PXD012924

PXD012924 is an original dataset announced via ProteomeXchange.

Title	Accurate quantitative proteomic analyses using metabolic labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS)
Description	Stable isotope labeling by amino acids in cell culture (SILAC) is routinely used to profile changes in protein and peptide abundance across different experimental paradigms. As with other quantitative proteomic approaches, the detection of peptide isotopomers can be limited by the presence of interference ions that ultimately affect the quality of quantitative measurements. Here, we evaluate high field asymmetric waveform ion mobility spectrometry (FAIMS) to improve the accuracy and dynamic range of quantitative proteomic analyses using SILAC. We compared quantitative measurements for tryptic digests of isotopically labeled protein extracts mixed in different ratios using LC-MS/MS with and without FAIMS. To further reduce sample complexity, we also examined the improvement in quantitative measurements when combining strong cation exchange (SCX) fractionation prior to LC-MS/MS analyses. Using the same amount of sample consumed, analyses performed using FAIMS provided more than 30% and 200% increase in the number of quantifiable peptides compared LC-MS/MS performed with and without SCX fractionation, respectively. Furthermore, FAIMS reduced the occurrence of interfering isobaric ions and improved the accuracy of quantitative measurements. We leveraged the application of FAIMS in phosphoproteomic analyses to profile dynamic changes in protein phosphorylation in HEK293 cells subjected to heat shock for periods up to 20 min. In addition to the enhanced phosphoproteomic coverage, FAIMS also provided the ability to separate phosphopeptide isomers that often co-elute and can be misassigned in conventional LC-MS/MS experiments.
HostingRepository	PRIDE
AnnounceDate	2019-05-28
AnnouncementXML	Submission_2019-05-28_07:36:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Francis McManus
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-01 02:11:23	ID requested
⏵ 1	2019-05-28 07:36:21	announced

Pfammatter S, Bonneil E, McManus FP, Thibault P, Accurate Quantitative Proteomic Analyses Using Metabolic Labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS). J Proteome Res, 18(5):2129-2138(2019) [pubmed]

curator keyword: Technical

submitter keyword: high field asymmetric waveform ion mobility spectrometry (FAIMS), Stable Isotope Labeling by Amino acids in Culture (SILAC), quantitative proteomics, phosphorylation

Pierre Thibault
contact affiliation	Institute for Research in Immunology and Cancer,Department of Chemistry, Université de Montréal, P.O. Box 6128, Station. Centre-ville, Montréal, Québec, Canada H3C 3J7
contact email	pierre.thibault@umontreal.ca
lab head
Francis McManus
contact affiliation	University of Montreal
contact email	francispmcmanus@gmail.com
dataset submitter

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.pride.ebi.ac.uk/pride/data/archive/2019/05/PXD012924

PRIDE project URI

• PRIDE
  1. PXD012924
     1. Label: PRIDE project
     2. Name: Accurate quantitative proteomic analyses using metabolic labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS)