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pmid:27408908

Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach.

Roberta Noberini · Giancarlo Pruneri · Saverio Minucci · Tiziana Bonaldi

Data in brief · 2016 doi:10.1016/j.dib.2016.02.028

Paper

complete

Experiment

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Data

partial

Analysis

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Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:27408908
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title
Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach.
doi
10.1016/j.dib.2016.02.028
pmid
27408908
authors array · 4 items
[0]
Roberta Noberini
[1]
Giancarlo Pruneri
[2]
Saverio Minucci
[3]
Tiziana Bonaldi
journal
Data in brief
year
2016
abstract
Aberrant histone post-translational modifications (hPTMs) have been implicated with various pathologies, including cancer, and may represent useful epigenetic biomarkers. The data described here provide a mass spectrometry-based quantitative analysis of hPTMs from formalin-fixed paraffin-embedded (FFPE) tissues, from which histones were extracted through the recently developed PAT-H-MS method. First, we analyzed FFPE samples from mouse spleen and liver or human breast cancer up to six years old, together with their corresponding fresh frozen tissue. We then combined the PAT-H-MS approach with a histone-focused version of the super-SILAC strategy-using a mix of histones from four breast cancer cell lines as a spike-in standard- to accurately quantify hPTMs from breast cancer specimens belonging to different subtypes. The data, which are associated with a recent publication (Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples (Noberini, 2015) [1]), are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002669.
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PT2(is) pNza
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18
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PT2 Pnd (sn)
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G2
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PT1a
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13
[6]
PT2 Pn3a
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G2
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[3]
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[4]
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[5]
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[6]
PT2 Pn1a
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G3
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G3
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60
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PT2 Pn1a
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[3]
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70
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PT2 Pn1a
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10 (TN)
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[3]
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16
[6]
PT1C Pn1mi (sn)
[7]
G2
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30
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PT1C Pn0 (sn)
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G3
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12 (HER)
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85
[6]
ypT3 ypN2a
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46
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PT1C Pn0
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G3
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14 (HER)
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rpT1c rpNx
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G3
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Pt3 (m) Pn0(sn)
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G3
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PT2 (m) Pn1a
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PT2 (m) PN0
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PT1b Pnd(sn)
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iomarkers. The data described here provide a mass spectrometry-based quantitative analysis of hPTMs from fo
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t publication (Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translation
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method. First, we analyzed FFPE samples from mouse spleen and liver or human breast cancer up t
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Complete file
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The data described here provide a mass spectrometry-based quantitative analysis of hPTMs from formalin-fixed paraffin-embedded (FFPE) tissues, from which histones were extracted through the recently developed PAT-H-MS method. First, we analyzed FFPE samples from mouse spleen and liver or human breast cancer up to six years old, together with their corresponding fresh frozen tissue. We then combined the PAT-H-MS approach with a histone-focused version of the super-SILAC strategy-using a mix of histones from four breast cancer cell lines as a spike-in standard- to accurately quantify hPTMs from breast cancer specimens belonging to different subtypes. The data, which are associated with a recent publication (Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples (Noberini, 2015) [1]), are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002669.", "claims": [{"id": "claim-method", "statement": "Acquired RAW data were analyzed by the MaxQuant software v.1.3.0.5 with the Andromeda search engine [4].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27408908", "locator": "sections[14] \"Data analysis\" paragraph 2", "quote": "Acquired RAW data were analyzed by the MaxQuant software v.1.3.0.5 with the Andromeda search engine [4]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw data corresponding to each experiment are reported in Table S1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27408908", "locator": "sections[14] \"Data analysis\" paragraph 2", "quote": "Raw data corresponding to each experiment are reported in Table S1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:27408908"], "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. 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The data described here provide a mass spectrometry-based quantitative analysis of hPTMs from fo", "t publication (Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translation"], "order_basis": "paper_text_order:280", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["method. First, we analyzed FFPE samples from mouse spleen and liver or human breast cancer up t", "s of FFPE and corresponding frozen tissue in mouse spleen or liver, stored for few weeks up to", "design⁎ Histone isolation from fresh-frozen mouse spleen and liver tissues (Fig. 1, Protocol 1", ", Protocol 1) Cells were obtained from fresh mouse spleen and liver as described above and hist"], "order_basis": "paper_text_order:509", "id": "assay:2"}]}