A searchable and exportable tab-separated table of the following metadata is now available.
| metadata | definition/examples | source |
|---|---|---|
| Project title | Name of the project | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Project description | Overall description of the project | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Contact information | person(s) responsible for contact including their affiliation | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1”, MIAPE (Taylor et al. (2007)) |
| Sample species | Species of the sample | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| PX_ID | Unique dataset identifier | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Instrument | Mass spectrometer & manufacturer | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Modifications | What post-translational modifications were done if applicable | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| File type | Type of file uploaded (e.g. RAW, SEARCH, RESULT, etc.) | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Ion source | ESI, MALDI or other ionisation source including relevant parameters | MIAPE (Taylor et al. (2007)) |
| DOI | ID number of the publication associated with the dataset | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Post source component | Analyzer & activation/dissociation type | MIAPE (Taylor et al. (2007)) |
| Comments/questions: |
|---|
| metadata | definition/examples | source |
|---|---|---|
| Sample processing protocol | short description of sample preparation including extraction, separation, enrichment, clean-up, digestion and mass spectrometry protocols | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1”, MIAPE (Taylor et al. (2007)) |
| Data processing protocol | short description of bioinformatics pipeline, software tools including versions, main search parameters and quantitative analysis | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1”, Adapted from MIAPE (Taylor et al. (2007)) |
| Growth protocol | description of the growth protocol or organism preparation | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Treatment protocol | description of the treatments applied to the organism prior to sample acquisition | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Extraction protocol | description of the extraction of proteins from the treated sample(s) | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Separation protocol | description of the separation of proteins and/or peptides | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Digestion protocol | description of the digestion of the proteins into peptides | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Acquisition protocol | description of the acquisition of mass spectra from the peptide sample | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Protocol parameters | list of parameter names | “Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1” |
| Comments/questions: |
|---|
| 🔹 Discussion question: one or two fields for protocols or more? -SS 02May2022 |
We also highly encourage the readers of this GitHub to look for examples of submitted proteomic samples and analyses in “PRIDE: PRoteomics IDEntifications Database”, “PeptideAtlas”, “MassIVE: Mass Spectrometry Interactive Virtual Environment”, “iProX: Integrated Proteome Resources” and read the publication and view the corresponding repository of jPOSTrepo: an international standard data repository for proteomes (Okuda et al. (2017)).
“Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1.” https://www.proteomexchange.org/docs/guidelines_px.pdf.
“iProX: Integrated Proteome Resources.” https://www.iprox.cn/page/helpEn.html#pag5.
“MassIVE: Mass Spectrometry Interactive Virtual Environment.” https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp.
Okuda, Shujiro, Yu Watanabe, Yuki Moriya, Shin Kawano, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, et al. 2017. “jPOSTrepo: An International Standard Data Repository for Proteomes.” Nucleic Acids Research 45 (D1): D1107–11. https://doi.org/10.1093/nar/gkw1080.
“PeptideAtlas.” https://peptideatlas.org/.
“PRIDE: PRoteomics IDEntifications Database.” https://www.ebi.ac.uk/pride/markdownpage/submitdatapage#submit_dataset.
Taylor, Chris, Norman Paton, Kathryn Lilley, Pierre-Alain Binz, Randall K Julian, Andrew R Jones, Weimin Zhu, Rolf Apweiler, Ruedi Aebersold, and Eric W Deutsch. 2007. “The Minimum Information about a Proteomics Experiment (MIAPE).” Nature Biotechnology 25 (8): 887–93. https://doi.org/10.1038/nbt1329.