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Lowerymass spectrometry imagingData-dependent acquisitionMass SpectrometryBottom-up proteomicsSalivary Gland CarcinomaEsophageal CarcinomaMucinous AdenocarcinomaColon Mucinous Adenocarcinomahttps://www.ebi.ac.uk/pride/archive/projects/PXD055865ColonSalivary GlandEsophagusGlass slides with formalin-fixed, paraffin-embedded tissue sections of mucinous tumors were heated, dewaxed, and rehydrated prior to antigen retrieval in citraconic anhydride buffer, pH 3, for 30 minutes at 95 °C. Following a water wash, slides were dried in a desiccator. PNGaseF PRIME (N-Zymes Scientific, Doylestown, PA) was applied to slides using an M5 Sprayer (HTX Technologies). Deglycosylation in proceeded for 2 hours at 37 °C, after which tissues were H&E stained. Cover slips were removed, then washed sequentially in 10 mM Tris pH 8.5, citraconic anhydride pH 3, and water. The M5 sprayer then applied StcE as above for overnight digestion at 37 °C and drying in a desiccator. Tissue regions were outlined using a hydrophobic pen (Sigma Aldrich, Z377821 or Z672548) and dried. Where indicated, a 0.05 mg/mL solution of StcE in fresh, 50 mM ammonium bicarbonate (AmBic) (Honeywell Fluka, 40867) was deposited via micropipette. Slides were incubated at 37 C for 13-23 hours. Glycopeptides were extracted with 3 different solvents: 0.1% FA in water, 4:1 ACN:0.1% FA in water, and 7:3 MeOH:0.1% FA in water. Each solvent was pipetted ten times on the slide surface, twice, for a total of six extractions. In some instances, StcE-derived glycopeptides were not collected prior to tryptic digestion. A 0.01 mg/mL solution of trypsin (Promega, V5113) in 50 mM AmBic was applied to slides as for the mucinase digestion. Slides were incubated at 37 C for 4-5 hours and peptides were extracted as above. All samples were dried and stored at -20 C. After resuspension in 50 mM AmBic, protein concentration was measured by NanoDrop One Microvolume UV-Vis Spectrophotometer (Thermo-Fisher). Samples were acidified, then desalted using 10 mg Strata-X 33 µm PRP SPE columns (Phenomenex, 8B-S100-AAK). Each column was activated with ACN, equilibrated with 0.1% FA, pre-eluted with 0.1% FA in 40% ACN, and re-equilibrated with 0.1% FA. Samples were applied and de-salted with two 150-µL rinses of 0.1% FA. Peptides were eluted with two 150 µL additions of 0.1% FA in 40% ACN. Samples were dried, and glycopeptide samples were resuspended in 0.1% FA for LC-MS. Tryptic peptides were fractionated with HILIC-based SPE using 12-μm, 300-Å PolyHYDROXYETHYL Aspartamide™ (PHEA) (PolyLC®, BMHY12-03) based on the StageTips design. Fractions were dried and resuspended in 0.1% FA in water for LC-MS. Samples were analyzed by nanoflow LC-MS/MS using an Orbitrap Eclipse coupled to a Dionex UltiMate 3000 HPLC (Thermo Fisher Scientific). A volume of 1-6 µL was injected onto an Acclaim PepMap 100 column packed with 2 cm of 5 µm C18 (Thermo Fisher, 164564) using 0.1% FA in water (solvent A). Peptides were separated on a 15 cm PepMap RSLC EASY-Spray C18 column packed with 2 µm of C18 (Thermo Fisher, ES904) using a gradient from 0-35% solvent B (0.1% FA with 80% ACN) in 60 min. For glycopeptide and trypsin Fraction 2 samples (and Fraction 1 for Colon 2 and the Salivary Gland), full scan MS1 spectra were collected at a resolution of 60,000, an automatic gain control (AGC) target of 3e5, and a mass range from 400-1500 m/z or 300-1500 m/z. Charge states 2-6 or 2-7 were selected for fragmentation. MS2s were generated at top speed for 3 s. Higher-energy collisional dissociation (HCD) was performed on all selected precursor masses with the following parameters: isolation window of 2 m/z, stepped collision fragmentation at 25-30-35% or 25-30-40% normalized collision energy (nCE), Orbitrap detection (resolution of 7,500), maximum inject time of 75 ms, and a standard AGC target. Dynamic exclusion was enabled with a repeat count of 2, repeat duration of 8 s, and exclusion duration of 8 s. Detection of at least 3 HexNAc or Neu5Ac fingerprint ions (126.055, 138.055, 144.07, 168.065, 186.076, 204.086, 274.092, 292.103, and 316.102) triggered additional fragmentation on precursors below 850 m/z using electron transfer dissociation (ETD), and fragments were detected in the ion trap. For precursors between 850-1300 m/z, detection of fingerprint ions triggered ETD with supplemental activation (EThcD) at 15% nCE, analyzed in the Orbitrap with a resolution of 7,500. Calibrated charge-dependent reaction times were used for ETD and EThcD. Dynamic exclusion was enabled with a repeat count of 2, repeat duration of 10 s, and exclusion duration of 10 s. For PHEA-enriched Fraction 1 samples of Colon 1 and the Esophagus, MS1 spectra were collected at a resolution of 60,000, an AGC target of 3e5, and a mass range from 400-1500 m/z or 300-1500 m/z. Charge states 2-6 were selected for fragmentation. MS2s were generated at top speed for 3 s. HCD was performed on all selected precursors with an isolation window of 2 m/z, stepped collision fragmentation at 27-29-31% or 25-30-35% nCE, Orbitrap detection (resolution of 15,000), 100 ms maximum inject time, and a standard AGC target. Dynamic exclusion was enabled with a repeat count of 2, repeat duration of 7 s, and exclusion duration of 8 s.PrideNot availableTryptic peptide *.raw files were searched against the human proteome with Byonic (Protein Metrics). Mass tolerances of 10 ppm, 20 ppm, and 0.3 Da were used for MS1, FTMS MS2, and ITMS MS2, respectively. Met oxidation was selected as a variable modification. The search was set to “fully specific” with proteolytic cleavage C-terminal to R and K, allowing 2 missed cleavages.Glycopeptide *.raw files for each tumor region were searched using O-Pair with MetaMorpheus (v1.0.2 or v1.0.3), using a manually curated protein database containing mucins of interest and StcE. The dissociation type was set to HCD, and EThcD was selected for child scan dissociation. Precursor and product ion mass tolerances were set to 10 ppm and 20 ppm, respectively. “Non-specific” protease cleavage was selected, and peptide length was set to 5-25 amino acids. A maximum of 6 O-glycans were allowed, using the “OGlycan.gdb” database. All glycopeptide identifications assigned Level 1 or 1b were validated by manual inspection of raw spectra using QualBrowser in XCalibur (v4.1.31.9).Colon 2 and Healthy Colon glycopeptide *.raw files were also searched with Byonic (v4.5.2). Separate searches were performed using focused databases created from searches of the two unmodified peptide fractions for each sample. “Fully specific” protease cleavage N-terminal to Ser and Thr residues was selected, allowing for a maximum of 6 missed cleavages. Precursor and product ion mass tolerances were set to 10 ppm and 20 ppm/0.35 Da (FTMS/ITMS), respectively. A custom O-glycan database that included the 6 most common O-glycans, glycan compositions manually identified in the Healthy Colon data, and mono-/di-/tri-acetylated versions of each sialylated O-glycans was used in each search. Glycopeptide identifications not found in original O-Pair searches were validated by manual inspection of raw spectra using QualBrowser in XCalibur (v4.1.31.9).ProteomicsStacy MalakerDepartment of Chemistry, Yale University, New Haven, CT 06520PARTIALHomo Sapiens (human)Not availablesarah.lowery@yale.eduYale UniversityUnited StatesfalseGlycosite Mapping and in situ Mass Spectrometry Imaging of MUC2 Glycopeptides via On-slide Mucinase DigestionAberrant mucin expression and glycosylation are hallmarks of cancer, but how these changes promote malignant processes are not well understood. Solid tumors are highly heterogeneous in their cellular and molecular composition, and many advanced spatial techniques have emerged in recent years to study the tumor microenvironment (TME) for better understanding disease progression. Spatially resolved glycoprotein analyses typically detect either the protein or glycan components, but not both. We developed a workflow using a dual mass spectrometry approach to map the location of intact glycopeptides in mucinous tumors, enabled by on-tissue digestion with the mucin-specific protease StcE. Future applications of this method on larger patient cohorts will enhance our understanding of glycans in malignancy, identify disease biomarkers, and define therapeutic targets.2026-04-062024-09-14PXD055865NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:145458NEWT:633149NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:9793NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:27457NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:452680NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:416348NEWT:11298NEWT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