PXD021440

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]

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

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/

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/