Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/M1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/F2.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/I2.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/E2.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/N1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/K1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/A2.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/H1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/L1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/G2.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/B1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/J2.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/O1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/P1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/D1.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/b1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/k1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/a2.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/h1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/n1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/j2.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/d1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/j2.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/g2.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/e2.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/p1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/f2.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/i2.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/g2.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/a2.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/l1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/h1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/k1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/m1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/p1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/n1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/d1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/m1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/f2.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/i2.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/b1.imzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/e2.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/o1.ibdftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/10/PXD021275/l1.ibdprimaryOK200B.P.A.M.Heijs@lumc.nlFanny BoyavalMass SpectrometryMass spectrometry imagingColon CancerNot availableGlycomicMass spectrometry imagingColorectal cancerhttp://www.ebi.ac.uk/pride/archive/projects/PXD021275ColonTissue section were cut at 6 µm thickness, mounted in pairs onto poly-L-lysine-coated indium tin oxide (ITO). paraffin was removed by heating the slides 1 h at 65°C followed by two consecutive washes in xylene (10 min and 5 min respectively). Tissues were rehydrated in ethanol baths (100% ethanol, twice for 2 min), followed by water baths (twice for 5 min) and dried for 10 min in a vacuum desiccator. On-tissue derivatization was performed by incubating the tissues slides in derivatization solution (250 mM EDC, 500 mM HOBt and 250 mM dimethylamine in DMSO) for 1 h at 60°C, followed by addition of a 25% ammonia solution (1:0.4 v/v derivatization solution–ammonia) and further incubation for 2 h at 60°C, both protected from evaporation. Following derivatization, tissue sections were rinsed thoroughly with 100% ethanol followed by sequential washes in 100% ethanol (2 × 2 min) and water (2 × 5 min). Slides were dried in a vacuum desiccator (10 min). On-tissue digestion was performed applying 10 layers at 10 μL/min of PNGase F (0.1 μg/μL in Tris buffer; from N-Zyme scientifics) using a SunCollect sprayer (Sunchrom, Friedrichsdorf, Germany). N-glycans were released overnight at 37°C in a humid environment. After incubation, slides were dried in a vacuum desiccator for 10 min, followed by matrix application (5 mg/mL CHCA in 50:49.9/0.1 (%v/v) ACN:mQ:TFA) using the SunCollect sprayer (6 layers at (1) 10 μL/min, (2) 20 μL/min, (3) 30 μL/min, (4+) 40 μL/min). N-glycan MALDI-MSI was performed in positive ion reflectron mode on a rapifleXTM MALDI-TOF/TOF-MS instrument (Bruker Daltonics) using a m/z range of 900 to 3300 Da, 1000 laser shots per pixel, 50 × 50 µm2 pixel size. MSI data acquisition was enabled by the flexImaging software (flexImaging 4.0 Build 32, Bruker Daltonics). After the MSI analysis, excess MALDI-matrix was removed by washing twice in 70% ethanol (5 min each), and tissues were stained with hematoxylin and eosin (H&E) following routine histopathological procedures.Pridecomplex glycosylationNot availableThe data were added to the ScilLab software from Bruker in the same depository, were the Imzml files from each tissue were extracted. The Imzml files can be found in this depositoryProteomicsHeijs, BramBruker Daltonics flex seriesCenter of Proteomics & metabolomics, Leiden University medical Center, Leiden, The netherlandsPARTIALHomo Sapiens (human)Not availableF.F.M.Boyaval@lumc.nlPhDNetherlandsDIMETHYL SULFOXIDE, Grain Alcohol, determination, instrument configuration, dimethylamine nitrate, FEZL, OFC11, Glykan, 1-hydroxyethane, mg/ml, alcohol, Cut, Ethanol, polisacarido, neutrophilic leucocyte, BANF, l(1)7Ba, l(1)7Bb, type I, neutrophil leukocyte, Parafilm, Alkohol, Impacts, Min, 4, Software Engineering, Environmental Impacts, 7, 9, R-717, Computer Program, DmelCG42273, ASD2, portion of tissue, ammoniac, Grain, C79325, PNGase F, TACHD, Ethyl, 2610036I19Rik, Open, Tissue, 2610510L13Rik, dimethyl sulphoxide, min, PNGase A, Computer Programs and Programming, dimethylammonium chloride, Glycane, Hemotoxylin, mAPC, mature neutrocyte, Aethanol, [CH2Me(OH)], Shots, CG11387, AI047805, Environmental Impact, Dehydrated ethanol, AMMONIA, fSAP152, spirit of hartshorn, ACN, polymorphonuclear leukocyte, polynuclear neutrophilic leucocyte, Acn, Glycan, CT, 10(6H)-pentol, bmp-4, Dimethylsulfoxid, spiritus vini, dimethylammonium formate, Ito, dimethylamine monosulfate, DMSO, N-glycanase activity, Alcohol, dimethyli sulfoxidum, Hydroxybrazilin, hi syndrome, dmso, N-oligosaccharide glycopeptidase activity, methylsulfinylmethane, Ct, Dmel_CG7826, Incontinentia pigmenti type 1, Th, Dimethylbenzenes, Xylene, Ethyl alcohol, Source Softwares, Software Tools, Absolute Alcohol, Glykane, Programs, Immunization, Program, Computer Applications, neutrocyte, (CH3)2SO, N-linked-glycopeptide-(N-acetyl-beta-D-glucosaminyl)-L-asparagine amidohydrolase activity, Dm1, Protease M, Computer Applications Software, Computer Applications Softwares, tissue portion, 11b-dihydro-, simple tissue, jack-bean glycopeptidase, Softwares, BcDNA:GH10590, ETHANOL, dimethylamine phosphate (3:1), [OEtH], Dmel_CG7835, Hydrogen Oxide, Mnb, MNB, ofc11, (methanesulfinyl)methane, Software Applications, dimethylamine sulfate (1:1), EtOH, instrument, mature neutrophil leukocyte, Source Software, AW124434, 2-d)pyran-3, alcohol etilico, Methylcarbinol, polysaccharides, Applications, 6a, peptide:N-glycanase, Ammonia, cis-(+)-., Computer Software Applications, polynuclear neutrophilic leukocyte, l(1)VE614, ammonia, hypomelanosis of Ito, Bath, amoniaco, xbmp4, etanol, Hematoxiline, glycans, dimethylsulfoxyde, ACINUS, Computer, thomson, Zyme, CG7826, Serine protease 18, Buffer, mass-to-charge ratio, Aethylalkohol, pigmentary mosaicism, TOF, bmp2b, zyme, Neurosin, CG7835, CG42273, PNGase, ZYME, Polysaccharide, ZNF312, Application, S(O)Me2, MCOPS6, sulfinylbis(methane), Open Source Softwares, Ito hypomelanosis, 3.4.21.-, Incontinentia pigmenti achromians, Acinus, Absolute, ethanol, Software Application, neutrophil leucocyte, Open Source Software, Hydroxybrasilin, neutrophilic leukocyte, dimethylamine, kf, Solution, BMP2B1, Computer Software Application, acinusL, bmp4, dimetil sulfoxido, C2H5OH, mature neutrophilic leucocyte, DmelCG11387, Tools, acinusS, glycopeptidase activity, azane, bmp2b1, FEZ, Applications Software, Open Source, DYRK1, XBMP-4, data, Computer Software, mature neutrophil leucocyte, dimethylamine hydrochloride, Ammoniak, Serine protease 9, Haematoxylon, buffer, mKIAA0670, light amplification by the stimulated emission of radiation, Tool, Impact, Environmental, Incontinentia pigmenti type 1 (formerly), Software Tool, chemical analysis, alcool ethylique, BMP2B, Dyrk1, Vacuums, Dimethyl sulfoxide, NH3, [NH3], Ito type, Software, dimethylamine perchlorate, OF-900, Ethyl Alcohol, AU020952, VSD1, polisacaridos, CC1, Engineering, dimethyl sulfoxide, Benz(b)indeno(1, mature neutrophilic leukocyte, Childhood, dimethylamine sulfate, ME-IV, incised, conjugate acid, Computer Programs, Incontinentia pigmenti, ZFP312, hydroxyethane, HMI, MALDI, SP59, Applications Softwares, humid, glycopeptide N-glycosidase activity, PMN, Environments, polymorphonuclear leucocyte, assay, poly, dimethyl sulfur oxide, SCH, IPA, polymorphonuclear neutrophil, formerlyApplications Software, Open Source Softwares, portion of tissue, Open Source, data, Software Applications, simple tissue., Computer Software, Source Software, Software Application, Open, Engineering, Tissue, Open Source Software, Computer Programs and Programming, Computer, Source Softwares, Software Tools, Computer Software Application, Tool, Programs, Computer Programs, Program, Computer Applications, Applications, Software Tool, Applications Softwares, Tools, Computer Applications Software, Computer Applications Softwares, tissue portion, Software Engineering, Softwares, Software, Computer Program, Application, Computer Software Applicationscarcinoma of large bowel, other disease, advanced, d230, malignant tumour of large bowel, Clr, developmental stage, carcinoma of colorectum, dTAFII250, malignant large bowel neoplasm, F20O9_210, EfW1, autosomal dominant, Relative, dmTAF[[II]]230, colorectal cancer, dATF-4, diseases, glycosylation, Glycosylation, dmTAF1, Taf230, malignant large intestine tumor, colorectum cancer, disease or disorder, anon-EST:Liang-2.17, diseases and disorders, anon-EST:Liang-2.11, Relapses, clone 2.11, preoperative procedures, malignant neoplasm of the large intestine, Atf4, TAF250, 929, DmelCG8669, portion of tissue, Taf200, human disease, malignant large intestine tumour, dTAF[[II]]250, simple tissue., TFIID TAF250, cel, clone 2.17, Recrudescences, cell, large bowel carcinoma, Recurrences, malignant tumour of the large intestine, malignant colorectal tumor, Scrb1, CG9429, Tissue, F20O9.210, Taf1p, CRUCIFERIN C, Ire1, large intestine cancer, cancer of the large intestine, non-neoplastic, dTAF250, malignant colorectal neoplasm, grupos, vartul, Clients, disorder, Homo sapiens disease, stage, operative procedures, carcinoma of the large bowel, carcinoma of large intestine, TAF, somatic mutation, colorectal (colon or rectal) cancer, malignant tumor of the large bowel, Relapse, malignant tumor of large intestine, dTAF[[II]]230, TAF[[II]]250, malignant large bowel tumor, grupo, Protein Glycosylation, SCRIB1, potp, disorders, TAF200, carcinoma of the large intestine, malignant neoplasm of large bowel, l(3)84Ab, intraoperative procedures, medical condition, BG:DS00004.13, large intestine carcinoma, eth, TAFII-250, somatic, TAF250/230, malignant large intestine neoplasm, Client, Cell, group, dTAF230, TAFII250, malignant neoplasm of large intestine, peroperative procedures, Recrudescence, p230, cancer of colorectum, Relative Risks, Protein, Diseases, TAF[[II]]250/230, tissue portion, condition, TFIID, CRC, Crc, l(2)crc, anon-EST:fe3D7, Adjuvant Chemotherapy, Relative Risk, large bowel cancer, Taf[[II]]250, colorectal cancer with chromosomal instability, cruciferin 3, malignant tumor of large bowel, TAF[[II]]230, Risk, operative therapy, susceptibility to, Risks, colorectum carcinoma, Rest, malignant colorectum neoplasm, operations, crc, TAF[II]250, CRIB, Adjuvant, CG17603, TAF[[II]], cancer of large bowel, malignant neoplasm of the large bowel, ATF-4, DmelCG9429, disease, Adjuvant Drug Therapy, crt, colon cancer, DmelCG17603, Drug Therapy, malignant colorectal tumour, Patient, Taf250, colorectal carcinoma, SR3-5, malignant neoplasm of colorectum, malignant tumour of the large bowel, perioperative procedures, malignant tumour of large intestine, cancer of the large bowel, malignant tumor of the large intestine, CG8669, cancer of large intestine, mKIAA0147, ATF4/crc, malignant large bowel tumour, groupe, TAF230, AI118201, Gruppe, invasive procedures, TAF1malignant tumor of the large bowel, Cancer Microenvironments, carcinoma of large bowel, malignant tumor of large intestine, advanced, malignant large bowel tumor, malignant tumour of large bowel, Cancer., Microenvironment, developmental stage, carcinoma of the large intestine, malignant neoplasm of large bowel, carcinoma of colorectum, malignant large bowel neoplasm, large intestine carcinoma, Tumor, somatic, malignant large intestine neoplasm, autosomal dominant, colorectal cancer, malignant neoplasm of large intestine, Cancer Microenvironment, Associations, malignant large intestine tumor, colorectum cancer, cancer of colorectum, CRC, Tumor Microenvironments, malignant neoplasm of the large intestine, large bowel cancer, colorectal cancer with chromosomal instability, malignant large intestine tumour, malignant tumor of large bowel, large bowel carcinoma, susceptibility to, malignant tumour of the large intestine, malignant colorectal tumor, colorectum carcinoma, malignant colorectum neoplasm, cancer of large bowel, large intestine cancer, malignant neoplasm of the large bowel, cancer of the large intestine, colon cancer, malignant colorectal neoplasm, malignant colorectal tumour, colorectal carcinoma, malignant neoplasm of colorectum, malignant tumour of the large bowel, malignant tumour of large intestine, cancer of the large bowel, malignant tumor of the large intestine, stage, cancer of large intestine, carcinoma of the large bowel, carcinoma of large intestine, Microenvironments, malignant large bowel tumour, somatic mutation, colorectal (colon or rectal) cancer, CancerfalseN-glycomic signature of stage II colorectal cancer and its association with the tumor microenvironmentThe choice for adjuvant chemotherapy in stage II colorectal cancer (CRC) is controversial as many patients are cured by surgery alone and it is difficult to identify patients with high-risk of recurrence of the disease. There is a need for better stratification of this group of patients. Mass spectrometry imaging could identify patients at risk. We report here the N-glycosylation signatures of the different cell populations in a group of stage II CRC tissue 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