More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

By Annette Michalski, Jüergen Cox, Matthias Mann. Journal of Proteome Research, 2011

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DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics (2015, neutral): “4 and 5 ).”
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis* (2012, background): “It does, however, have limited quantification capabilities on large sample sets because of stochastic and irreproducible precursor ion selection (11) and under-sampling (12).”
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics (2016, background): “40| Set the minimum length for a peptide to be considered for identification, as well as the maximum peptide mass. 41| Set the minimum and the maximum peptide lengths in case of unspecific search (i.e., without digestion enzyme) if applicable.”
Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer (2011, background): “) The number of isotope patterns detected was close to 150,000, a very high number considering that the gradient was not particularly long (4, 5), presumably because of the short MS and MS/MS cycle time of 1 s.”
A multi-center study benchmarks software tools for label-free proteome quantification (2016, background): “Outlier log-ratios that are out of validity range are dropped and remaining log-ratios are shifted by the median log-ratio of the predefined background species to center the data (Supplementary Table 9).”