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MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides.

ABSTRACT: Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. Although achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on prescheduled mass-to-charge and retention time windows. Here we set out to unify these two concepts by a global targeting approach in which an arbitrary number of precursors of interest are detected in real-time, followed by standard fragmentation or advanced peptide-specific analyses. We made use of a fast application programming interface to a quadrupole Orbitrap instrument and real-time recalibration in mass, retention time and intensity dimensions to predict precursor identity. MaxQuant.Live is freely available (www.maxquant.live) and has a graphical user interface to specify many predefined data acquisition strategies. Acquisition speed is as fast as with the vendor software and the power of our approach is demonstrated with the acquisition of breakdown curves for hundreds of precursors of interest. We also uncover precursors that are not even visible in MS1 scans, using elution time prediction based on the auto-adjusted retention time alone. Finally, we successfully recognized and targeted more than 25,000 peptides in single LC-MS runs. Global targeting combines the advantages of two classical approaches in MS-based proteomics, whereas greatly expanding the analytical toolbox.

SUBMITTER: Wichmann C

PROVIDER: S-EPMC6495250 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides.

Wichmann Christoph C Meier Florian F Virreira Winter Sebastian S Brunner Andreas-David AD Cox Jürgen J Mann Matthias M

Molecular & cellular proteomics : MCP 20190212 5

Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. Although achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, ...[more]

PMID: 30755466

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Project description:PurposeTo identify postoperative complications and risk factors associated with hip fracture and dislocation following primary arthroscopic surgical management of femoroacetabular impingement (FAI) syndrome.MethodsMarketScan was queried to identify patients who underwent FAI surgery from 2007 to 2016. Patients were stratified into 2 groups: acetabuloplasty only or femoroplasty only. A subanalysis of combined acetabuloplasty and femoroplasty also was undertaken. Surgical outcomes were followed postoperatively for 180 days. Multivariate logistic regression was used to control for with an alpha value of 0.05 set as significant.ResultsThis study identified 13,809 patients (mean age, 36.3 years) who underwent primary acetabuloplasty or femoroplasty. We also identified 10,026 patients who underwent both procedures. Postoperative complication rates were similar between the cohorts (acetabuloplasty 17.1%, femoroplasty 19.9%, P = .0622). Rates of hip fracture (femoroplasty: 2.4% vs acetabuloplasty: 2.0%, P = .0302) and heterotopic ossification (femoroplasty: 11.3% vs acetabuloplasty: 8.8%, P < .0001) were greater in the femoroplasty-only cohort. Combined acetabuloplasty and femoroplasty was associated with the greatest complication burden of 21.6% (P < .0001). After multivariate regression, differences in age, sex, comorbid status, or procedure type did not influence odds in risk for postoperative hip dislocation. Adjusted data showed that neither femoroplasty nor acetabuloplasty influenced odds of hip fracture (P > .05). Patients who were aged younger than 20 years old were significantly less likely to fracture their hips postoperatively than patients aged 60+ years (odds ratio 0.3, 95% confidence interval 0.1-0.8). Hypertension was independently associated with increased odds of hip fracture (odds ratio 1.7, 95% confidence interval 1.2-3.5).ConclusionsOlder age, male sex, and hypertension all carry increased risk for a hip fracture following acetabuloplasty or femoroplasty. Patient- and procedure-specific factors that could be assessed with this database did not influence risk for hip dislocation.Level of evidenceLevel III; retrospective comparative observation trial.

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MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides.

Publications

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides.

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