PXD005573 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results |
Description | Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we identified and quantified 6,383 proteins in human cell lines using 2-or-more peptides/protein and over 7,100 proteins when including the 717 proteins that were identified on the basis of a single peptide sequence. 7,739 proteins were identified in mouse tissues using 2-or-more peptides/protein and 8,121 when including the 382 proteins that were identified on the basis of a single peptide sequence. Missing values for proteins were within 0.3 to 2.1% and median coefficients of variation of 4.7 to 6.2% among technical triplicates. In very complex mixtures, we could quantify 10,780 proteins and 12,192 proteins when including the 1,412 proteins that were identified on the basis of a single peptide sequence. Using this optimized DIA, we investigated large-protein networks before and after the critical period for whisker experience-induced synaptic strength in the murine somatosensory cortex 1 barrel field. This work shows that parallel mass spectrometry enables proteome profiling for discovery with high coverage, reproducibility, precision and scalability. |
HostingRepository | PRIDE |
AnnounceDate | 2017-11-06 |
AnnouncementXML | Submission_2017-11-06_05:24:09.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Roland Bruderer |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue; acetylated residue; deamidated residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2016-12-15 06:37:06 | ID requested | |
1 | 2017-04-24 04:56:01 | announced | |
2 | 2017-10-27 00:14:10 | announced | Updated project metadata. |
3 | 2017-11-01 08:51:38 | announced | Updated publication reference for PubMed record(s): 29070702. |
⏵ 4 | 2017-11-06 05:24:10 | announced | Updated project metadata. |
Publication List
Bruderer R, Bernhardt OM, Gandhi T, Xuan Y, Sondermann J, Schmidt M, Gomez-Varela D, Reiter L, Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results. Mol Cell Proteomics, 16(12):2296-2309(2017) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: human DIA proteomics |
Contact List
Lukas Reiter |
contact affiliation | Biognosys AG |
contact email | lukas.reiter@biognosys.com |
lab head | |
Roland Bruderer |
contact affiliation | Biognosys AG |
contact email | roland.bruderer@biognosys.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD005573
- Label: PRIDE project
- Name: Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results