{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/combined_protein.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/combined_ion.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/combined_peptide.tsv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0294.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0292.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0307.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0298.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0303.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0301.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0291.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0296.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0306.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0295.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0308.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0297.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0299.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0304.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0293.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0300.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0302.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/GV0305.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/fragpipe-files.fp-manifest","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065433/chpl.fas"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["ikchudinov@gmail.com"],"submitter":["Ivan Chudinov"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Metabarcoding","Proteogenomics","Proteomics","Food quality control","Food safety"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD065433"],"sample_protocol":["For this study, 7 samples were obtained from Russian retailers, 2 samples (IC01 and IC23) were declared as pure Epilobium angustifolium L., while 5 others contain additives (including other herbs) according to the manufacturer's declaration.  To ensure the use of a representative sample portion, we performed sample homogenization prior to protein extraction. An amount of ~2 g of each sample was homogenized by grinding with a sterile power mill in the presence of PVP (7% w/w). 100 ± 10 mg of the resulting mixture was transferred to a 2 mL tube, filled with 1 mL 10% SDS 10 mM Tris-HCl (pH 8.0) and subjected to an ultrasonic homogenizer - 40% power, 15 seconds on, 30 seconds off, 6 minutes cycle.   The resulting mixture was centrifuged at 15,000g for 10 minutes, 500 µL of supernatant was collected and transferred to a clean 2 mL tube. An adapted chloroform-methanol extraction was performed.   A 12.5% polyacrylamide gel, 1 mm thick, was loaded with 6 µL each of a 1:1 mixture of protein sample and 4X Laemmli buffer, and 3 µL of RAV-11 marker. SDS-PAGE was performed in tris-glycine buffer. The gel was then stained with Coomassie (G-250) solution for 20 minutes, followed by washing in 10% acetic acid for 12-16 hours. Imaging was performed on an iBright 1500.  Stained protein bands were excised with a blade, cut into 1x1 mm2 pieces and washed with wash solution (50% acetonitrile in 100mM NH₄HCO₃), dehydrated with 100% acetonitrile. Incubated for 30 minutes, 56°C, with 10 mM DTT in 100 mM NH₄HCO₃, incubated for 20 minutes at room temperature in the dark with 55 mM IAA in 100 mM NH₄HCO₃, followed by 30 minutes with 10 mM DTT in 100 mM NH₄HCO₃. The gel was then dried with 100% acetonitrile.   Chemically modified, methylation-stabilized, and purified laboratory-made trypsin was used for protein digestion. Trypsinolysis solution (200 mM NH₄HCO₃, H2O MQ, acetonitrile, trypsin in 50 mM acetic acid) was added to the dried gel on ice and samples were left for incubation at 37°C for 16 hours. Trypsinolysis was stopped with 50% formic acid, then centrifuged at 16,000g for 5 minutes at 20°C. 50% acetonitrile was added and incubated for 15 minutes. 20% formic acid was added with the following incubation for 25 minutes, 100% acetonitrile was added with the following incubation for 15 minutes, centrifuged at 16,000 g for 5 minutes at 20°C, supernatant collected in a tube and dried on a Speedvac at 2000 rpm, 45°C.  Peptide samples were dissolved in 5% ACN + 0.1% formic acid and separated using UltiMate 3000 nano-flow HPLC system coupled to an Orbitrap Exploris 480 mass spectrometer. Peptide separation was performed on a Peaky-C18 column 500 mm х 75 µm, 1.9 µm particle size in a gradient from 5% to 10% mobile phase B (80% ACN, 0.1% FA) over 0.75 min, then from 10% to 45% mobile phase B over 13. 5 min, then from 45% to 65% of mobile phase B over 0.75 min at 0.25 µL/min, followed by washing the column with 100% of mobile phase B for 2 min and post-analytical equilibration with 5% solvent B for 15 min.  Ion source parameters were as follows: spray voltage of 2200 V, an Ion Transfer Tube temperature of 275°C. Mass spectra were acquired in positive ionization mode with a resolution of 60,000 (at m/z 200) for MS and 15000 for MS/MS scans. The survey MS scan was followed by MS/MS acquisition of a series of automatically selected precursors, which can be acquired in a cycle time of 1 second. Higher energy collisional dissociation (HCD) at 30% was used to generate fragment ions. The signal threshold for precursor ions was set to 100,000 and ions were isolated within a 1.4 m/z window. Tandem mass spectra were acquired within a scan range set to auto."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Sequences of all chloroplast proteins of plant genera identified in the metagenomic study were downloaded from NCBI Protein using the edirect (v20.3) software package (accessed July 7, 2024). The genus Spinacia, which did not appear in the metagenomic results and was included as a control in the proteomic study, was added to the set of genera.  Each of the chloroplast protein sets was preprocessed as follows:  All amino acid sequences containing letters that did not match the IUPAC code were excluded. The amino acid sequence of the protein was subjected to in silico trypsinolysis using the pyteomics (v4.7.2) software package (peptides of 5 to 50 amino acids, 3 missing trypsinolysis sites). If a set of protein peptides was found to be empty as a result of cleavage, such a protein was not included in further analysis. All proteins represented by the same set of peptides were excluded except for the first occurrence. For the set of genus peptides, a scikit-learn (v1.5.1) CountVectorizer model was created to represent each protein by a set of unit vectors in the space of all possible peptides. By iterating over each protein within a genus, proteins that could be represented by a peptide linear combination of all proteins in the genus except that one, i.e., proteins that do not contain a unique peptide, were excluded.  The final protein sets for each of the genera were combined into a single FASTA, which was supplemented with sequences of natural contaminant proteins and converted into a computational database using Philosopher (v5.1.1).   Identification and label free quantification was performed with FragPipe workflow (v22.0) in a closed search mode with match between runs (MBR), trypsin digestion mode, 3 missed cleavages. Fixed modification of cysteine — 57.02146 mass delta), variable modifications – oxidation of methionine (15.9949 mass delta, max 3 occurrences), N-terminal acetylation (42.0106 mass delta, max 1 occurrences), phosphorylation (79.96633 mass delta, max 3 occurrences), pyro-Glu from Q or loss of ammonia at peptide N-terminal (-17.0265, max 1 occurrences), pyro-Glu from E (-18.0106, max 1 occurrences), acrylamide adduct (71.03712 mass delta, max 1 occurrences). Max variable modification combinations — 5000, max variable modifications per peptide — 5. Ion false discovery rate (FDR) for MBR 1%, filtering FDR 5%."],"omics_type":["Proteomics"],"labhead":["Ivan Chudinov"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Scientific Research Institute for Systems Biology and Medicine"],"species":["Food Metagenome"],"publication":["41673033 Chudinov IK, Krinitsina AA, Petukhova DA, Lukina-Gronskaya AV, Korneenko EV, Gremyacheva VD, Kovalenko AV, Fedorov OV, Kozhemyakin GL, Mironov KS, Antipin MI, Butenko IO, Logacheva MD, Speranskaya AS. Proteogenomic investigation of plant constituents in herbal beverages. NPJ Sci Food. 2026 10(1):99 10.1038/s41538-026-00747-1"],"submitter_mail":["ikchudinov@gmail.com"],"submitter_affiliation":["Scientific Research Institute for Systems Biology and Medicine"],"submitter_country":["Russia"],"pubmed_abstract":["Manufacturing adulteration is the major cause of discrepancies between the declared and actual composition of food products. While high-throughput sequencing (HTS) of DNA barcodes is a promising method to identify adulterants, its practical application is hampered by technical challenges. Food pre-processing and differences in GC composition can lead to unequal amplification or complete loss of DNA barcode components. Consequently, HTS results require independent confirmation using an orthogonal method based on very different physical principles than DNA sequencing. To address this, we evaluated the suitability of a multi-omic approach that coupled DNA barcode HTS analysis with proteomic analysis, to enhance the detection of food fraud in herbal beverages. To resolve discrepancies between genomic and proteomic findings, we employed traditional botanical morphology as an arbiter. Among the samples studied, the combined approach revealed two main adulterations of Epilobium with Lythrum - a substitution potentially hazardous to consumers - as well as several minor substitutions, all confirmed by orthogonal methods. Our findings demonstrate that proteomic analysis provides enhanced confidence for verifying the presence or absence of plant components identified by HTS. However, its effective application is guided by prior sequencing to define specific targets for subsequent proteomic verification. This study established that a multimodal analytical approach is not only beneficial, but essential for the reliable and comprehensive characterization of components in complex plant mixtures."],"pubmed_title":["Proteogenomic investigation of plant constituents in herbal beverages."],"pubmed_authors":["Chudinov Ivan K IK, Krinitsina Anastasia A AA, Petukhova Diana A DA, Lukina-Gronskaya Aleksandra V AV, Korneenko Elena V EV, Gremyacheva Veronika D VD, Kovalenko Alexey V AV, Fedorov Oleg V OV, Kozhemyakin Grigory L GL, Mironov Kirill S KS, Antipin Maxim I MI, Butenko Ivan O IO, Logacheva Maria D MD, Speranskaya Anna S AS"],"additional_accession":[]},"is_claimable":false,"name":"Proteogenomic investigation of plant constituents in herbal beverages","description":"Manufacturing adulteration is the major cause of discrepancies between the declared and actual composition of food products. The use of high-throughput sequencing of DNA barcodes is a promising method to identify adulterants, but is not yet widely used in practice. Food pre-processing and differences in GC composition can lead to unequal amplification or complete loss of DNA barcode components, so the results of genomic analysis require an independent confirmation method. Perhaps the most promising way to increase the accuracy of food ingredient identification is to use an orthogonal method based on very different physical principles than DNA sequencing, which involves the analysis of other plant cell components, to verify the results of HTS analysis.  In this work, we decided to evaluate the suitability of a multi-omic approach, including coupled DNA barcode HTS analysis and proteomic analysis, to estimate food fraud in herbal beverages. To resolve disputed discordant results obtained during genomic and proteomic investigation of samples, we used traditional botanical morphology method. Among the samples studied, the combined approach revealed two adulterations of Epilobium with Lythrum, which could be dangerous for the unsuspecting consumer.","dates":{"publication":"2026-03-30","submission":"2025-06-25"},"accession":"PXD065433","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:192875","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:4432","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NEWT:2246","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:333760","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:1226408","NEWT:40479","NEWT:43989","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:4084","NEWT:63577","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8655","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:207559","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:40674","NEWT:1194669","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:214053","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476","NEWT:6669","NEWT:9935","NEWT:89453","NEWT:287889",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