Adding Intro, identifications and PTMs - #11
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julianu
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julianu
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I like your structuring and adding this as a first effort to fill up some content. I guess, for the current state we also said, going with ideas and filling in the gaps later is ok.
Maybe we should think of a way to assess the current state, though, like adding some progress or TODO flags to the chapters/sections. Let's discuss in the upcoming meeting.
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| ## Mass Spectrometry Fundamentals | ||
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| A mass spectrometer consists of three main components: an ionization source, a mass analyzer, and a detector [@Dass2007-gs]. Several mass spectrometers have been developed, including the Orbitrap Exploris 480 [@Bekker-Jensen2020-xw; @Denisov2021-bk] and the Orbitrap Astral [@Heil2023-qh; @Guzman2024-gk]. During injection into the instrument, peptides are ionized using electrospray ionization (ESI), which imparts one or more electrical charges to the peptide molecules [@Fenn1989-bt]. These charged peptide ions, referred to as precursor ions, are transferred to the mass analyzer, where electromagnetic fields separate them according to their mass-to-charge (*m/z*) ratios [@McDonald2002-hy]. The instrument then records a full mass spectrum (MS1), which measures the *m/z* values and relative abundances of the precursor ions. |
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Maybe either mention two more different machines (a timsTOF and an orbi-based machine?), or no specifc, just mentioning "many different kinds"?
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| ## Data Acquisition Strategies | ||
| There are several data acquisition method to select peptides from the MS1 for further fragmentation into MS2. There are three main acquisition types in proteomics, in which the precursors are selected from the MS1. The three main data collection strategies are: targeted analysis, data-dependent acquisition (DDA) [@Stahl1996-wd], and data-independent acquisition (DIA). |
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Adding examples for targeted, like SRM/MRM/PRM?
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