PXD001900

PXD001900 is an original dataset announced via ProteomeXchange.

Title	Multiplexed, scheduled high resolution sMRM-HR acquisition on full scan MS/MS instruments
Description	Advances in software and high resolution, high mass accuracy mass spectrometers have expanded their functionality beyond traditional data dependent acquisition (DDA) methods. Using a single platform, an orthogonal quadrupole time-of flight (QqTOF) mass spectrometer, the TripleTOF 5600, we have investigated the feasibility of implementing large-scale targeted quantitative assays, derived from discovery type data sets, using scheduled, high resolution multiple reaction monitoring (sMRM-HR) mass spectrometry. We assessed the selectivity and reproducibility of MRM-HR, also referred to as parallel reaction monitoring (PRM), measuring standard peptide concentration curves as well as system suitability assays. We specifically compared the robustness and accuracy of MRM-HR assays to traditional SRM workflows on triple quadrupole instruments. To determine the utility of sMRM-HR for large-scale targeted quantitative assays, we retention time scheduled over 500 peptides in a single LC-MS acquisition. High resolution and high mass accuracy of the full scan MS/MS spectra resulted in sufficient selectivity to monitor numerous MS/MS fragment ions per analyte precursor and provided flexibility for post-acquisition assay refinement and optimization. To demonstrate its applicability to biological samples, whole cell lysates from several E. coli wild-type and mutant strains were quantitatively assayed by sMRM-HR to confirm a previously generated candidate list of differentially expressed proteins. The ease of developing and implementing sMRM-HR assays derived directly from DDA discovery workflows on the same high resolution instrument platform facilitates downstream validation studies targeting many peptides for MS/MS level quantitation. This work provides a robust MRM-HR workflow for rapidly moving from discovery analysis to large-scale, multiplexed, targeted quantitation.
HostingRepository	MassIVE
AnnounceDate	2015-09-29
AnnouncementXML	Submission_2015-09-29_10:53:31.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Birgit Schilling
SpeciesList	scientific name: Bos taurus; common name: cattle; NCBI TaxID: 9913; scientific name: Saccharomyces cerevisiae; common name: baker's yeast; NCBI TaxID: 4932; scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2015-03-10 12:15:50	ID requested
⏵ 1	2015-09-29 10:53:32	announced

Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW, Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows. Anal Chem, 87(20):10222-9(2015) [pubmed]

submitter keyword: MRM high resolution, PRM, data independent acquisition (DIA), label free quantification, time-scheduled acquisitions

Bradford W. Gibson
lab head
Birgit Schilling
contact affiliation	Buck Institute
contact email	bschilling@buckinstitute.org
dataset submitter

MassIVE dataset URI

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