate (M.W. 200 kDa), calcium chloride dihydrate, gentamicin sulfate (GM), citric acid (CA), and chitosan (75–85% degree of deacetylation, M.W. 50–190 kDa) were obtained from Sigma-Aldrich (St. Louis, MO, USA). Phosphate buffer saline (PBS) was purchased from Gibco (Carlsbad, CA, USA). Acetonitrile and trifluoroacetic acid were purchased from Biosolve (Valkenvaard, The Netherlands), and formic acid was obtained from Merck (Darmstadt, Germany).
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