Blog

Articles tagged: statistics

Return to blog archive

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 [...]

Full article and comments form

Posted by John Cottrell (March 14, 2016)

Some peaks are more equal than others

When you look at the details of a peptide match in the Mascot Peptide View report, only a small number of the peaks may be labelled in the spectrum graphic and highlighted in the table of fragment masses. We often got challenged about this: "Why haven’t you labelled these other peaks that clearly match?". So, in Mascot 2.3, we added [...]

Full article and comments form

Posted by John Cottrell (July 15, 2015)

Search only for peptides we care about?

The July issue of Nature Methods contains a commentary from William Noble with the slightly provocative title "Mass spectrometrists should search only for peptides they care about". At first sight, this seems to contradict our general advice to include contaminant sequences when searching a single organism database or when using a taxonomy filter. One of Noble’s examples is a study [...]

Full article and comments form

Posted by John Cottrell (November 22, 2013)

Does protein FDR have any meaning?

Its easy to grasp the concept of using a target/decoy search to estimate peptide false discovery rate. You search against a decoy database where there are no true matches available, so the number of observed matches provides a good estimate of the number of false matches in the results from the target. People debate implementation details, such as whether the [...]

Full article and comments form

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 [...]

Full article and comments form

Posted by John Cottrell (December 17, 2012)

High mass accuracy: fragments

In an earlier post, we looked at the implications for database search of very accurate precursor m/z. In this post, we discuss what to expect from high accuracy measurement of fragment m/z. It can come as a surprise that the accuracy of the fragment m/z values in an MS/MS spectrum has only a modest effect on the score for a [...]

Full article and comments form

Posted by John Cottrell (December 1, 2012)

High mass accuracy: precursors

High performance instruments can deliver low ppm accuracy for both precursors and fragments. How does this impact database search? In this post, the first of two, we’ll look at the implications of very accurate precursor m/z. High mass accuracy and high resolution have transformed mass spectrometry over the last few years. Apart from increasing file sizes, and maybe the time [...]

Full article and comments form