PXD056868
PXD056868 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Database Search Strategy affects Protein-Identification Outputs and Statistical Comparisons in Comparative Proteomics Experiments |
| Description | Comparative proteomics experiments reveal biomarkers by using statistical tests to determine proteins expressed with higher abundance in one sample versus another. However, comparative experiments can be complicated by variability from all aspects of proteomics workflows. To account for variability, software for database searching contains retention-time alignment and imputation algorithms to correct for retention-time shifts and assign abundances to missing proteins. While these algorithms improve quantification and reduce processing time, we hypothesize that they alter statistical comparisons between samples when samples are searched together. Herein, we search different cleanup methods or single proteins separately versus together in Progenesis Qi for proteomics database searching software. Our results show that searching samples together increases the number of identifications by each sample, enhances protein similarity between samples, and leads to false transfers. Further, we demonstrate that searching samples together affects protein abundance, differentially expressed proteins, and confidence scores due to retention-time alignment and imputation algorithms. Ultimately, we highlight that careful consideration of the search design is necessary to determine biomarkers in comparative proteomics experiments. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-05-01 |
| AnnouncementXML | Submission_2025-05-01_16:20:37.094.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Jessica Conforti |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Chicken Egg White; scientific name: Equine Heart; scientific name: Equine Skeletal Muscle; scientific name: Bovine Blood; scientific name: bovine erythrocytes; |
| ModificationList | L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine |
| Instrument | nanoACQUITY UPLC; Synapt G2-S HDMS |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-10-16 11:36:01 | ID requested | |
| ⏵ 1 | 2025-05-01 16:20:37 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Database Searching, Imputation, Missing Proteins, Proteomics, Retention-time Alignment, Stochasticity, DatasetType:Proteomics |
Contact List
| Elyssia Gallagher | |
|---|---|
| contact affiliation | Baylor University |
| contact email | elyssia_gallagher@baylor.edu |
| lab head | |
| Jessica Conforti | |
| contact affiliation | Baylor University |
| contact email | jess_conforti1@baylor.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v08/MSV000096112/ |
to receive all new ProteomeXchange dataset release announcements!
