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Posted by John Cottrell (June 17, 2020)

Using the Quantitation Summary to create reports and charts

An earlier article described how to create a Quantitation Summary in Mascot Daemon. This is a spreadsheet-like text file, where the rows correspond to proteins and the columns contain expression data for various samples in the form of abundances or ratios of abundances. A Quantitation Summary can be opened and manipulated in a spreadsheet program such as Excel, and it [...]

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Posted by John Cottrell (May 19, 2020)

Tabulate expression data from multiple analyses with Mascot Daemon

Studies that use mass spectrometry-based quantitation often contain large numbers of individual analyses: samples from different sources or treatments or time points, possibly fractionated, with replicates and so forth. Using statistical methods to combine the analyses, extract meaningful information, and report it as charts and tables is a complex task that usually requires custom scripting in a language such as [...]

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Posted by Patrick Emery (August 22, 2019)

The three Ds: Diethylation, Dimethylation and the Deuterium effect

Dimethylation Mascot Server and Mascot Distiller support a number of precursor intensity based quantitation techniques using a number of different techniques and chemistries. The software also allows you to flexibly define your own methods, allowing you to implement quantitation protocols which we have not supplied ‘out of the box’. One isotope labelling method which Distiller supports ‘out of the box’ [...]

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Posted by Patrick Emery (October 15, 2018)

Back to basics 3: Quantitation statistics

Mascot Server and Distiller support a number of different quantitation methods. These methods are carried out at the peptide level, the peptides are then grouped into protein families, and the peptide quantitation results used to calculate protein ratio values. Mascot and Distiller perform a number of statistical procedures and tests to give you an indication of the quality and reliability [...]

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Posted by Ville Koskinen (May 24, 2018)

Higher accuracy for oxidation profiles

Earlier this year, Reest et al. described a quantitation workflow based on light and heavy iodoacetamide labels, which they named SICyLIA [1]. The workflow was used for analysing cysteine oxidation levels between wild-type and redox-stressed mouse cells. At its core, SICyLIA is a precursor protocol with two components, light and heavy, where the labels are simply light and heavy carbamidomethyl on [...]

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Posted by Patrick Emery (February 12, 2018)

MS3 reporter ion quantitation with Mascot Distiller

A common issue encountered when carrying out reporter ion quantitation methods, such as TMT and iTRAQ, is that of interfering ion signals in the reporter region. One commonly used strategy which can be taken to mitigate against this is to reisolate the most abundant ion in the MS/MS spectrum and refragment it. The resultant reporter ion signals in the MS3 [...]

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Posted by John Cottrell (October 14, 2013)

Modifications round-up, part 2

This is the second of two articles dealing with topics relating to modifications. The first can be found here. Note that Site analysis was covered in an earlier article. Why aren’t amino acid substitutions listed in the search form? Amino acid substitutions are rare and there are lots of them, so the only practical way to use them is in [...]

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Posted by John Cottrell (August 2, 2013)

Current challenges in quantitative proteomics

"Current challenges in software solutions for mass spectrometry-based quantitative proteomics" is a recent paper in Amino Acids by a group of expert authors that describes ten areas of particular difficulty in data processing for quantitation. Full text is available online at Springer Link. I would argue that Mascot Distiller meets almost all of these challenges. Obviously, I have to declare [...]

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Posted by John Cottrell (January 5, 2013)

Quantify then identify or identify then quantify?

Quantitation in Mascot Distiller is identification driven. All of the MS/MS data is searched then all of the identified peptides that meet the requirements of the method are quantified. Conventional wisdom is that a feature driven approach is more efficient: first look for features that indicate up or down regulation between samples, then target these for quantitation. The reasoning is [...]

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