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OM, MacLean B, Ro ¨st HL, Tate SA, Tsou
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Y,
Nesvizhskii
AI,
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34:1130–1136
133. MacLean B, Tomazela DM, Shulman N,
Chambers M, Finney GL, Frewen B, Kern
R, Tabb DL, Liebler DC, MacCoss MJ
(2010) Skyline: an open source document
editor for creating and analyzing targeted
proteomics experiments. Bioinformatics
26:966–968
134. R€ ast HL, Rosenberger G, Navarro P, Gillet L,
Miladinovia ¨ SM, Schubert OT, OpenSWATH
enables automated, targeted analysis of dataindependent acquisition MS data. Nat Biotechnol 32:219–223
SWATH-MS Protocols in Human Diseases
141
ON, Podtelejnikov AV, Neubauer G,
Mortensen P, Mann M (1996) A strategy for
identifying gel-separated proteins in sequence
databases by MS alone. Biochem Soc Trans
24:893–896
119. Schilling B, Gibson BW, Hunter CL (2018)
Management. Manage Entrep:15–38
120. Bereman MS (2015) Tools for monitoring
system suitability in LC MS/MS centric proteomic experiments. Proteomics 15:891–902
121. Bruderer R, Bernhardt OM, Gandhi T, Reiter
L (2016) High-precision iRT prediction in
the targeted analysis of data-independent
acquisition and its impact on identification
and quantitation. Proteomics 16:2246–2256
122. Ro ¨st HL, Aebersold R, Schubert OT (2017)
Management. Manage Entrep 1550:15–38
123. Lam H, Aebersold R (2011) Building and
searching tandem mass (MS/MS) spectral
libraries for peptide identification in proteomics. Methods 54:424–431
124. Zi J, Zhang S, Zhou R, Zhou B, Xu S, Hou G,
Tan F, Wen B, Wang Q, Lin L, Liu S (2014)
Expansion of the ion library for mining
SWATH-MS data through fractionation proteomics. Anal Chem 86:7242–7246
125. Lam H (2012) Spectral library searching for
peptide identification in proteomics. Stat
Interface 5:39–46
126. Schubert OT, Gillet LC, Collins BC,
Navarro P, Rosenberger G, Wolski WE,
Lam H, Amodei D, Mallick P, Maclean B,
Aebersold R (2015) Building high-quality
assay libraries for targeted analysis of
SWATH MS data. Nat Protoc 10:426–441
127. Deutsch EW, Perez-riverol Y, Chalkley RJ,
Wilhelm M, Sachsenberg T, Walzer M,
K€ all L, Delanghe B, Schymanski EL,
Wilmes P, Dorfer V, Kuster B (2019) Expanding the use of spectral libraries in proteomics.
J Proteome Res 17:4051–4060
128. Escher C, Reiter L, Maclean B, Ossola R,
Herzog F, Maccoss MJ, Rinner O (2014)
Using iRT, a normalized retention time for
more targeted measurement of peptides. Proteomics 12:1111–1121
129. Manadas B, Mendes VM, English J, Dunn MJ
(2010) Peptide fractionation in proteomics
approaches.
Expert
Rev
Proteomics
7:655–663
130. Bekker-Jensen DB, Kelstrup CD, Batth TS,
Larsen SC, Haldrup C, Bramsen JB, Sørensen
KD, Høyer S, Ørntoft TF, Andersen CL,
Nielsen ML, Olsen JV (2017) An optimized
shotgun strategy for the rapid generation of
comprehensive human proteomes. Cell Syst
4:587–599.e4
131. Barkovits K, Pacharra S, Pfeiffer K,
Steinbach S, Eisenacher M, Marcus K, Uszkoreit J (2019) Reproducibility, specificity
and accuracy of relative quantification using
spectral
library-based
data-independent
acquisition. Mol Cell Proteomics 2019:mcp.
RA119.001714
132. Navarro P, Kuharev J, Gillet LC, Bernhardt
OM, MacLean B, Ro ¨st HL, Tate SA, Tsou
CC, Reiter L, Distler U, Rosenberger G,
Perez-Riverol
Y,
Nesvizhskii
AI,
Aebersold R, Tenzer S (2016) A multicenter
study benchmarks software tools for label-free
proteome quantification. Nat Biotechnol
34:1130–1136
133. MacLean B, Tomazela DM, Shulman N,
Chambers M, Finney GL, Frewen B, Kern
R, Tabb DL, Liebler DC, MacCoss MJ
(2010) Skyline: an open source document
editor for creating and analyzing targeted
proteomics experiments. Bioinformatics
26:966–968
134. R€ ast HL, Rosenberger G, Navarro P, Gillet L,
Miladinovia ¨ SM, Schubert OT, OpenSWATH
enables automated, targeted analysis of dataindependent acquisition MS data. Nat Biotechnol 32:219–223
SWATH-MS Protocols in Human Diseases
141