← All .science files
pmid:28540588
Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga Guillardia theta cultured under different light intensities.
Thomas Kieselbach · Otilia Cheregi · Beverley R Green · Christiane Funk
Photosynthesis research · 2018 doi:10.1007/s11120-017-0400-0
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 4 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
[2] object · 6 fields
evidence array · 6 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[3] object · 3 fields
[4] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 5 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 24 items
[0] array · 4 items
[1] array · 15 items
[2] array · 16 items
[3] array · 16 items
[4] array · 16 items
[5] array · 16 items
[6] array · 16 items
[7] array · 16 items
[8] array · 16 items
[9] array · 16 items
[10] array · 16 items
[11] array · 16 items
[12] array · 16 items
[13] array · 16 items
[14] array · 16 items
[15] array · 16 items
[16] array · 16 items
[17] array · 16 items
[18] array · 16 items
[19] array · 16 items
[20] array · 16 items
[21] array · 16 items
[22] array · 16 items
[23] array · 16 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 86 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 7 items
[12] array · 7 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 7 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 7 items
[23] array · 6 items
[24] array · 7 items
[25] array · 6 items
[26] array · 6 items
[27] array · 6 items
[28] array · 6 items
[29] array · 7 items
[30] array · 6 items
[31] array · 6 items
[32] array · 6 items
[33] array · 6 items
[34] array · 7 items
[35] array · 6 items
[36] array · 7 items
[37] array · 7 items
[38] array · 6 items
[39] array · 6 items
[40] array · 6 items
[41] array · 6 items
[42] array · 6 items
[43] array · 6 items
[44] array · 6 items
[45] array · 6 items
[46] array · 6 items
[47] array · 6 items
[48] array · 7 items
[49] array · 6 items
[50] array · 6 items
[51] array · 6 items
[52] array · 7 items
[53] array · 6 items
[54] array · 6 items
[55] array · 6 items
[56] array · 6 items
[57] array · 7 items
[58] array · 6 items
[59] array · 6 items
[60] array · 7 items
[61] array · 6 items
[62] array · 6 items
[63] array · 6 items
[64] array · 6 items
[65] array · 6 items
[66] array · 7 items
[67] array · 6 items
[68] array · 7 items
[69] array · 6 items
[70] array · 6 items
[71] array · 6 items
[72] array · 6 items
[73] array · 7 items
[74] array · 6 items
[75] array · 6 items
[76] array · 6 items
[77] array · 6 items
[78] array · 7 items
[79] array · 6 items
[80] array · 6 items
[81] array · 6 items
[82] array · 7 items
[83] array · 7 items
[84] array · 6 items
[85] array · 7 items
gaps array · 0 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 0 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28540588", "kind": "science-record", "revision": 6, "content_hash": "sha256:2eff992832cdc01814e24b3702fc03d5860fab91576037d07dde271bb6e40843", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga Guillardia theta cultured under different light intensities.", "doi": "10.1007/s11120-017-0400-0", "pmid": "28540588", "authors": ["Thomas Kieselbach", "Otilia Cheregi", "Beverley R Green", "Christiane Funk"], "journal": "Photosynthesis research", "year": 2018, "abstract": "Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active α1β·α2β-tetramer. In all cryptophyte algae investigated so far, the α-subunits have duplicated and diversified into a large gene family. Although there is transcriptional evidence for expression of all these genes, the X-ray structures determined to date suggest that only two of the α-subunit genes might be significantly expressed at the protein level. Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light. The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied. GtcpeA10 seems to be a special member of the α-subunit family, because it consists of two similar N- and C-terminal domains, which likely are the result of a partial tandem gene duplication. The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.", "claims": [{"id": "claim-method", "statement": "In this study, we used a semiquantitative evaluation by peptide counting to test if individual α-subunits are regulated by the different intensities of the white growth light, under which the algae were grown.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28540588", "locator": "sections[14] \"Proteomics analysis\" paragraph 9", "quote": "In this study, we used a semiquantitative evaluation by peptide counting to test if individual α-subunits are regulated by the different intensities of the white growth light, under which the algae were grown."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using semiquantitative peptide counting, the study found that all 20 PE545 α-subunits of Guillardia theta were expressed under white light; their relative abundances did not significantly change across low, standard, and high light, indicating regulation of the antenna pool size rather than individual α-subunits. The proteomics source data were deposited with ProteomeXchange/PRIDE under PXD006301 and 10.6019/PXD006301.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light."}, {"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied."}, {"asset": "source:pmid:28540588", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301."}, {"asset": "source:pmid:28540588", "locator": "sections[9] \"Mass spectrometry analysis and bioinformatics\" paragraph 5", "quote": "A semiquantitative analysis of the relative expression of the α- and β-subunits was performed according to Dowle et al. (2016)."}, {"asset": "source:pmid:28540588", "locator": "sections[14] \"Proteomics analysis\" paragraph 10", "quote": "The result of this evaluation is that the relative ratios of each α- and β-subunit do not change significantly under LL, SL or HL conditions within the limits of the standard deviations of our quantization."}, {"asset": "source:pmid:28540588", "locator": "sections[14] \"Proteomics analysis\" paragraph 10", "quote": "It therefore appears that the PE545 antennas function as a pool that is regulated by light intensity."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using semiquantitative peptide counting, the study found that all 20 PE545 α-subunits of Guillardia theta were expressed under white light; their relative abundances did not significantly change across low, standard, and high light, indicating regulation of the antenna pool size rather than individual α-subunits. The proteomics source data were deposited with ProteomeXchange/PRIDE under PXD006301 and 10.6019/PXD006301.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28540588"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28540588", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s11120-017-0400-0", "sha256": "sha256:ad3d19db104f211533596b9827836bffdf76960b1493b8c784fdf914d0c145bf", "bytes": 53529, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s11120-017-0400-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5784005", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:28540588:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d8e1b5204df94ff834b2ff2b6ed1d8d329ab6d344d87a8e355b3748f95ef648", "bytes": 532, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab1", "version": null, "note": "Photosynthetic parameters of cells grown under different light intensities", "structure": {"pmcid": "PMC5784005", "section_index": 12, "section_title": "Growth and light acclimation of G. theta", "row_count": 5, "column_count": 4}, "table": {"label": "Table 1", "caption": "Photosynthetic parameters of cells grown under different light intensities", "rows": [["", "Low light (LL)", "Standard light (SL)", "High light (HL)"], ["Chl/cell (pg/cell)", "0.776 (±0.016)", "1.300 (±0.07)", "0.441 (±0.007)"], ["Chl a/Chl c", "3.56 (±0.17)", "4.4 (±0.63)", "6.2 (±0.3)"], ["Fv/Fm", "0.77(±0)", "0.77(±0.01)", "0.72 (±0.01)"], ["NPQ", "0.30 (±0.04)", "0.59 (±0.03)", "0.57 (±0.02)"]], "row_count": 5, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28540588:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f304a5e76a49999fe81951505e1d58154544fe45946333479e72fed4b39f30e9", "bytes": 2523, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab2", "version": null, "note": "Phycoerythrins of G. theta expressed under different light growth conditions", "structure": {"pmcid": "PMC5784005", "section_index": 14, "section_title": "Proteomics analysis", "row_count": 24, "column_count": 16}, "table": {"label": "Table 2", "caption": "Phycoerythrins of G. theta expressed under different light growth conditions", "rows": [["Gene model", "Low-light growth conditions", "Standard-light growth conditions", "High-light growth conditions"], ["1", "2", "3", "4", "5", "1", "2", "3", "4", "5", "1", "2", "3", "4", "5"], ["GtcpeA1", "988", "1298", "478", "700", "697", "1421", "667", "730", "1390", "860", "971", "733", "495", "802", "855"], ["GtcpeA2", "102", "130", "106", "47", "42", "204", "181", "68", "280", "276", "", "", "26", "", ""], ["GtcpeA3", "511", "453", "254", "274", "369", "983", "423", "423", "669", "394", "86", "453", "172", "313", "183"], ["GtcpeA4", "208", "256", "83", "67", "116", "387", "226", "172", "205", "89", "", "", "", "", ""], ["GtcpeA5", "138", "223", "169", "138", "184", "466", "223", "297", "378", "285", "", "64", "62", "176", "48"], ["GtcpeA6", "342", "673", "299", "563", "379", "653", "256", "439", "753", "810", "332", "423", "216", "581", "377"], ["GtcpeA8", "158", "270", "136", "18", "200", "327", "262", "239", "368", "365", "", "42", "", "", ""], ["GtcpeA9", "", "909", "", "", "381", "", "", "", "", "", "", "", "", "", ""], ["GtcpeA10", "858", "1037", "384", "537", "539", "1421", "621", "554", "1553", "876", "81", "509", "194", "220", "178"], ["GtcpeA11", "365", "411", "134", "236", "191", "612", "324", "223", "716", "535", "240", "323", "202", "302", "244"], ["GtcpeA12", "576", "825", "325", "500", "301", "613", "298", "425", "728", "426", "133", "412", "237", "560", "583"], ["GtcpeA13", "31", "89", "", "", "25", "172", "102", "93", "92", "93", "", "50", "35", "42", "18"], ["GtcpeA14", "381", "440", "213", "332", "290", "750", "283", "292", "812", "646", "162", "189", "224", "367", "152"], ["GtcpeA15", "355", "477", "205", "333", "281", "484", "210", "332", "581", "441", "231", "194", "130", "278", "318"], ["GtcpeA16", "774", "1679", "810", "700", "1019", "1913", "779", "793", "1461", "996", "1026", "925", "889", "1592", "909"], ["GtcpeA17", "78", "359", "165", "98", "159", "567", "479", "217", "253", "147", "", "", "", "", ""], ["GtcpeA18", "516", "968", "381", "589", "610", "1448", "953", "440", "529", "507", "263", "301", "460", "811", "438"], ["GtcpeA19", "", "975", "269", "", "404", "", "", "370", "1136", "852", "404", "375", "278", "", ""], ["GtcpeA9 or GtcpeA19", "", "", "", "323*", "", "754*", "", "", "", "", "", "", "", "477*", ""], ["GtcpeA20", "543", "1031", "375", "675", "615", "1282", "573", "605", "1514", "900", "638", "447", "405", "558", "608"], ["GtcpeA21", "973", "1241", "469", "681", "677", "1283", "660", "702", "1320", "816", "883", "730", "463", "767", "848"], ["Gt-Beta", "2308", "3619", "2077", "2400", "1500", "2869", "1151", "1437", "4407", "4133", "1443", "1304", "1139", "1768", "1581"]], "row_count": 24, "column_count": 16, "numeric_cells": 305, "header_rows": 2, "locator": "section[14]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:28540588:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d9f8853dfb57f1e9852e97c4fd7b15475a36842553cca1b438f9a05876166079", "bytes": 6278, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab3", "version": null, "note": "Experimentally detected unique peptides of the phycobiliproteins of G. theta", "structure": {"pmcid": "PMC5784005", "section_index": 14, "section_title": "Proteomics analysis", "row_count": 86, "column_count": 7}, "table": {"label": "Table 3", "caption": "Experimentally detected unique peptides of the phycobiliproteins of G. theta", "rows": [["Protein", "Start and end in precursor", "Start and end in predicted mature protein", "Unique tryptic peptide", "Highest peptide score", "Lowest peptide expectation value", "Spectra with expectation values <0.05"], ["Beta", "", "1–7", "MLDAFSR (N-terminus)", "47.64", "1.70E−05", "14"], ["", "", "16–28", "AAYVGGADLQALK", "117.63", "1.70E−12", "90"], ["", "16–29", "AAYVGGADLQALKK", "90.98", "8.10E−10", "147"], ["", "85–91", "DGEIILR", "39.35", "0.00012", "6"], ["", "92–108", "YVSYALLSGDSSVLEDR", "155.02", "3.20E−16", "289"], ["", "115–129", "ETYSSLGVPANSNAR", "120", "1.00E−12", "230"], ["", "130–149", "AVSIMKACAVAFINNTASQR", "145.61", "2.80E−15", "30"], ["", "136–149", "ACAVAFINNTASQR", "155.02", "3.20E−16", "160"], ["", "150–171", "KLSTPQGDCSGLASECASYFDK", "114.82", "3.30E−12", "31"], ["", "151–171", "LSTPQGDCSGLASECASYFDK", "155.02", "3.20E−16", "26"], ["GtcpeA1", "42–51", "9–18", "APVITVFDHR", "73.05", "5.00E−08", "181"], ["GtcpeA2", "59–68", "1–10", "IPLGTQIAGK (N-terminus)", "25.67", "0.0027", "30"], ["75–88", "17–30", "ANFYAPEVTIFDHR", "76.29", "2.40E−08", "6"], ["102–112", "44–54", "TGDQDDEMLVR", "89.35", "1.20E−09", "10"], ["118–127", "60–69", "VFCPEAEAAK", "13.82", "0.041", "1"], ["128–137", "70–79", "VLASTLSVLK", "77.34", "1.80E−08", "39"], ["GtcpeA3", "45–54", "9–19", "APVVTVFDHR", "91.3", "7.40E−10", "35"], ["62–80", "26–44", "NTEYQGLPANSQDDEMLVK", "155.02", "3.20E−16", "90"], ["61–80", "25–44", "RNTEYQGLPANSQDDEMLVK", "18.77", "0.013", "1"], ["86–105", "50–69", "VAINEAAATDLVQQLLGTLK", "120.64", "8.60E−13", "16"], ["86–106", "50–70", "VAINEAAATDLVQQLLGTLKK (C-terminus)", "106.65", "2.20E−11", "13"], ["GtcpeA4", "43–55", "6–18", "SNTAPIVQIFDHR", "92.01", "6.30E−10", "35"], ["84–104", "47–67", "VIPAPEALAASVLQVTVGNLK", "93.35", "4.60E−10", "12"], ["GtcpeA5", "63–74", "6–17", "AIAPVITIFDHR", "112.95", "5.10E−12", "20"], ["88–98", "31–41", "ANTYDDYMLVK", "58.6", "1.40E−06", "16"], ["87–98", "30–41", "KANTYDDYMLVK", "58.06", "1.60E−06", "8"], ["101–124", "44–52", "GEVITVSTSTAASVLAETFGLLDR", "37.6", "0.00017", "1"], ["99–124", "42–67", "VKGEVITVSTSTAASVLAETFGLLDR", "141.73", "6.70E−15", "32"], ["GtcpeA6", "78–89", "9–20", "GFLAPQSYQSYR", "91.23", "7.50E−10", "120"], ["90–106", "21–37", "KGQLLNIAPVIQVHDER", "55.2", "3.00E−06", "16"], ["91–106", "22–37", "GQLLNIAPVIQVHDER", "97.83", "1.60E−10", "16"], ["120–132", "51–63", "VGTEDDAMCVSVK", "132.58", "5.50E−14", "174"], ["135–161", "66–92", "AIPANTNLAASILSDFQIYCQDGSCPK (C-terminus)", "126.81", "2.10E−13", "129"], ["GtcpeA8", "77–90", "25–38", "EYVGPASGDEDDNR", "76.52", "2.20E−08", "6"], ["99–117", "47–65", "ITVSETEAAAALQEFISYR", "154.66", "3.40E−16", "41"], ["GtcpeA9", "98–107", "48–57", "IAVSEGDAAK", "26.6", "0.0022", "3"], ["GtcpeA10", "34–46", "2–14", "AAGYSTASPYSSK (N-terminus)", "28.85", "0.0013", "3"], ["47–64", "15–32", "NSNMGPAFAPVITIFDNR", "155.02", "3.20E−16", "71"], ["79–89", "47–57", "AGDENDEMLVK", "28.24", "0.0015", "10"], ["95–107", "63–75", "IPFPTDDVVNEFR", "145.05", "3.10E−15", "50"], ["95–108", "63–76", "IPFPTDDVVNEFRR", "25.22", "0.003", "7"], ["109–120", "77–88", "ENLAIQGNLDLR", "67.25", "1.90E−07", "18"], ["109–130", "77–98", "ENLAIQGNLDLRAPQITIFDHR", "26.91", "0.002", "3"], ["121–130", "89–98", "APQITIFDHR", "125.77", "2.60E−13", "79"], ["144–154", "112–122", "AGTYDDEMLVK", "32.63", "0.00055", "29"], ["166–179", "134–147", "LAQQVLEQTIGVLK", "84.23", "3.80E−09", "29"], ["166–181", "134–149", "LAQQVLEQTIGVLKAK (C-terminus)", "31.42", "0.00072", "1"], ["GtcpeA11", "59–68", "8–17", "APEITIFDHR", "89.96", "1.00E−09", "61"], ["82–92", "31–41", "AGTSDDEMCVK", "42.6", "5.50E−05", "10"], ["98–107", "47–56", "VEASLTLAEK", "27.29", "0.0019", "25"], ["119–129", "68–78", "GIDGDYTGVVK", "70.2", "9.50E−08", "55"], ["GtcpeA12", "64–79", "8–23", "VQTQSSFGVINDNMGK", "129.58", "1.10E−13", "51"], ["80–91", "24–35", "GAMPVITVFDHR", "67.79", "1.70E−07", "14"], ["105–115", "49–59", "SGDQDDEMCVK", "32.64", "0.00054", "6"], ["120–129", "64–73", "TPYTYPQYTR", "52.09", "6.20E−06", "52"], ["130–145", "74–89", "QATALLNEIIGVTYTK", "155.02", "3.20E−16", "50"], ["GtcpeA13", "79–90", "18–29", "NFAPVITVFDHR", "66.65", "2.20E−07", "11"], ["105–115", "44–54", "SNDENDEMLVK", "18.13", "0.015", "2"], ["141–149", "80–88", "GTFYQYPIR", "64.48", "3.60E−07", "32"], ["GtcpeA14", "67–84", "1–18", "IGEGPSNTFSGQNGIATK (N-terminus)", "131.28", "7.50E−14", "65"], ["85–99", "19–33", "TANGLLGTSIVGVGK", "146.89", "2.00E−15", "46"], ["107–118", "41–52", "NFAPMITIFDAR", "95.41", "2.90E−10", "43"], ["132–142", "66–76", "AGTTDDEMLVK", "28.18", "0.0015", "1"], ["150–160", "84–94", "VPEYQAAAFTR", "73.4", "4.60E−08", "51"], ["161–171", "95–105", "EQLGYTYPTTR", "57.5", "1.80E−06", "55"], ["GtcpeA15", "78–89", "17–28", "NAAPVITIFDHR", "96.09", "2.50E−10", "55"], ["98–114", "37–53", "EYTGAPSNDYNDEMLVK", "155.02", "3.20E−16", "60"], ["GtcpeA16", "66–81", "4–19", "MPADSYTPIITIFDAR", "155.02", "3.20E−16", "96"], ["86–105", "24–43", "GAGEYEGSPAGDNNDEMAVK", "155.81", "2.60E−16", "186"], ["111–122", "49–60", "LEPDTGFAEQIK", "57.2", "1.90E−06", "7"], ["110–122", "48–60", "KLEPDTGFAEQIK", "88.18", "1.50E−09", "31"], ["111–131", "49–69", "LEPDTGFAEQIKAETLGLMSK", "19.97", "0.01", "1"], ["GtcpeA17", "44–55", "8–19", "GVAPIITVFDHR", "44.81", "3.30E−05", "3"], ["60–81", "24–45", "GKADSEYQGALANGPEDEMLVK", "28.48", "0.0014", "3"], ["62–81", "26–45", "ADSEYQGALANGPEDEMLVK", "154.68", "3.40E−16", "31"], ["87–96", "51–60", "VPLSAGFADK", "35.26", "0.0003", "3"], ["97–113", "61–77", "VLQQTLGTFGQAPAGAK", "155.02", "3.20E−16", "21"], ["GtcpeA18", "59–75", "4–20", "TMPADGYAPVITVFDHR", "113.61", "4.40E−12", "81"], ["89–99", "34–44", "SNDMEDGMLVK", "54.99", "3.20E−06", "54"], ["107–126", "52–71", "VTESYAASLLQEQLGYINDK", "153.61", "4.40E−16", "60"], ["107–127", "52–72", "VTESYAASLLQEQLGYINDKA (C-terminus)", "154.66", "3.40E−16", "64"], ["GtcpeA19", "98–107", "48–57", "IAVSEGDAAR", "51.02", "7.90E−06", "15"], ["GtcpeA20", "77–93", "25–41", "EYTGGLSNTQDDQMCVK", "155.02", "3.20E−16", "84"], ["109–120", "57–68", "LLQENLSSMFGK (C-terminus)", "153.03", "5.00E−16", "56"], ["GtcpeA21", "42–51", "9–18", "APVVTIFDHR", "66.35", "2.30E−07", "176"]], "row_count": 86, "column_count": 7, "numeric_cells": 428, "header_rows": 1, "locator": "section[14]/table-wrap[2]#Tab3"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "semiquantitative evaluation by peptide counting", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this study, we used a semiquantitative evaluation by peptide counting to test if individual α-subunits are regulated by the different intensities of the white growth light, under which the algae were grown."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (semiquantitative evaluation by peptide counting), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD006301 and 10.6019/PXD006301"], "resolved_accessions": [], "statements": ["The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301."], "basis": "The paper names PXD006301 and 10.6019/PXD006301, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28540588", "asset:table:pmid:28540588:1", "asset:table:pmid:28540588:2", "asset:table:pmid:28540588:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:20Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 116559, "completion_tokens": 3402, "cached_tokens": 2080}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:28540588", "type": "paper", "label": "pmid:28540588"}, {"id": "source:pmid:28540588", "type": "manuscript", "label": "PMID 28540588 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28540588", "type": "paper", "label": "pmid:28540588"}, {"id": "source:pmid:28540588", "type": "manuscript", "label": "PMID 28540588 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28540588", "type": "extraction", "used": ["source:pmid:28540588"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:28540588", "parent_hash": "sha256:1b38456316953fdbccbc6e73fe1129f2aab8d2389f40649e3c5158bc0d5dedf7", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}