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I began reading this paper ( and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere. Consider the following line:

"The resulting peptide signals in the LC-MS map are referred to as features while the selection of features for fragmentation with MS/MS is called precursor ion selection."

I'm not sure what an LC-MS map is, so I can't properly understand what features or precursor ion selection are: can someone define these terms for me with examples?

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LC-MS stands for Liquid chromatography–mass spectrometry. The LC-MS map shows the separation of samples by polarity and mass. – Mys_721tx Jan 8 '14 at 6:21
As I understand precursor ion refers to the tryptic peptide ions prior to fragmentation after the first round of MS. – WYSIWYG Jan 8 '14 at 9:13

LC-MS map they refer to is the projection of two separation method (Liquid Chromatography - Mass Spectroscopy) results into an imaginary plane. It's a conceptual map. From this map, peptide signals referred to as "features" (article uses this term) are selected for the next level of fragmentation and then MS again.

Figure 1 of the article you cite simulates a small fraction of this larger map.

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In a liquid chromatography coupled to mass spectrometry (LC-MS) analysis, as analytes elute from the chromatographic column they are sprayed through a hypodermic needle maintained at a high potential difference relative to the mass spectrometer. Combination of this potential difference and the pH of the LC buffers causes the analyte molecules to pick charge. Analyte ions are then pulled into the MS and guided using lenses. Then these ions are separated based on their m/z (mass-to-charge) ratios inside an analyser and then detected using a detector.

At any given time, detected signals are typically represented on a 2-D map/graph between m/z on the x-axis and ion intensity/relative abundance on the y-axis. This is called as MS1 scan or precursor ion scan. Now, depending on the mode in which LC-MS analysis is being carried out, precursors are selected for fragmentation and further MS measurements, which is called as MS/MS or MS2 or product ion scan. Several of these MS1 or MS2 snap-shots can be used to construct a elution time profile for every ion. For an ion having a specific m/z ratio, this can be represented as a 2-D map between retention time on the x-axis and ion intensity on the y-axis. Area under this profile can be used to estimate the ion current of an analyte and under the given conditions it is proportional to the abundance of the analyte in the sample.

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