Dataset Information

Parallel reaction monitoring using quadrupole-orbitrap mass spectrometer: principle and applications

ABSTRACT: The PRM dataset corresponds to the raw data files supporting the comparison between conventional database search using Mascot and spectral matching strategy (Figure 3). The PRM and DDA raw data files support the comparison between these two acquisition methods using the spectral matching strategy to corroborate the identity of the peptides (Figure 4D). The data were generated from the triplicate analyses of a dilution series of 778 SIL peptides spiked in a yeast tryptic digest at concentrations ranging from 50 amol/µL to 37 fmol/µL.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Adèle Bourmaud

LAB HEAD: Bruno Domon

PROVIDER: PXD003781 | Pride | 2016-05-09

REPOSITORIES: Pride

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Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: Principle and applications.

Bourmaud Adele A Gallien Sebastien S Domon Bruno B

Proteomics 20160527 15-16

Targeted mass spectrometry-based approaches are nowadays widely used for quantitative proteomics studies and more recently have been implemented on high resolution/accurate mass (HRAM) instruments resulting in a considerable performance improvement. More specifically, the parallel reaction monitoring technique (PRM) performed on quadrupole-Orbitrap mass spectrometers, leveraging the high resolution and trapping capabilities of the instrument, offers a clear advantage over the conventional select ...[more]

PMID: 27145088

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Project description:Being inspired by metabolomic data processing, we have developed a bioinformatic pipeline that optimizes the processing of mass spectral data obtained from isobaric Tandem Mass Tag (TMT) experiments. Our method focuses on the tandem mass spectral level by first quantifying and then identifying (QtI), while preserving unidentified spectra for further investigations. The raw datasets were previously generated [1, 2]. Two-proteome model experiments were considered where identical pools of human CSF or plasma samples were mixed with E. coli samples at different concentrations. E. coli protein extract was spiked in 400 µL of CSF at amounts of 0, 2, 3, 5, 6.25, and 7.5 µg. Such sets of 6 spiked CSF samples were prepared in triplicate for comparison using sixplex isobaric tagging and analyzed in triplicates on two independent but identical LC MS/MS, for a total of 18 raw files [1]; this experiment is called “CSF-E.coli”. E. coli protein extract was spiked at 0, 2.5, 5, 6.25, 12.5, and 25 µg in 30 µL human plasma. Such sets of 6 spiked plasma samples were prepared in quadruplicate for comparison using sixplex isobaric tagging and analyzed in triplicates on one LC MS/MS, for a total of 12 raw files [2]; this experiment is referred as “Plasma-E.coli”.The so-called “96samples-CSF” experiment consists of 16 replicate TMT sixplex experiments measuring identical CSF samples from the pool described above [2], analyzed in triplicates on one LCMS/MS for a total of 48 raw files. The so-called “96samples-plasma” experiment consists of 16 replicate TMT sixplex experiments measuring identical plasma samples from the pool described before, analyzed in triplicates on one LC MS/MS for a total of 48 raw files [1]. References: [1] Dayon, L., Núñez Galindo, A., Corthésy, J., Cominetti, O. & Kussmann, M. Comprehensive and scalable highly automated MS-based proteomic workflow for clinical biomarker discovery in human plasma. J. Proteome Res. 13, 3837-3845 (2014). [2] Núñez Galindo, A., Kussmann, M. & Dayon, L. Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery. Anal. Chem. 87, 10755-10761 (2015).

Dataset Information

Parallel reaction monitoring using quadrupole-orbitrap mass spectrometer: principle and applications

Publications

Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: Principle and applications.

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