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pmid:26693171
Delineating the glycoproteome of elongating cotton fiber cells.
Saravanan Kumar · Pankaj Pandey · Krishan Kumar · Vijayalakshmi Rajamani · Kethireddy Venkata Padmalatha · Gurusamy Dhandapani · Mogilicherla Kanakachari · Sadhu Leelavathi · Polumetla Ananda Kumar · Vanga Siva Reddy
Data in brief · 2015 doi:10.1016/j.dib.2015.10.015
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Experiment
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Complete file
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Utilizing species specific protein sequence databases in proteomic approaches often leads to additional information that may not be obtained using cross-species databases. In this context we have reanalyzed our glycoproteome dataset with the Gossypium arboreum, Gossypium raimondii (version 2.0) and Gossypium hirsutum protein databases that has led to the identification of 21 N-linked glycosylation sites and 18 unique glycoproteins that were not reported in our previous study. 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Oxidation (M)", "47"], ["", "Cotton_A_00858_BGI-A2_v1.0", "", "", "", "", ""], ["", "CotAD_24219", "", "", "", "", ""], ["", "Cotton_D_gene_10024539", "", "", "", "", ""], ["8", "Cotton_A_24352_BGI-A2_v1.0", "PREDICTED: PI-PLC X domain-containing protein At5g67130 [Gossypium raimondii]", "2409.0506", "7", "Q.NYFPTNPN(+.98)ETAACAENSAPLVK.M+Deamidated (NQ)", "152"], ["", "CotAD_35067", "", "", "", "", ""], ["", "Gorai.007G214400.1", "", "", "", "", ""], ["9", "Gorai.004G201700.1", "PREDICTED: protein YLS3-like [Gossypium raimondii]", "2572.1033", "10", "S.CYPYLNN(+.98)ATAKPEDDCCNPIR.Q+Deamidated (NQ)", "47"], ["", "Cotton_A_36086_BGI-A2_v1.0", "", "", "", "", ""], ["", "CotAD_48188", "", "", "", "", ""], ["10", "Gorai.007G021100.2", "PREDICTED: lipid transfer-like protein VAS [Gossypium raimondii]", "1560.7793", "12", "F.ASLN(+.98)ISTAQALN(+.98)VTR.E+2 Deamidated (NQ)", "135"], ["", "CotAD_02614", "", "", "", "", ""], ["11", "Gorai.008G216800.1", "PREDICTED: acid beta-fructofuranosidase-like [Gossypium raimondii]", "2176.928", "9", "R.PLN(+.98)TSDGSLETYFCADETR.S+Deamidated (NQ)", "50"], ["", "CotAD_31849", "", "", "", "", ""], ["12", "Cotton_A_11565_BGI-A2_v1.0", "PREDICTED: GDSL esterase/lipase At5g14450-like [Gossypium raimondii]", "1686.8147", "9", "R.RPN(+.98)ETIYEYGISPF.G+Deamidated (NQ)", "103"], ["", "Gorai.001G266600.1", "", "", "", "", ""], ["", "CotAD_07905", "", "", "", "", ""], ["13", "Gorai.006G117500.1", "PREDICTED: protein STRICTOSIDINE SYNTHASE-LIKE 3-like [Gossypium raimondii]", "1061.3817", "3", "K.DFAYTSSN(+.98)R.S+Deamidated (NQ)", "45"], ["", "CotAD_27689", "", "", "", "", ""], ["14", "Cotton_A_36266_BGI-A2_v1.0", "Hydantoin utilization C [Gossypium arboreum] Isoform of S.NO 25", "1622.6905", "3", "K.TTVDGQN(+.98)ISFLEAAR.S+Deamidated (NQ)", "51"], ["", "CotAD_68215", "", "", "", "", ""], ["15", "Gorai.003G061600.1", "PREDICTED: lysM domain receptor-like kinase 3 isoform X1 [Gossypium raimondii]", "1288.691", "1", "K.NYATN(+.98)TTFTVR.S+Deamidated (NQ)", "47"], ["", "CotAD_65258", "", "", "", "", ""], ["", "Cotton_A_27440_BGI-A2_v1.0", "", "", "", "", ""], ["16", "CotAD_16513", "Proline--tRNA ligase [Gossypium arboreum]", "3367.4499", "6", "S.GVN(+.98)YSSSVGMKLSCN(+.98)SSSSSSEAGFSQATSFR.M+Carbamyl (N-term); 2 Deamidated (NQ); Oxidation (M)", "150"], ["", "Cotton_A_23586_BGI-A2_v1.0", "", "", "", "", ""], ["", "Gorai.001G140300.3", "", "", "", "", ""], ["17", "CotAD_72223", "PREDICTED: beta-xylosidase/alpha-L-arabinofuranosidase 2 [Gossypium raimondii]", "1502.7566", "4", "T.AASFN(+.98)TSLYETIGK.V+Deamidated (NQ)", "50"], ["", "Cotton_A_27349_BGI-A2_v1.0", "", "", "", "", ""], ["", "Gorai.005G218000.2", "", "", "", "", ""], [""]], "row_count": 53, "column_count": 7, "numeric_cells": 144, "header_rows": 0, "locator": "section[5]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26693171:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1ddf95bafd9e62e23a5ad16ae0dcb58cbe3732c53de3320d41b1bb87893747af", "bytes": 3289, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#t0010", "version": null, "note": "Additional protein identified in the current study using Gossypium species specific protein sequence databases.", "structure": {"pmcid": "PMC4652025", "section_index": 15, "section_title": "Data analysis using Scaffold and bioinformatic tools", "row_count": 21, "column_count": 7}, "table": {"label": "Table 2", "caption": "Additional protein identified in the current study using Gossypium species specific protein sequence databases.", "rows": [["Sl no.", "Accession no.", "Protein ID – [Source]", "Mole Wt (kDa)", "Observedmass(M+H)+", "Peptides sequenced by MS/MS", "MOWSE score"], [""], ["1", "Gorai.002G207900.1", "Predicted:Separase isoform X1 [Gossypium raimondii] Pepridase_C50", "215.624", "1140.65", "S.ADHLSEDVVR.D", "58"], ["2", "CotAD_40266 Gorai.004G002500.1", "Predicted:cucumisin-like [Gossypium raimondii] Peptidase_S8_3", "144.236", "2049.08", "K.LAGNNTSCPKNSTKMLPR.D+Carbamyl (L), Carbamidomethyl (C), Oxidation (M)", "54"], ["3", "CotAD_03361 Gorai.009G100400.1", "Predicted: heat shock cognate 70 kDa protein 2 like [Gossypium raimondii]", "71.222", "1568.80", "K.QFAAEEISSMVLMK.M+Ammonia-loss (Q)", "45"], ["4", "Cotton_A_01713", "Aldehyde oxidase 4-like protein [Gossypium arboreum]", "145.122", "2283.38", "K.QMTAYGLGLVKCGGTQDLLEK.V+Carbamidomethyl (C)", "57"], ["5", "Cotton_A_01770", "Predicted:Cysteine proteinase inhibitor like [Gosyypium raimondii]", "11.388", "2357.10", "M.ATLGGISQVDGSANSLEIENLAR.F+Acetyl (A)", "62"], ["6", "Cotton_A_01738", "Predicted:Auxin response factor 4-like isoform X1 [Gosyypium raimondii]", "84.086", "1429.76", "P.RASHAEFVIPFR.K", "65"], ["7", "Cotton_A_01780", "Predicted:crt homolog 1 isoform X3 [Gosyypium raimondii] CRT-Chlorouine resistance transporter", "47.582", "1165.45", "P.VGRSEGGDCTK.K+Carbamidomethyl (C)", "58"], ["8", "Cotton_A_01799", "Ribonuclease I [Gossypium arboreum]", "104.392", "1026.56", "V.TGGSGSIYER.F", "63"], ["9", "CotAD_36535 Cotton_A_04276", "Protein disulfide isomerase-like 1-4 [Gossypium arboreum]", "65.760", "1619.74", "Y.FFVDGKHKPYPGAR.N", "59"], ["10", "CotAD_73953", "Predicted:Protein disulfide-isomerase-like [Gossypium raimondii]", "52.851", "1748.81", "I.EDATANDIVGENFDVR.G", "90"], ["11", "CotAD_38843", "PREDICTED: heat shock cognate 70 kDa protein 2-like isoform X1 [Gossypium raimondii]", "70.793", "1740.73", "K.ETAEAYLGSTVKNGVVT.V", "90"], ["12", "CotAD_45862", "Fructokinase [Gossypium hirsutum]", "34.965", "1616.77", "K.QNGVSGDGILFDQGAR.T+Ammonia-loss (Q)", "72"], ["13", "CotAD_44107 Gorai.002G182000.1", "Predicted:nuclear transport factor 2 [Gossypium raimondii]", "13.373", "1705.87", "K.AFVDHYYSTFDANR.A", "42"], ["14", "CotAD_24219 Gorai.013G030200.1", "PREDICTED: probable receptor protein kinase TMK1 [Gossypium raimondii]", "102.438", "1692.79", "R.LNGTIEVIQNMSSLR.E+2 Deamidated (N); Oxidation (M) (Glycopeptide)", "47"], ["15", "CotAD_02614 Gorai.007G021100.2", "PREDICTED: lipid transfer-like protein VAS [Gossypium raimondii]", "15.572", "1560.77", "F.ASLNISTAQALNVTR.E+2 Deamidated (NQ) (Glycopeptide)", "135"], ["16", "CotAD_27689 Gorai.006G117500.1", "PREDICTED: protein STRICTOSIDINE SYNTHASE-LIKE 3-like [Gossypium raimondii]", "43.827", "1061.38", "K.DFAYTSSNR.S+Deamidated (N) (Glycopeptide)", "45"], ["17", "CotAD_68215 Cotton_A_36266", "Hydantoin utilization C [Gossypium arboreum]", "51.739", "1622.69", "K.TTVDGQNISFLEAAR.S+Deamidated (N) (Glycopeptide)", "51"], ["18", "CotAD_65258 Gorai.003G061600.1", "PREDICTED: lysM domain receptor-like kinase 3 isoform X1 [Gossypium raimondii]", "73.564", "1288.69", "K.NYATNTTFTVR.S+Deamidated (N) (Glycopeptide)", "47"], [""]], "row_count": 21, "column_count": 7, "numeric_cells": 103, "header_rows": 0, "locator": "section[15]/table-wrap[1]#t0010"}}], "gaps": ["asset:data:geo:PXD000178 not downloaded", "asset:data:geo:PXD000178 licence not read", "asset:data:geo:PXD002849 not downloaded", "asset:data:geo:PXD002849 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), 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": "R1", "reachable": true, "accessions": ["PXD000178", "PXD002849"], "resolved_accessions": ["PXD000178", "PXD002849"], "statements": ["The data is accessible via this article, via the related research article [1], and at the ProteomeXchange Consortium via the PRIDE partner repository [2] using the dataset identifier PXD000178 and PXD002849. (http://proteomecentral.proteomexchange.org)"], "basis": "The paper names PXD000178, PXD002849 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26693171", "data:geo:PXD000178", "asset:table:pmid:26693171:1", "asset:table:pmid:26693171:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000178"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:06:44Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 16712, "completion_tokens": 1254, "cached_tokens": 512}}, "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:26693171", "type": "paper", "label": "pmid:26693171"}, {"id": "source:pmid:26693171", "type": "manuscript", "label": "PMID 26693171 full text"}, {"id": "data:geo:PXD000178", "type": "dataset", "label": "GEO PXD000178"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26693171", "type": "paper", "label": "pmid:26693171"}, {"id": "source:pmid:26693171", "type": "manuscript", "label": "PMID 26693171 full text"}, {"id": "data:geo:PXD000178", "type": "dataset", "label": "GEO PXD000178"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26693171", "type": "extraction", "used": ["source:pmid:26693171"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000178", "type": "accession_resolution", "used": ["data:geo:PXD000178"], "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:26693171", "parent_hash": "sha256:88c19e842cc075118f27ab4e21d7b325e1488fb77e38e88b7c683aaa3eb893e6", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD000178 licence not read", "asset:data:geo:PXD000178 not downloaded", "asset:data:geo:PXD002849 licence not read", "asset:data:geo:PXD002849 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"]}