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How exactly does Match-between-runs work in MaxQuant? I understand that MBR works by getting information from a previously identified peptide and transferring it to another based on m/z, charge state, RT, CCS data, etc. But I am unsure what the "runs" mean, and what types of runs can be used in MBRs.

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How do I assess when to use "match between runs" for LFQ analysis on Maxquant? Hi Proteomics enthusiasts, I am currently analyzing DNA pulldown data (treated vs non-treated) using Label-free.

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Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable.

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To address this issue, several approaches have been developed including computational methods such as MaxQuant's match-between-runs (MBR) algorithm. Often dozens of runs are all considered at once by MBR, transferring identifications from any one run to any of the others.

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Label-free quantification is commonly used to perform proteome-wide quantification in large biological cohorts. To reliably interpret the data, ID-transfer between runs is vital to reduce false missing values. False missing values are generated by the stochasticity of data-dependent acquisition (DDA) or the difficulty in interpreting MS2.

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Match- between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable. Though

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'Match between runs' is a feature of MaxQuant and is used to check for the signal of a peptide identified in one sample but not in another, by using high mass accuracy and a narrow retention time window. If such a signal is found it will be marked 'by matching' rather than 'by MS/MS'. Designed for quantitative experiments. References

Accuracy of matching between runs. a. Retention time match difference

Match-between-runs (MBR) is a commonly used approach to quantify additional features by . transferring information across different samples. It largely miti gates the missing value problem .

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Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference.

Labelfree quantification with FDRcontrolled matchbetweenruns bioRxiv

Using "match between runs" in Spectronaut enabled peptides to be quantified across replica even without being initially detected in every single replica. In the 1x sample, this yielded 292 (70%) quantified URPs out of 414 identified URPs. The same injection amount (1.5 μg) of HSA, albeit alone and not in mixture with six other proteins.

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Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable.

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Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable.

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Match-Between-Runs Authors Fengchao Yu, Sarah E. Haynes, and Alexey I. Nesvizhskii Correspondence Graphical Abstract [email protected] In Brief Match-between-runs is a powerful approach to mitigate the missing value problem in label-free quantification. It transfers features identified by MS/MS from one run to the other, but previously.

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Also, as the 'match-between-runs' function had not yet been included in the DIA-NN version we used for this study, the obtained results should be revisited for newer DIA-NN versions.

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To address this issue, several approaches have been developed including computational methods such as MaxQuant's match-between-runs (MBR) algorithm. Often dozens of runs are all considered at once by MBR, transferring identifications from any one run to any of the others.

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Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable.