References
Bekker-Jensen, Dorte B, Ana Martínez-Val, Sophia Steigerwald, et al.
2020. “A Compact Quadrupole-Orbitrap Mass Spectrometer with
FAIMS Interface Improves Proteome Coverage in Short
LC Gradients.” Mol. Cell. Proteomics 19
(4): 716–29.
Benjamini, Yoav, and Yosef Hochberg. 1995. “Controlling the False
Discovery Rate: A Practical and Powerful Approach to Multiple
Testing.” J. R. Stat. Soc. Series B Stat. Methodol. 57
(1): 289–300.
Cox, Jürgen, and Matthias Mann. 2008. “MaxQuant
Enables High Peptide Identification Rates, Individualized p.p.b.-Range
Mass Accuracies and Proteome-Wide Protein Quantification.”
Nat. Biotechnol. 26 (12): 1367–72.
Cox, Jürgen, Nadin Neuhauser, Annette Michalski, Richard A Scheltema,
Jesper V Olsen, and Matthias Mann. 2011. “Andromeda: A Peptide
Search Engine Integrated into the MaxQuant
Environment.” J. Proteome Res. 10 (4): 1794–805.
Dass, Chhabil. 2007. Fundamentals of Contemporary Mass
Spectrometry. Wiley Series on Mass Spectrometry. Wiley-Blackwell.
Denisov, Eduard, Eugen Damoc, and Alexander Makarov. 2021.
“Exploring Frontiers of Orbitrap Performance for Long
Transients.” Int. J. Mass Spectrom. 466 (116607):
116607.
Elias, Joshua E, and Steven P Gygi. 2007. “Target-Decoy Search
Strategy for Increased Confidence in Large-Scale Protein Identifications
by Mass Spectrometry.” Nat. Methods 4 (3): 207–14.
Eng, Jimmy K, Ashley L McCormack, and John R Yates. 1994. “An
Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino
Acid Sequences in a Protein Database.” J. Am. Soc. Mass
Spectrom. 5 (11): 976–89.
Fenn, John B, Matthias Mann, Chin Kai Meng, Shek Fu Wong, and Craig M
Whitehouse. 1989. “Electrospray Ionization for Mass Spectrometry
of Large Biomolecules.” Science 246 (4926): 64–71.
Guzman, Ulises H, Ana Martinez-Val, Zilu Ye, et al. 2024.
“Ultra-Fast Label-Free Quantification and Comprehensive Proteome
Coverage with Narrow-Window Data-Independent Acquisition.”
Nat. Biotechnol. 42 (12): 1855–66.
Heil, Lilian R, Eugen Damoc, Tabiwang N Arrey, et al. 2023.
“Evaluating the Performance of the Astral Mass Analyzer for
Quantitative Proteomics Using Data-Independent Acquisition.”
J. Proteome Res. 22 (10): 3290–300.
Kim, Sangtae, and Pavel A Pevzner. 2014. “MS-GF+
Makes Progress Towards a Universal Database Search Tool for
Proteomics.” Nat. Commun. 5 (1): 5277.
Kong, Andy T, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya
Mellacheruvu, and Alexey I Nesvizhskii. 2017.
“MSFragger: Ultrafast and Comprehensive Peptide
Identification in Mass Spectrometry-Based Proteomics.” Nat.
Methods 14 (5): 513–20.
Lange, Vinzenz, Paola Picotti, Bruno Domon, and Ruedi Aebersold. 2008.
“Selected Reaction Monitoring for Quantitative Proteomics: A
Tutorial.” Mol. Syst. Biol. 4: 222. https://doi.org/10.1038/msb.2008.61.
Lennon, J J, and K A Walsh. 1999. “Locating and Identifying
Posttranslational Modifications by in-Source Decay During
MALDI-TOF Mass Spectrometry.”
Protein Sci. 8 (11): 2487–93.
McDonald, W Hayes, and John R Yates 3rd. 2002. “Shotgun Proteomics
and Biomarker Discovery.” Dis. Markers 18 (2): 99–105.
McLafferty, Fred W. 1981. “Tandem Mass Spectrometry.”
Science 214 (4518): 280–87.
Meier, Florian, Andreas-David Brunner, Scarlet Koch, et al. 2018.
“Online Parallel Accumulation-Serial Fragmentation
(PASEF) with a Novel Trapped Ion Mobility Mass
Spectrometer.” Mol. Cell. Proteomics 17 (12): 2534–45.
https://doi.org/10.1074/mcp.TIR118.000900.
Olsen, Jesper V, Boris Macek, Oliver Lange, Alexander Makarov, Stevan
Horning, and Matthias Mann. 2007. “Higher-Energy
C-Trap Dissociation for Peptide Modification
Analysis.” Nat. Methods 4 (9): 709–12.
Peters-Clarke, Trenton M, Joshua J Coon, and Nicholas M Riley. 2024.
“Instrumentation at the Leading Edge of Proteomics.”
Anal. Chem. 96 (20): 7976–8010.
Peterson, Amelia C, Jason D Russell, Derek J Bailey, Michael S
Westphall, and Joshua J Coon. 2012. “Parallel Reaction Monitoring
for High Resolution and High Mass Accuracy Quantitative, Targeted
Proteomics.” Mol. Cell. Proteomics 11 (11): 1475–88. https://doi.org/10.1074/mcp.O112.020131.
Roepstorff, P, and J Fohlman. 1984. “Proposal for a Common
Nomenclature for Sequence Ions in Mass Spectra of Peptides.”
Biomed. Mass Spectrom. 11 (11): 601.
Sinitcyn, Pavel, Jan Daniel Rudolph, and Jürgen Cox. 2018.
“Computational Methods for Understanding Mass Spectrometry-Based
Shotgun Proteomics Data.” Annu. Rev. Biomed. Data Sci. 1
(July): 207–34.
Stahl, David C, Kathryn M Swiderek, Michael T Davis, and Terry D Lee.
1996. “Data-Controlled Automation of Liquid Chromatography/Tandem
Mass Spectrometry Analysis of Peptide Mixtures.” J. Am. Soc.
Mass Spectrom. 7 (6): 532–40.
Steen, Hanno, and Matthias Mann. 2004. “The ABC’s
(and XYZ’s) of Peptide Sequencing.” Nat. Rev.
Mol. Cell Biol. 5 (9): 699–711.
Storey, John D, and Robert Tibshirani. 2003. “Statistical
Significance for Genomewide Studies.” Proc. Natl. Acad. Sci.
U. S. A. 100 (16): 9440–45.
The UniProt Consortium. 2018. “UniProt: The Universal
Protein Knowledgebase.” Nucleic Acids Res. 46 (5): 2699.
Tyanova, Stefka, Tikira Temu, and Juergen Cox. 2016. “The
MaxQuant Computational Platform for Mass Spectrometry-Based
Shotgun Proteomics.” Nat. Protoc. 11 (12): 2301–19.