9. Aebersold R, Mann M (2003) Mass
spectrometry-based proteomics. Nature
422:198–207
10. Hu A, Noble WS, Wolf-Yadlin A (2016)
Technical advances in proteomics: new developments in data-independent acquisition.
F1000Res 5:F1000 Faculty Rev-419
11. Michalski A, Cox J, Mann M (2011) More
than 100,000 detectable peptide species
elute in single shotgun proteomics runs but
the majority is inaccessible to data-dependent
LC-MS/MS. J Proteome Res 10:1785–1793
12. Meyer JG, Schilling B (2017) Clinical applications of quantitative proteomics using targeted and untargeted data-independent
acquisition techniques. Expert Rev Proteomics 14:419–429
13. Doerr A (2014) DIA mass spectrometry. Nat
Methods 12:35
14. Wolf-Yadlin A, Hu A, Noble WS (2016)
Technical advances in proteomics: new developments in data-independent acquisition.
F1000Res 5:1–12
15. Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J (2019) Data-independent acquisition
improves quantitative cross-linking mass spectrometry. Mol Cell Proteomics 18:786–795
16. Gillet LC, Navarro P, Tate S, Ro ¨st H,
Selevsek N, Reiter L, Bonner R, Aebersold R
(2012) Targeted data extraction of the
MS/MS spectra generated by dataindependent acquisition: a new concept for
consistent and accurate proteome analysis.
Mol Cell Proteomics 11:1–17
17. Chapman JD, Goodlett DR, Masselon CD
(2014) Multiplexed and data-independent
tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev
33:452–470
18. Kang Y, Burton L, Lau A, Tate S (2017)
SWATH-ID: an instrument method which
combines identification and quantification in
a single analysis. Proteomics 17:e1500522
19. Lin Q, Tan HT, Chung MCM (2019) Mass
spectrometry of proteins. Methods Mol Biol
1977:3–15
20. Shilov IV, Seymour SL, Patel AA, Loboda A,
Tang WH, Keating SP, Hunter CL, Nuwaysir
LM, Schaeffer DA (2007) The Paragon Algorithm, a next generation search engine that
uses sequence temperature values and feature
probabilities to identify peptides from tandem
mass spectra. Mol Cell Proteomics
6:1638–1655
21. Ro ¨st HL, Aebersold R, Schubert OT (2017)
Automated swath data analysis using targeted
extraction of ion chromatograms. Methods
Mol Biol 1550:289–307
22. Lin Q, Tan HT, Chung MCM (2019) Methods in molecular biology. Humana,
New York, pp 3–15
23. Wang J, Pe ´rez-Santiago J, Katz JE, Mallick P,
Bandeira N (2010) Peptide identification
from mixture tandem mass spectra. Mol Cell
Proteomics 9:1476–1485
24. Parker SJ, Rost H, Rosenberger G, Collins
BC,
Malmstro ¨m
L,
Amodei
D,
Venkatraman V, Raedschelders K, Van Eyk
JE, Aebersold R (2015) Identification of a
set of conserved eukaryotic internal retention
time standards for data independent acquisition mass spectrometry. Mol Cell Proteomics
14:2800–2813
25. Holewinski RJ, Parker SJ, Matlock AD,
Venkatraman V, Van Eyk JE (2016) Methods
for SWATH™: data independent acquisition
on triplet of mass spectrometers. Methods
Mol Biol 1410:265–279
26. Ludwig C, Gillet L, Rosenberger G, Amon S,
Collins BC, Aebersold R (2018) Dataindependent acquisition-based SWATH - MS
for quantitative proteomics: a tutorial. Mol
Syst Biol 14:1–23
27. Ahn SM, Simpson RJ (2007) Body fluid proteomics: prospects for biomarker discovery.
Proteomics Clin Appl 1:1004–1015
28. Manuscript A (2010) Human body fluid proteome analysis. Proteomics 6:6326–6353
29. Cso ˝sz E ´ , Kallo ´ G, Ma ´rkus B, Dea ´k E,
Csutak A, To ˝zse ´r J (2017) Quantitative body
fluid proteomics in medicine—a focus on
minimal
invasiveness.
J
Proteomics
153:30–43
30. Humphrey SP, Williamson RT (2001) A
review of saliva normal composition, flow,
and function. J Prosthet Dent 85:162–169
31. De Almeida PDV, Gre ´gio AMT, Machado
MA ˆ N, De Lima AAS, Azevedo LR (2008)
Saliva composition and functions: a comprehensive review. J Contemp Dent Pract
9:072–080
32. Schulz BL, Cooper-White J, Punyadeera CK
(2013) Saliva proteome research: current status and future outlook. Crit Rev Biotechnol
33:246–259
33. Shaila M, Pai GP, Shetty P (2013) Salivary
protein concentration, flow rate, buffer capacity and pH estimation: a comparative study
among young and elderly subjects, both normal and with gingivitis and periodontitis. J
Indian Soc Periodontol 17:42–46
34. Ventura TM d S, Ribeiro NR, Dionizio AS,
Sabino IT, Buzalaf MAR (2018) Standardization of a protocol for shotgun proteomic analysis of saliva. J Appl Oral Sci 26:e20170561
136
Maria del Pilar Chantada-Va ´ zquez et al.
spectrometry-based proteomics. Nature
422:198–207
10. Hu A, Noble WS, Wolf-Yadlin A (2016)
Technical advances in proteomics: new developments in data-independent acquisition.
F1000Res 5:F1000 Faculty Rev-419
11. Michalski A, Cox J, Mann M (2011) More
than 100,000 detectable peptide species
elute in single shotgun proteomics runs but
the majority is inaccessible to data-dependent
LC-MS/MS. J Proteome Res 10:1785–1793
12. Meyer JG, Schilling B (2017) Clinical applications of quantitative proteomics using targeted and untargeted data-independent
acquisition techniques. Expert Rev Proteomics 14:419–429
13. Doerr A (2014) DIA mass spectrometry. Nat
Methods 12:35
14. Wolf-Yadlin A, Hu A, Noble WS (2016)
Technical advances in proteomics: new developments in data-independent acquisition.
F1000Res 5:1–12
15. Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J (2019) Data-independent acquisition
improves quantitative cross-linking mass spectrometry. Mol Cell Proteomics 18:786–795
16. Gillet LC, Navarro P, Tate S, Ro ¨st H,
Selevsek N, Reiter L, Bonner R, Aebersold R
(2012) Targeted data extraction of the
MS/MS spectra generated by dataindependent acquisition: a new concept for
consistent and accurate proteome analysis.
Mol Cell Proteomics 11:1–17
17. Chapman JD, Goodlett DR, Masselon CD
(2014) Multiplexed and data-independent
tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev
33:452–470
18. Kang Y, Burton L, Lau A, Tate S (2017)
SWATH-ID: an instrument method which
combines identification and quantification in
a single analysis. Proteomics 17:e1500522
19. Lin Q, Tan HT, Chung MCM (2019) Mass
spectrometry of proteins. Methods Mol Biol
1977:3–15
20. Shilov IV, Seymour SL, Patel AA, Loboda A,
Tang WH, Keating SP, Hunter CL, Nuwaysir
LM, Schaeffer DA (2007) The Paragon Algorithm, a next generation search engine that
uses sequence temperature values and feature
probabilities to identify peptides from tandem
mass spectra. Mol Cell Proteomics
6:1638–1655
21. Ro ¨st HL, Aebersold R, Schubert OT (2017)
Automated swath data analysis using targeted
extraction of ion chromatograms. Methods
Mol Biol 1550:289–307
22. Lin Q, Tan HT, Chung MCM (2019) Methods in molecular biology. Humana,
New York, pp 3–15
23. Wang J, Pe ´rez-Santiago J, Katz JE, Mallick P,
Bandeira N (2010) Peptide identification
from mixture tandem mass spectra. Mol Cell
Proteomics 9:1476–1485
24. Parker SJ, Rost H, Rosenberger G, Collins
BC,
Malmstro ¨m
L,
Amodei
D,
Venkatraman V, Raedschelders K, Van Eyk
JE, Aebersold R (2015) Identification of a
set of conserved eukaryotic internal retention
time standards for data independent acquisition mass spectrometry. Mol Cell Proteomics
14:2800–2813
25. Holewinski RJ, Parker SJ, Matlock AD,
Venkatraman V, Van Eyk JE (2016) Methods
for SWATH™: data independent acquisition
on triplet of mass spectrometers. Methods
Mol Biol 1410:265–279
26. Ludwig C, Gillet L, Rosenberger G, Amon S,
Collins BC, Aebersold R (2018) Dataindependent acquisition-based SWATH - MS
for quantitative proteomics: a tutorial. Mol
Syst Biol 14:1–23
27. Ahn SM, Simpson RJ (2007) Body fluid proteomics: prospects for biomarker discovery.
Proteomics Clin Appl 1:1004–1015
28. Manuscript A (2010) Human body fluid proteome analysis. Proteomics 6:6326–6353
29. Cso ˝sz E ´ , Kallo ´ G, Ma ´rkus B, Dea ´k E,
Csutak A, To ˝zse ´r J (2017) Quantitative body
fluid proteomics in medicine—a focus on
minimal
invasiveness.
J
Proteomics
153:30–43
30. Humphrey SP, Williamson RT (2001) A
review of saliva normal composition, flow,
and function. J Prosthet Dent 85:162–169
31. De Almeida PDV, Gre ´gio AMT, Machado
MA ˆ N, De Lima AAS, Azevedo LR (2008)
Saliva composition and functions: a comprehensive review. J Contemp Dent Pract
9:072–080
32. Schulz BL, Cooper-White J, Punyadeera CK
(2013) Saliva proteome research: current status and future outlook. Crit Rev Biotechnol
33:246–259
33. Shaila M, Pai GP, Shetty P (2013) Salivary
protein concentration, flow rate, buffer capacity and pH estimation: a comparative study
among young and elderly subjects, both normal and with gingivitis and periodontitis. J
Indian Soc Periodontol 17:42–46
34. Ventura TM d S, Ribeiro NR, Dionizio AS,
Sabino IT, Buzalaf MAR (2018) Standardization of a protocol for shotgun proteomic analysis of saliva. J Appl Oral Sci 26:e20170561
136
Maria del Pilar Chantada-Va ´ zquez et al.