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Articles tagged: quantitation

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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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