Accelerating scanning speed of mass spectrometers over time: looking good for personal proteomics!

The main driver of biological research today is genome sequencing and consequently the mainstream type of bioinformatics deals with genomics/sequencing. Personal genomics is already moving away from microarray genotyping platforms to sequencing methods. The possibility and potential growth of personal proteomics is dependent on many things and today I try to talk about only the high-throughput sequencing capacity of mass spec machines in the form of a semi-log plot. I won’t talk about things like sensitivity, mass range, isolation/trapping efficiency, and cost. The idea of the plot is coming from the famousNHGRI sequencing cost graph dubbed as one of the main genomics/sequencing conference bingo card by @dgmacarthur.

In tandem mass spectrometry a MS survey scan is followed by multiple MS/MS scans in the so-called data-dependent acquisition mode. That is a fancy way of saying that the n most intense m/z peaks of ionised peptides are picked from the survey scan and those peptides are subject to n MS/MS scans in which they are fragmented. Each MS/MS scan can potentially identify a peptide.  So n peptides can be identified per cycle. The time in seconds to complete a cycle is the scanning speed (alternatively scan rate) and in the plot below a full scan is 1 survey MS scan + 10 subsequent MS/MS scans. The instruments labelled are Thermo mass spectrometers. There are two types of labels. The triangles show the sequencing rate for CID-type fragmentation, which has been the mainstay of shotgun proteomics since its inception[1]. The circles shows the sequencing rate for HCD-type fragmentation, which is available in Orbitrap analyzers. With the Q-Exactive HCD sequencing speed has caught up to CID[2]. This is notable because HCD fragmentation with detection in the Orbitrap analyzer permits measurement of the fragment ions at high mass accuracy and high mass resolution, significantly increasing peptide identification confidence. In turn, this will enable even more rapid sequencing via “data-independent acquisition” or “all-ion fragmentation” methods[3,4].

Please let us know on Twitter (@attilacsordas & @brianbalgley) if the data is wrong or can be complemented.


This post was done together by me and Brian Balgley. I came up with the idea of a chart like this, Brian provided the concept, the metric, the mass spec background and references and I made the plot. Both of us worked on the text.

One response to “Accelerating scanning speed of mass spectrometers over time: looking good for personal proteomics!

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