PXD021440-2
PXD021440 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | timsTOF Pro datasets for CCS prediction |
Description | The contribution of peptide amino-acid sequence to collision cross-section values (CCS) has been investigated using a dataset of ~134,000 peptides of four different charge states (1+ to 4+). The migration data collection was acquired using a two-dimensional LC/trapped ion mobility spectrometry/quadrupole/time-of-flight MS analysis of HeLa cell digests created using 7 different proteases and converted to CCS values. Following the previously reported modeling approaches using intrinsic size parameters, we extended this methodology to encode the position of individual residues within a peptide sequence. A generalized prediction model was built by dividing the dataset into 8 groups (four charges for both tryptic/non-tryptic peptides). Position dependent intrinsic size parameters were independently optimized for the eight subsets of peptides, resulting in prediction accuracy of ~0.98 for the entire population of peptides. |
HostingRepository | jPOST |
AnnounceDate | 2021-09-06 |
AnnouncementXML | Submission_2022-09-18_02:46:57.530.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Chih-Hsiang Chang |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide; monohydroxylated tryptophan; deamidated L-asparagine; deamidated L-glutamine; unknown modification; unknown modification; unknown modification |
Instrument | timsTOF Pro |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2020-09-13 05:51:30 | ID requested | |
1 | 2021-09-06 06:12:03 | announced | |
⏵ 2 | 2022-09-18 02:46:58 | announced | 2022-09-18: Updated FTP location. |
Publication List
Chang CH, Yeung D, Spicer V, Ogata K, Krokhin O, Ishihama Y, Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry. J Proteome Res, ():(2021) [pubmed] |
Keyword List
submitter keyword: trapped ion mobility, CCS prediction, SSICalc |
Contact List
Yasushi Ishihama | |
---|---|
lab head | |
Chih-Hsiang Chang | |
contact affiliation | Kumamoto university |
dataset submitter |
Full Dataset Link List
jPOST 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://ftp.jpostdb.org/JPST000959/ |