#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** Corinne Spickett

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** Aston University

#  DATA COLLECTION

**What data will you collect or create?**

Liquid chromatography mass spectrometry (LC-MS) data, including fragmentation
(MS/MS) data as raw data in the proprietary vendor format and as derived peak
lists in a standard format.

SDS-PAGE and western blots for protein separation and oxidation as image
files.

Activity assays for purified and oxidant-treated enzymes.

Chemical analytical data.

**How will the data be collected or created?**

LC-MS/MS analyses

SDS-PAGE and western blotting

Spectrophotometric or fluorimetric assays

HPLC assays

Chemical analysis as appropriate to the samples

#  DOCUMENTATION AND METADATA

**What documentation and metadata will accompany the data?**

Sample name and treatment type, basic methodological information as
appropriate for experiments in vitro.

For clinical samples, only the condition, severity and sample handling
information, without any patient or personal information.

For MS data, the metadata will be reported according to the applicable
standards and controlled vocabularies of the established Human Proteome
Organization’s Proteomics Standards Initiative (HUPO PSI).

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

Ethical issues relating to the analysis of clinical samples may arise in the 2
nd  half of the project. It will be handled by anonymising any data from
patient and volunteer samples to ensure that it cannot be linked to
individuals in any way, and will only be made publicly available if this is
approved by the relevant ethical committees. Data that cannot be separated
from personal data or clinical records will not be made publicly available.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

This will be handled by Aston University’s legal team, if applicable.

IPR would be divided between the applicants and researcher, according to
intellectual input. Access to MS data that is to be disseminated via
established online repositories (ProteomeXchange for proteomics data, and
MetaboLights for small molecule data) is to be free to all users, as per the
licensing policy of the European Bioinformatics Institute. See also below.

Green open access route is likely to be used for any publication of the data.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Data that will be deposited in public repositories will be stored and backed
up in these repositories. In addition, and exclusively for data that falls
under ethical or privacy regulations, the data will be stored on local
infrastructure at the site of acquisition.

**How will you manage access and security?**

Data will be on secure Aston University computers and at this stage will only
be accessed by members of staff. After manuscript submission and during peer
review, data that are not subject to ethical or privacy rules will be
privately shared with the journal editor and anonymous peer reviewers through
the established public repositories. After publication of the associated
manuscript, all data in established public repositories will become publicly
available.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?**

Currently, all MS data has intrinsic long-term value, as evidenced by several
published data mining approaches that are based on data mining and/or re-
analysis of public data sets. Moreover, the data sets to be acquired during
this project will be of considerable interest as oxidized biomolecules
(peptides and small molecules) are not yet well represented in these
repositories.

**What is the long-term preservation plan for the dataset?**

The publicly available data will be disseminated through the established
repositories. Copies of the data, as well as data that is subjected to ethical
and privacy regulations, will also be archived locally for at least 7 years.

#  DATA SHARING

**How will you share the data?**

MS data sharing will happen through the established, standard repositories
(ProteomeXchange for proteomics data; MetaboLights for metabolite data) hosted
at the European Bioinformatics Institute (EMBL-EBI). Exceptions apply to data
sets that cannot be made publicly available due to applicable ethical or
privacy regulations.

All data that is deposited in the abovementioned, established repositories
will be publicly accessible without restrictions for re-use as per the
licenses employed by EMBL-EBI for all data in its public repositories.

**Are any restrictions on data sharing required?**

Possibly, if patentable compounds or materials are produced. Note that these
potential restrictions are compatible with the free access to the data
deposited in public repositories because a specific clause in their licenses
states that users of the data should ensure that they do not violate any
patent rights held by the original data submitter.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Prof Andrew R. Pitt

**What resources will you require to deliver your plan?**

Facilities for storage of large data sets at Aston University. Submission
support from the relevant public data repositories. Software to convert the
data into standardized form and to provide the required metadata annotation.
Software to aid the submission of large volumes of data to the repository.

6\. Addendum 2 – Data Management Plan for P2 - UAVR

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** Pedro Domingues

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** Aveiro University

#  DATA COLLECTION

**What data will you collect or create?**

Liquid chromatography mass spectrometry (LC-MS) data, including fragmentation
(MS/MS) data as raw data in the proprietary vendor format and as derived peak
lists in a standard format.

Western blots for protein oxidation as image files.

Thin layer chromatography for lipid oxidation as image files.

Inflammatory panel of samples.

**How will the data be collected or created?**

LC-MS/MS analyses

Western blotting

Spectrophotometric assays

Chemical analysis as appropriate to the samples

#  DOCUMENTATION AND METADATA

**What documentation and metadata will accompany the data?**

Sample name and treatment type, basic methodological information as
appropriate.

For MS data, the metadata will be reported according to the applicable
standards and controlled vocabularies of the established Human Proteome
Organization’s Proteomics Standards Initiative (HUPO PSI) and Lipid Maps.

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

No ethical issues that we are aware of.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

This will be handled by Aveiro University’s legal team, if applicable.

IPR would be divided between the applicants and researcher, according to
intellectual input. Access to MS data that is to be disseminated via
established online repositories (ProteomeXchange for proteomics data, and
MetaboLights for small molecule data) is to be free to all users, as per the
licensing policy of the European Bioinformatics Institute. See also below.

Green open access route is likely to be used for any publication related to
the data.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Data that will be deposited in public repositories will be stored and backed
up in these repositories. In addition, and exclusively for data that falls
under ethical or privacy regulations, the data will be stored on local
infrastructure at the site of acquisition.

**How will you manage access and security?**

Data will be on secure Aveiro University computers and at this stage will only
be accessed by members of staff. After manuscript submission and during peer
review, data that are not subject to ethical or privacy rules will be
privately shared with the journal editor and anonymous peer reviewers through
the established public repositories. After publication of the associated
manuscript, all data in established public repositories will become publicly
available.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?**

Currently, all MS data has intrinsic long-term value, as evidenced by several
published data mining approaches that are based on data mining and/or re-
analysis of public data sets. Moreover, the data sets to be acquired during
this project will be of considerable interest as oxidized biomolecules
(peptides, lipids and small molecules) are not yet well represented in these
repositories.

**What is the long-term preservation plan for the dataset?**

The publicly available data will be disseminated through the established
repositories. Copies of the data, as well as data that is subjected to ethical
and privacy regulations, will also be archived locally for at least 2 years.

#  DATA SHARING

**How will you share the data?**

MS data sharing will happen through the established, standard repositories
(ProteomeXchange for proteomics data; MetaboLights for metabolite data) hosted
at the European Bioinformatics Institute (EMBL-EBI). Exceptions apply to data
sets that cannot be made publicly available due to applicable ethical or
privacy regulations.

All data that is deposited in the abovementioned, established repositories
will be publicly accessible without restrictions for re-use as per the
licenses employed by EMBL-EBI for all data in its public repositories.

**Are any restrictions on data sharing required?**

Possibly, if patentable compounds or materials are produced. Note that these
potential restrictions are compatible with the free access to the data
deposited in public repositories because a specific clause in their licenses
states that users of the data should ensure that they do not violate any
patent rights held by the original data submitter.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Dr Pedro Domingues

**What resources will you require to deliver your plan?**

Facilities for storage of large data sets at Aveiro University. Submission
support from the relevant public data repositories. Software to convert the
data into standardized form and to provide the required metadata annotation.
Software to aid the submission of large volumes of data to the repository.

7\. Addendum 3 – Data Management Plan for P3 - ULEI

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** Maria Fedorova

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** Leipzig University

#  DATA COLLECTION

**What data will you collect or create?**

Liquid chromatography mass spectrometry (LC-MS) data, including fragmentation
(MS/MS) data as raw data in the proprietary vendor format and as derived peak
lists in a standard format.

Western blots for protein oxidation as image files

Microscopy data as image files

Chemical analytical data

**How will the data be collected or created?**

LC-MS/MS analyses

Western blotting

Microscopy imaging

Chemical analysis as appropriate to the samples

#  DOCUMENTATION AND METADATA

**What documentation and metadata will accompany the data?**

Sample name and treatment type, basic methodological information as
appropriate.

For MS data, the metadata will be reported according to the applicable
standards and controlled vocabularies of the established Human Proteome
Organization’s Proteomics Standards Initiative (HUPO PSI).

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

Ethical issues relating to the analysis of clinical samples will be handled by
anonymising any data from patient and volunteer samples to ensure that it
cannot be linked to individuals in any way, and will only be made publicly
available if this is approved by the relevant ethical committees. Data that
cannot be separated from personal data or clinical records will not be made
publicly available.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

This will be handled by Leipzig University’s legal team, if applicable.

IPR would be divided between the applicants and researcher, according to
intellectual input. Access to MS data that is to be disseminated via
established online repositories (ProteomeXchange for proteomics data, and
MetaboLights for small molecule data) is to be free to all users, as per the
licensing policy of the European Bioinformatics Institute. See also below.

Green open access route is likely to be used for any publication of the data.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Data that will be deposited in public repositories will be stored and backed
up in these repositories. In addition, and exclusively for data that falls
under ethical or privacy regulations, the data will be stored on local
infrastructure at the site of acquisition.

**How will you manage access and security?**

Data will be on secure Leipzig University computers and at this stage will
only be accessed by members of staff. After manuscript submission and during
peer review, data that are not subject to ethical or privacy rules will be
privately shared with the journal editor and anonymous peer reviewers through
the established public repositories. After publication of the associated
manuscript, all data in established public repositories will become publicly
available.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?**

Currently, all MS data has intrinsic long-term value, as evidenced by several
published data mining approaches that are based on data mining and/or re-
analysis of public data sets. Moreover, the data sets to be acquired during
this project will be of considerable interest as oxidized biomolecules
(lipids, peptides and small molecules) are not yet well represented in these
repositories.

**What is the long-term preservation plan for the dataset?**

The publicly available data will be disseminated through the established
repositories. Copies of the data, as well as data that is subjected to ethical
and privacy regulations, will also be archived locally for at least 10 years.

#  DATA SHARING

**How will you share the data?**

MS data sharing will happen through the established, standard repositories
(ProteomeXchange for proteomics data; MetaboLights for metabolite data) hosted
at the European Bioinformatics Institute (EMBL-EBI). Exceptions apply to data
sets that cannot be made publicly available due to applicable ethical or
privacy regulations.

All data that is deposited in the abovementioned, established repositories
will be publicly accessible without restrictions for re-use as per the
licenses employed by EMBL-EBI for all data in its public repositories.

**Are any restrictions on data sharing required?**

Possibly, if patentable compounds or materials are produced. Note that these
potential restrictions are compatible with the free access to the data
deposited in public repositories because a specific clause in their licenses
states that users of the data should ensure that they do not violate any
patent rights held by the original data submitter.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Dr Maria Fedorova

**What resources will you require to deliver your plan?**

Facilities for storage of large data sets at Leipzig University. Submission
support from the relevant public data repositories. Software to convert the
data into standardized form and to provide the required metadata annotation.
Software to aid the submission of large volumes of data to the repository.

8\. Addendum 4 – Data Management Plan for P4 - UMIL

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** Giancarlo Aldini

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** University of Milan

#  DATA COLLECTION

**What data will you collect or create?**

LC-ESI-MS raw data generated by Thermo instruments.

Gel electrophoresis images acquired by using Molecular Image Versa Doc Biorad

Data analyses generated by using GraphPad software and Proteome discoverer

**How will the data be collected or created?**

Data will be created and collected automatically by LC-ESI-MS instruments

Data will be created by analysing raw data using data analysis software

#  DOCUMENTATION AND METADATA

All the activities and procedures will be recorded in a bound notebook which
will be signed daily by the scientist and lab manager. Raw data and analysed
data will be classified according to the day and time of data generation,
sample name and treatment type, basic methodological information as
appropriate.

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

No ethical issues that we are aware of.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

This will be handled by the University of Milan’s legal team, if applicable.

IPR would be divided between the applicants and researcher, according to
intellectual input.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Public data will be uploaded stored and backed up in repositories according to
their rules. Data that will not be made publicly available will be stored on
local infrastructure of the University of Milan and suitably backed-up. Data
will also be stored for all the duration of MASSTRPLAN on the QNAP systems
available in the data room located in the lab managed by Giancarlo Aldini.

**How will you manage access and security?**

Data will be on secure on the University of Milan computers and storage
systems. Dedicated QNAP backup systems which are password protected and
encrypted will also be used. Each member of the staff will have the access to
the data through an encrypted password. Access will be recorded in a log file
and backup will be performed every day.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?** All the generated raw data and analysed data will be long-term
stored in the University of Milan storage system.

**What is the long-term preservation plan for the dataset?**

The publicly available data will be disseminated through the established
repositories. Copies of the data, as well as data that is subjected to ethical
and privacy regulations, will also be archived locally for at least 5 years.

#  DATA SHARING

**How will you share the data?**

MS data sharing will happen through the established, standard repositories
(ProteomeXchange for proteomics data; MetaboLights for metabolite data) hosted
at the European Bioinformatics Institute (EMBL-EBI). Exceptions apply to data
sets that cannot be made publicly available due to applicable ethical or
privacy regulations. Data generated in the lab managed by Giancarlo Aldini
that will not be made publicly available will be shared among the other
MASSTRPLAN members through a Synology cubestation system.

**Are any restrictions on data sharing required?**

Possibly, if patentable compounds or materials are produced.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Dr. Giancarlo Aldini

**What resources will you require to deliver your plan?**

Data Facilities for storage of large data sets at University of Milan (Big
Data facility). QNAP systems for 8 terabyte and backup system are already
available in the data centre of the research lab managed by Giancarlo Aldini.

9\. Addendum 5 – Data Management Plan for P6 - CSIC

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** Dolores Pérez-Sala

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** Consejo Superior de Investigaciones Científicas

#  DATA COLLECTION

**What data will you collect or create?**

We will collect data in the form of text files (.dat or .txt) or excel
spreadsheets generated by fluorescence and absorbance plate readers,
spectrofluorometers, analytical ultracentrifuges, scattering and other
specialized instruments. We will also collect .jpg and .tif images generated
by fluorescence and electron microscopes and by scan of SDS-PAGE gels. We will
create, as well, text files (.dat or .txt) or excel spreadsheets corresponding
to modelling of the raw data acquired by using specific software for analysis.
We will also generate data from proteomic analysis in the form of datasheets
of peaks from MALDI-TOF MS and MS-MS.

**How will the data be collected or created?**

Directly by the instruments and by the software used for data fitting or
simulation. Western blotting followed by scan of blots. Fluorescence
microscopy-generated tiff or videos.

#  DOCUMENTATION AND METADATA

Images from fluorescence microscopy and from proteomic analysis will be
identified by date of acquisition, user name and a code related to sample
identity. Likewise, data files for biophysical and biochemical experiments
will be identified by date, user and sample identity codes.

#  ETHICS AND LEGAL COMPLIANCE

Ethical issues could arise from the use of primary cells derived from patients
suffering from genetic diseases obtained from the Coriell Institute for
Biomedical Research (NIH, USA). These cells will be used according to the
conditions established by the Coriell Repository. This Institution already
takes care of anonymization. Therefore, no data from donors are associated to
the use of these cells. Any potential human samples will be obtained from
Official Biobanks and will be used according to their regulations and
subjected to approval by their committees and that of CSIC for Bioethical and
Biosafety issues.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

All data generated at CSIC and/or by CSIC researchers belong to the
Institution (copyright holder). Subjects on IPR are dealt by the CSIC Office
of Transfer of Technology. Therefore, in principle, all data generated are
considered confidential. We foresee sharing with other ITN teams specific sets
of data obtained during secondments and those directly related to
collaborative publications. Data will not be available in principle to the
general audience before publication, which we will try to do in Open Access
form.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Data will be stored in computer and external hard drives. Upon publication,
accepted manuscripts are posted by the Digital CSIC Repository.

**How will you manage access and security?**

Access to computers will be generally by password. External hard drives will
be safely kept in the lab. All drives are equipped with software for password
protection of their contents.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?** Image and other experimental data may be subject to re-analysis
in the mid-long term to assess parameters different from those originally
analysed. Data on proteomic analysis may prove valuable in broader contexts or
meta-analysis. Therefore, the metadata for MS data will be reported according
to the applicable standards and controlled vocabularies of the established
Human Proteome Organization’s Proteomics Standards Initiative (HUPO PSI).

**What is the long-term preservation plan for the dataset?**

The minimal storage time for data obtained at CSIC is 5 years. During that
time, laboratory notebooks and hard drives with security copies of data will
be kept at CIB-CSIC.

#  DATA SHARING

**How will you share the data?**

Among teams, data will be shared under a confidentiality basis. Data will be
available to the public upon publication. MS data from proteomic
identifications will be shared through the established, standard repositories
(ProteomeXchange for proteomics data) hosted at the European Bioinformatics
Institute (EMBL-EBI). For other data, and when applicable, we will follow the
recommendations of the journals regarding the presentation of raw data or of
deposit in public repositories

(http://www.nature.com/sdata/data-policies/repositories). For instance, image
data may be shared through Figshare (https://figshare.com/). For some
journals, deposit is made at the time of submission and data are made public
upon manuscript acceptance. In addition, all published works will be available
in accepted author version at the open access repository of our Institution
Digital CSIC (https:// **digital** . **csic** .es/). This is mandatory for our
Institution. Non-published data will remain confidential.

**Are any restrictions on data sharing required?**

Yes, results or materials can be transferred on a royalty-free basis only for
research purposes, on a confidential basis and upon signing of an MTA with
CSIC. Results or materials will not be used for commercial purposes, they will
be subject to confidentiality and their use will require the signature of an
MTA with CSIC.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Dr. Dolores Pérez-Sala

**What resources will you require to deliver your plan?**

Facilities for temporary storage of image data are available at CIB-CSIC. We
will increase our storage capacity through the acquisition of external hard-
drives and computers protected by passwords.

10\. Addendum 6 – Data Management Plan for P7 - CCM

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** Cristina Banfi

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** Centro Cardiologico Monzino

#  DATA COLLECTION

**What data will you collect or create?**

Clinical data of patients recruited at Centro Cardiologico Monzino.
Specifically, data are related to full clinical assessment, including
pulmonary function and lung diffusion for carbon monoxide (DLco), maximal
cardiopulmonary exercise test and measurements of circulating proteins,
including immature and mature forms of SP-B. Liquid chromatography mass
spectrometry (LC-MS) data, including fragmentation (MS/MS) data as raw data in
the proprietary vendor format and as derived peak lists in a standard format.

**How will the data be collected or created?**

All clinical data will be treated in confidence. Any information relates to
subject recruited in the study will be acquired and used solely for the
purposes described in the disclosure and in a manner consistent with current
legislation on protection of personal data (Legislative Decree 196/03). By
signing the informed consent form, the subject gives permission to have direct
access to his medical records. The doctor who follows the study will identify
the subjects with a code: the data collected during the study, with the
exception of the name will be recorded, processed and stored together with
this code, the date of birth, sex, weight and height. Only the doctor and
authorized entities may link this code to the name. Surname(s), first name(s)
and date of birth of the patient will be present only in the source document
(medical records). Any information or biological material will be identified
by a unique code that will allow to associate clinical data with laboratory
results but, in any case, with the patient's identity

Other data will be collected by LC-MS/MS analyses and biochemical assays on
clinical samples.

#  DOCUMENTATION AND METADATA

**What documentation and metadata will accompany the data?**

Sample name and treatment type, basic methodological information as
appropriate.

For MS data, the metadata will be reported according to the applicable
standards and controlled vocabularies of the established Human Proteome
Organization’s Proteomics Standards Initiative (HUPO PSI).

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

The Study will be conducted in full respect for human dignity and fundamental
human rights as dictated by the "Helsinki Treaty", as amended, by the
standards of "Good Clinical Practice" (GCP) issued by the European Community
and in accordance with all laws and local rules regarding the clinical trials

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

This will be handled by CCM’s legal team, if applicable.

IPR would be divided between the applicants and researcher, according to
intellectual input. Access to MS data that is to be disseminated via
established online repositories (ProteomeXchange for proteomics data, and
MetaboLights for small molecule data) is to be free to all users, as per the
licensing policy of the European Bioinformatics Institute.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Sensitive data, managed on computer, will be treated accordingly to
legislation and then the personal data will be separated from those that
determine a patient's medical condition. The original data will be kept for
seven years by the investigators. The reference that links clinical data to a
patient will be kept in a Microsoft Excel file, protected by passwords, on the
personal computer of the doctor responsible of the project. The patient
demographics are not of interest for the trial in question.

LC-MS/MS data will be deposited in public repositories and will be stored and
backed up in these repositories.

**How will you manage access and security?**

Data will be on secure Centro Cardiologico Monzino computers and at this stage
will only be accessed by members of staff with personal account protected by
password. After manuscript submission and during peer review, data that are
not subject to ethical or privacy rules will be privately shared with the
journal editor and anonymous peer reviewers through the established public
repositories. After publication of the associated manuscript, all data in
established public repositories will become publicly available.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?**

Currently, all MS data has intrinsic long-term value, as evidenced by several
published data mining approaches that are based on data mining and/or re-
analysis of public data sets. Moreover, the data sets to be acquired during
this project will be of considerable interest as oxidized biomolecules
(peptides and small molecules) are not yet well represented in these
repositories. In addition, clinical data, in anonymous form, will be shared in
order to correlate oxidised biomolecule levels with clinical parameters.

**What is the long-term preservation plan for the dataset?**

The publicly available data will be disseminated through the established
repositories. Copies of the data, as well as data that are subjected to
ethical and privacy regulations, will also be archived locally for at least 7
years.

#  DATA SHARING

**How will you share the data?**

The data, processed using electronic tools will be disclosed only in strictly
anonymous form, such as through scientific papers, statistics and scientific
conferences.

MS data sharing will happen through the established, standard repositories
(ProteomeXchange for proteomics data; MetaboLights for metabolite data) hosted
at the European Bioinformatics Institute (EMBL-EBI). Exceptions apply to data
sets that cannot be made publicly available due to applicable ethical or
privacy regulations.

All data that is deposited in the abovementioned, established repositories
will be publicly accessible without restrictions for re-use as per the
licenses employed by EMBL-EBI for all data in its public repositories.

**Are any restrictions on data sharing required?**

Possibly, if patentable compounds or materials are produced. Note that these
potential restrictions are compatible with the free access to the data
deposited in public repositories because a specific clause in their licenses
states that users of the data should ensure that they do not violate any
patent rights held by the original data submitter. Data that falls under
ethical or privacy regulations will be shared only in anonymous form.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

For the clinical data Prof Piergiuseppe Agostoni, director of the Heart
Failure Unit, and Dr Cristina Banfi will be responsible for scientific data.

**What resources will you require to deliver your plan?**

Facilities for storage of large data sets at CCM. Submission support from the
relevant public data repositories. Software to convert the data into
standardized form and to provide the required metadata annotation. Software to
aid the submission of large volumes of data to the repository.

11\. Addendum 7 Data Management Plan for P8 - CHUC

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** Artur Paiva

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** Centro Hospitalar e Universitário de Coimbra

#  DATA COLLECTION

**What data will you collect or create?**

Flow cytometry data in the format provided by FACSDiva software (Becton
Dickinson Biosciences). Gene expression data in the format provided by
LightCycler software (Roche Diagnostics).

**How will the data be collected or created?**

Flow cytometry.

Real time polymerase chain reaction.

#  DOCUMENTATION AND METADATA

Sample name, patient diagnosis, cell stimulation conditions, and basic
methodological information as appropriate.

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

To comply with legal and ethics requirements, no patient data will be shared
or any data that can be linked to patients or their personal and medical
history. However, analytical data that has been anonymised and cannot be
linked to individual patients will be shared.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

This will be handled by Centro Hospitalar e Universitário de Coimbra’s legal
team, if applicable.

IPR would be divided between the applicants and researchers, according to
intellectual input. Green open access route is likely to be used for any
publication of the data.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

The data will be stored on local infrastructure at the site of acquisition.

**How will you manage access and security?**

Data will be on secure Centro Hospitalar e Universitário de Coimbra computers
and at this stage will only be accessed by members of staff. After manuscript
submission and during peer review, data that are not subject to ethical or
privacy rules will be privately shared with the journal editor and anonymous
peer reviewers through the established public repositories. After publication
of the associated manuscript, all data in established public repositories will
become publicly available.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?** All data is considered worthy of archiving.

**What is the long-term preservation plan for the dataset?**

Copies of the data, as well as data that is subjected to ethical and privacy
regulations, will be archived locally for at least 5 years.

#  DATA SHARING

**How will you share the data?**

Relevant data will be shared among the MASSTRPLAN beneficiaries.

Publication related flow cytometry and RT-PCR data sharing will happen through
public repositories. Exceptions apply to data sets that cannot be made
publicly available due to applicable ethical or privacy regulations.

**Are any restrictions on data sharing required?**

Possibly, if patentable compounds or materials are produced. Note that these
potential restrictions are compatible with the free access to the data
deposited in public repositories because a specific clause in their licenses
states that users of the data should ensure that they do not violate any
patent rights held by the original data submitter.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Dr. Artur Paiva

**What resources will you require to deliver your plan?**

Facilities for data storage at Centro Hospitalar e Universitário de Coimbra

12\. Addendum 8 Data Management Plan for P9 - MOL

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** John Wilkins

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** Mologic Ltd, Bedford, UK

#  DATA COLLECTION

**What data will you collect or create?**

Laboratory research notes on the development of antibodies, synthetic peptides
and immunochromatographic assays and formats.

Comparative ELISA or Lateral Flow (LF) assay data, obtained using
spectrophotometers or lab readers, with commercial or in-house assays.

Experimental data, such as HPLC and mass spectrometric (MS) data, as raw data
files in proprietary instrument manufacturer format, or as summary
spreadsheets.

**How will the data be collected or created?**

Significant data will be summarised and presented in Mologic research reports
and MASSTRPLAN documents.

MS files are archived and kept at Mologic for 5 years.

#  DOCUMENTATION AND METADATA

**What documentation and metadata will accompany the data?**

Sample name and treatment type, plus basic methodological information, as
appropriate. For MS data, the metadata will be reported according to the
applicable standards and controlled vocabularies of the established Human
Proteome Organization’s Proteomics Standards Initiative (HUPO PSI).

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

Human clinical samples may be required for method development and validation
of commercial assays, e.g. using urines or blood samples from healthy local
volunteers, and from patients of known disease/health status. Mologic adheres
to ethical procedures (informed consent, patient anonymity etc.), and is in
the process of applying for an HTA licence (UK Human Tissue Authority) to
allow local sample storage.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

Mologic will identify any IP opportunities that arise during the research
conducted at the Mologic premises. IP rights will be allocated equitably
between consortium members according to intellectual input.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Mologic will ensure that laboratory data and reports are archived locally and
held for a minimum of 5 years.

**How will you manage access and security?**

Data will be held on the secure Mologic computer system, and will only be
accessed by authorised members of staff.

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?**

After any IP opportunities have been evaluated and protected, significant MS
data (i.e. of scientific interest or novelty) will be summarised and presented
in MASSTRPLAN documents and in scientific publications. These published data
will be made publicly available.

**What is the long-term preservation plan for the dataset?**

The data generated at Mologic will be archived locally for at least 5 years.

#  DATA SHARING

**How will you share the data?**

Mologic MS data will be shared with consortium members. Data related to
Mologic’s proprietary method development will be kept private, until IP
opportunities have been explored.

**Are any restrictions on data sharing required?**

Data related to Mologic’s proprietary method development will be kept private,
until IP opportunities have been explored and resolved.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Dr John Wilkins

**What resources will you require to deliver your plan?**

No additional resources will be required, as Mologic already has computer data
and laboratory notebook archive systems.

13\. Addendum 9 Data Management Plan for P10 - THERMO

#  ADMIN DETAILS

**Project Name** : MASS spectrometry TRaining in Protein Lipoxidation ANalysis
for Inflammation

**Principal Investigator / Researcher:** (Dr Ken Cook)

**Funder:** European Commission’s REA with the H2020 MSCA

**Institution:** (Thermofisher Scientific)

#  DATA COLLECTION

**What data will you collect or create?**

Chromatography data and Mass Spectrometry data from various protein and lipid
samples

**How will the data be collected or created?**

Data will be in Chromeleon files and Excalibur file format. There will be
presentation material in powerpoint and publications in word / PDF

#  DOCUMENTATION AND METADATA

Data will be collected and stored via the instrument data collection software.
This will include instrument settings, run time and date, sample information
and injection amounts. The collected data from the instrument will include raw
data from all detection systems and the final report.

#  ETHICS AND LEGAL COMPLIANCE

**How will you manage any ethical issues?**

We will not be collecting data from patients or any other source involving
ethical issues unless in collaboration with another institute, in which case
applicable regulations of the partner site will be followed.

**How will you manage copyright and Intellectual Property Rights (IPR)
issues?**

We do not anticipate any IPR issues. We would hope to publish findings from
the project.

#  STORAGE AND BACKUP

**How will the data be stored and backed up during the research?**

Data will be stored on local computers and backed up on the Thermofisher
network.

**How will you manage access and security?**

Thermofisher have their own secure network protocols. Data access to useful
data will be shared through the consortium. Publishable data will be made
publicly available via established repositories (ProteomeXchange and
MetaboLights).

#  SELECTION AND PRESERVATION

**Which data are of long-term value and should be retained, shared, and/or
preserved?**

Any publishable results or presentation worthy material will be shared and
preserved. We will also retain material which led to such discoveries.

**What is the long-term preservation plan for the dataset?**

Data will be shared with the consortium and data will also be stored on the
local computer and the Thermofisher network. Publishable data will be stored
and made publically available via established repositories in the field
(ProteomeXchange and MetaboLights), in addition to long term storage with the
consortium.

#  DATA SHARING

**How will you share the data?**

Data will be made available to the consortium and a shared facility can be
used for consortium members who request it. Any data published will then be
publically available.

**Are any restrictions on data sharing required?**

Only on data that may be used in an upcoming publication until it is
submitted, when free access will be available. Such data may also be shared
early with consortium members if useful and needed.

#  RESPONSIBILITIES AND RESOURCES

**Who will be responsible for data management?**

Dr Ken Cook, Dr Madalina Oppermann and the appointed Student

**What resources will you require to deliver your plan?** None other than
those already available.