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Allsup"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Phagosomal proteome","Phagosome proteome","Phagosome lumen","Phagosomal lumen","Hrp","Apex2","Phagosome","Turboid","Proximity labeling"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD055598"],"tissue":["Macrophage"],"sample_protocol":["For TMT experiments (iBMDM PhagoID, hMDM PhagoID, FLAM IFN stimulation, TFEB/LAMP1 KO, iBMDM timecourse):Macrophages (immortalized murine bone-marrow derived or primary human monocyte-derived)  were seeded into one 10cm dish ~24 hrs prior to experiment for each condition. 250e6 HRP- or BSA-beads were prepared per condition by washing 3x in cell culture medium. Fresh medium containing 250e6 beads was added to each dish, followed by 1 minute of agitation to evenly disperse beads, then 2 minutes with cells resting at room temperature to allow beads to settle with minimal internalization. Plates were then transferred to 37° C and allowed to internalize beads for 30 minutes. To synchronize phagocytosis, non-internalized beads were removed with 5x warm DPBS washes, then warm media was re-added and phagosomes were allowed to mature for an additional 30 minutes at 37° C. AP was spiked in to a final concentration of 500 μM 15 minutes prior to labeling. After 30 minutes of phagosome maturation, 100 mM H2O2 was prepared in DPBS and added to a final concentration of 1 mM for each dish, followed by 1 minute of gentle agitation, then rapidly removing the media and washing 3x with ice-cold quencher solution. Cells were then scraped in ice-cold quenching buffer and transferred to tubes, then pelleted and washed once more with ice-cold quenching buffer. Cells were pelleted again and supernatant was removed, then cell pellets were frozen at -80° C. Cell pellets were thawed at room temp for 5 minutes, then vortexed briefly before adding 225 uL of 1% SDS lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM sodium ascorbate, 5 mM trolox, 1 mM PMSF, 1:1000 benzonase, 1:100 HALT protease inhibitor cocktail (ThermoFisher)) and incubating at RT for 3 minutes. Samples were boiled in 1% SDS lysis buffer at 95° C for 5 minutes, then 4 volumes of ice-cold RIPA (no SDS) were added and incubated for 5 minutes further at room temperature. Lysates were clarified by centrifugation at 10,000xg for 10 minutes at 4C and the clarified supernatant was quantified using the 660 nm Protein Assay with the Ionic Compatibility Detergent Reagent (ThermoFisher).   All samples were normalized to equivalent concentration in 1% SDS lysis buffer. The click reaction was conducted with a 29x click master mix (resulting in final concentrations of 500 μM CuSO4, 1 mM BTTAA, 2.5 mM sodium L-ascorbate, 100 μM biotin-PEG3-azide) as described at 37° C with rotation for 2 hours, then precipitated with 5 volumes of cold methanol overnight at -80° C. Precipitated protein was pelleted by centrifugation at 8000xg for 3 minutes at 4C, followed by 2x cold methanol washes. Lysate pellets were dried for 10 minutes, then resuspended in 100 uL of RIPA containing 2% SDS. 900 uL of RIPA containing no SDS was added and lysates were transferred to fresh tubes prior to biotin enrichment by streptavidin beads. 75 uL of Pierce™ Streptavidin Magnetic Beads were washed 2x in RIPA then added to each sample and incubated at 4C with rotation overnight. Beads were then washed on ice with ice-cold buffers as follows: 2x washes with RIPA, once with 1M KCl, once with 0.1 M Na2CO3, once with 2 M Urea in 10 mM Tris-HCl (pH 8), and 2x with RIPA. Following the final RIPA wash, beads were transferred to fresh tubes and delivered to the Koch Institute Proteomics Core for further preparation for mass spectrometry.   Proteins were reduced with 10mM dithiothreitol (Sigma) for 1h at 56° C and then alkylated with 20mM iodoacetamide (Sigma) for 1h at 25° C in the dark. Samples were incubated with PNGaseF for 2 h at 37° C. Proteins were then digested with modified trypsin (Promega) in 100mM ammonium bicarbonate, pH 8 at 25° C overnight. Trypsin activity was halted by addition of formic acid (99.9%, Sigma) to a final concentration of 5%. Peptides were desalted using Pierce Peptide Desalting Spin Columns(cat#89852) then vacuum centrifuged. After digestion the samples were TMT labeled according to the manufacturer's protocol (ThermoFisher). Each fraction was separately resuspended in 0.2% formic acid and injected onto a column. The peptides were separated by reverse phase HPLC (Thermo Ultimate 3000) using a Thermo PepMap RSLC C18 column(2um tip, 75umx50cm PN# ES903) over a gradient before nano-electrospray using a Orbitrap Exploris 480 mass spectrometer (Thermo). Solvent A was 0.1% formic acid in water and solvent B was 0.1% formic acid in acetonitrile. The gradient conditions were 1% B (0-10 min at 300nL/min) 1% B (10-15 min, 300 nL/min to 200 nL/min) 1-10% B (15-20 min, 200nL/min), 10-25% B (20-65 min, 200nL/min), 25-36% B (65-75 min, 200nL/min), 36-80% B (75-75.5 min, 200 nL/min), 80% B (75.5-80 min, 200nL/min), 80-1% B (80-80.1 min, 200nL/min), 1% B (80.1-100 min, 200nL/min).  The mass spectrometer was operated in a data-dependent mode. The parameters for the full scan MS were: resolution of 120,000 across 375-1600 m/z and maximum IT 25 ms. The full MS scan was followed by MS/MS for as many precursor ions in a two seconds cycle with a NCE of 36, dynamic exclusion of 30 s and resolution of 45,000.For LFQ experiment (E coli vs bead PhagoID):10 million iBMDMs for each condition were seeded across 2 wells of a 6-well dish for each condition ~18 hours prior to the initiation of PhagoID. To account for the different settling times of beads and bacteria, the cell culture media was replaced with cold D10 containing beads (5 beads per macrophage) and/or bacteria (20 bacteria per macrophage), gently agitated for 1 minute for equal distribution, then incubated on ice for 60 minutes. Plates were then transferred to a shallow water bath within the 37C incubator to rapidly warm macrophages and induce phagocytosis, which proceeded for 25 minutes. As E. coli are expected to induce a more significant ROS burst in the phagosome compared to inert beads, alkyne phenol was added to the well only 5 minutes prior to labeling to minimize non-temporally restricted proximity labeling catalyzed by endogenous H2O2 production. At the 30 minute timepoint, EGCG was added to a final concentration of 200 uM to block labeling from extracellular beads or bacteria, followed immediately by the addition of 1mM H2O2 for 1 minute. Samples were quenched, washed, detached, and lysed as described above. The click reaction and streptavidin enrichment was conducted as described above with an input of 500 ug in 1 mL reaction volume. Mass spectrometry for the LFQ experiments (E. coli PhagoID) was conducted identically as described above for TMT experiments, with the following modifications: 1) PNGase F treatment was omitted to avoid expanding the search space for LFQ database calling, as LFQ experiments are more sporadic with missing detection and expanded search space can increase false hits. 2) Each LFQ samples was run as a single shot: tryptic peptides were desalted, then immediately injected onto a column without fractionation. 3) The gradient length was increased to maximize the number of peptides analyzed: The gradient conditions were 1% B (0-20 min at 300nL/min) 1% B (20-25 min, 300 nL/min to 200 nL/min) 1-5% B (25-30 min, 200nL/min), 5-15% B (30-115 min, 200nL/min), 15-25% B (115-128 min, 200nL/min), 25-80% B (128-128.5 min, 200 nL/min), 80% B (128.5-130 min, 200nL/min), 80-1% B (130-130.1 min, 200nL/min), 1% B (130.1-150 min, 200nL/min). 4) The full MS scan was followed by MS/MS for as many precursor ions in a three seconds cycle with a NCE of 28, dynamic exclusion of 20 s and resolution of 15,000."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["For TMT experiments (iBMDM PhagoID, hMDM PhagoID, FLAM IFN stimulation, TFEB/LAMP1 KO, iBMDM timecourse):Raw mass spectral data files (.raw) were searched using Sequest HT in Proteome Discoverer (ThermoFisher). Sequest search parameters were: 10 ppm mass tolerance for precursor ions; 0.05 Da for fragment ion mass tolerance; 2 missed cleavages of trypsin; fixed modification were carbamidomethylation of cysteine and TMT modification on the lysines and peptide N-termini; variable modifications were methionine oxidation, methionine loss at the N-terminus of the protein, acetylation of the N-terminus of the protein. As all samples included PNGaseF digestion, an additional variable modification of deamidation of asparagine because PNGaseF digestion of N-linked glycans results in the deamidation of the glycosylated asparagine. Data was searched against an Uniprot Mouse database (Proteome ID: UP000000589) or Uniprot Human database (Proteome ID: UP000005640) and a contaminate database made in house.For LFQ experiment (E coli vs bead PhagoID):Thermo .raw files were searched using MaxQuant (v2.7.5) with fully default settings other than these parameters: enabled LFQ quantification, LFQ min ratio set to 2 (for more stringent quantification requiring 2 peptide ratios for quantification of any protein); match-between-runs set to 1 minute; enabled Classical LFQ for single shots; up to 2 missed cleavages; enabled ID of 2nd peptides; fixed modification Carbamidomethyl (C); variable modifications Oxidation (M), Acetyl (protein N-term). Fasta files included for MaxQuant search were 1) reference murine proteome UP000000589 “one sequence per gene” .fasta file , retrieved on April 21 2026, 2) reference E. coli K12 proteome UP000000625 “one sequence per gene” .fasta file , retrieved on April 21 2026, and 3) a custom .fasta file containing the amino acid sequences of eCPX-SpyTag2, SpyCatcher, and HRP.  Following MaxQuant our data analysis pipeline for the LFQ experiments comparing 4 conditions (HRP-Beads, HRP-E. coli, BSA-Beads, and E. coli (no HRP)) is described in Figure S7."],"omics_type":["Proteomics"],"labhead":["Bryan Bryson"],"instrument_platform":[""],"labhead_affiliation":["Department of Biological Engineering, MIT, Cambridge, USA Ragon Institute of Mass General, Harvard, and MIT, Cambridge, USA"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)","Mus Musculus (mouse)"],"submitter_mail":["allsup@mit.edu"],"publication":["10.1126/SCIADV.AEE3876"],"submitter_affiliation":["Massachussetts Institute of Technology"],"submitter_country":["United States"],"doi":["10.6019/PXD055598"],"additional_accession":[]},"is_claimable":false,"name":"PhagoID: Quantitative in situ proximity labeling defines the proteomes of bead- and microbe-containing phagosome lumina across species, maturation, and immune activation","description":"The phagosome is an immune organelle that integrates signals from diverse cargos to drive pathogen killing, tissue homeostasis, and antigen presentation. How this compartment coordinates such diverse functions remains incompletely understood. A comprehensive view of phagosomal composition across cell states and perturbations could accelerate insight into its regulation. Here, we establish PhagoID, a modular proximity labeling approach that enables in situ proteomic profiling of the phagosome lumen in living cells. Applying PhagoID to murine and human macrophages, we define conserved and species-specific phagosomal proteomes that include both canonical lysosomal components and unexpected contributors from nuclear, mitochondrial, and endoplasmic reticulum compartments. Integrating these proteomes with 25 genome-scale CRISPR screens of phagosomal phenotypes, we identify a network of lumenal proteins that regulate cargo uptake, acidification, antigen presentation, and microbial control highlighting previously unrecognized phagosomal effectors. We next adapt PhagoID to profile the microbe-containing phagosome and compare the sterile bead-containing phagosome to the E. coli-containing phagosome, demonstrating a modest E. coli signature of phagosome remodeling. Comparative analyses further reveal that loss of LAMP1 enhances recruitment of ER-derived proteins to the phagosome, whereas loss of TFEB minimally perturbs the lumenal proteome despite its established role in lysosomal biogenesis. Finally, cytokine stimulation remodels the phagosome lumen to enrich for proteins involved in antigen presentation and antimicrobial activity in response to type I and II interferons. Together, these data demonstrate that PhagoID delivers a high-confidence, quantitative, and integrative map of the phagosome lumen, revealing new axes of organellar communication and regulatory control in innate immunity.","dates":{"publication":"2026-10-02","submission":"2024-09-05"},"accession":"PXD055598","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:57577","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:1584","NEWT:36630","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:29064","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:273791","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:34878","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:237610","NEWT:95486","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:172271","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:595495","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:1613","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCB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