Cell Proteomics 17(9):1685–1701. https://
doi.org/10.1074/mcp.RA118.000821
18. Duncan C, Jamieson FB, Troudt J, Izzo L,
Bielefeldt-Ohmann H, Izzo A, Mehaffy C
(2017) Whole transcriptomic and proteomic
analyses of an isogenic M. tuberculosis clinical
strain with a naturally occurring 15 kb genomic
deletion. PLoS One 12(6):e0179996. https://
doi.org/10.1371/journal.pone.0179996
19. Mehaffy C, Hess A, Prenni JE, Mathema B,
Kreiswirth B, Dobos KM (2010) Descriptive
proteomic analysis shows protein variability
between closely related clinical isolates of Mycobacterium
tuberculosis.
Proteomics
10:1966–1984.
https://doi.org/10.1002/
pmic.200900836
20. Bereman MS, Beri J, Sharma V, Nathe C,
Eckels J, MacLean B, MacCoss MJ (2016) An
automated pipeline to monitor system performance in liquid chromatography-tandem mass
spectrometry proteomic experiments. J Proteome Res 15(12):4763–4769. https://doi.org/
10.1021/acs.jproteome.6b00744
21. Bereman MS, Johnson R, Bollinger J, Boss Y,
Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ (2014) Implementation of statistical
process control for proteomic experiments via
LC MS/MS. J Am Soc Mass Spectrom 25
(4):581–587.
https://doi.org/10.1007/
s13361-013-0824-5
22. Bielow C, Mastrobuoni G, Kempa S (2016)
Proteomics quality control: quality control
software for MaxQuant results. J Proteome
Res 15(3):777–787. https://doi.org/10.
1021/acs.jproteome.5b00780
23. Dogu E, Mohammad-Taheri S, Abbatiello SE,
Bereman MS, MacLean B, Schilling B, Vitek O
(2017) MSstatsQC: longitudinal system suitability monitoring and quality control for targeted proteomic experiments. Mol Cell
Proteomics 16(7):1335–1347. https://doi.
org/10.1074/mcp.M116.064774
24. Taverner T, Karpievitch YV, Polpitiya AD,
Brown JN, Dabney AR, Anderson GA, Smith
RD (2012) DanteR: an extensible R-based tool
for quantitative analysis of -omics data. Bioinformatics 28(18):2404–2406. https://doi.
org/10.1093/bioinformatics/bts449
25. Bourmaud A, Gallien S, Domon B (2015) A
quality control of proteomic experiments based
on multiple isotopologous internal standards.
EuPA Open Proteom 8:16–21. https://doi.
org/10.1016/j.euprot.2015.07.010
26. Perez-Riverol Y, Alpi E, Wang R,
Hermjakob H, Vizcaino JA (2015) Making
proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 15(5–6):930–949. https://
doi.org/10.1002/pmic.201400302
27. Riffle M, Eng JK (2009) Proteomics data repositories.
Proteomics
9(20):4653–4663.
https://doi.org/10.1002/pmic.200900216
28. Demeure K, Quinton L, Gabelica V, De Pauw
E (2007) Rational selection of the optimum
MALDI matrix for top-down proteomics by
in-source
decay.
Anal
Chem
79
(22):8678–8685. https://doi.org/10.1021/
ac070849z
29. Guray MZ, Zheng S, Doucette AA (2017)
Mass spectrometry of intact proteins reveals
+98 u chemical artifacts following precipitation
in acetone. J Proteome Res 16(2):889–897.
https://doi.org/10.1021/acs.jproteome.
6b00841
30. Link AJ, LaBaer J (2011) Trichloroacetic acid
(TCA) precipitation of proteins. Cold Spring
Harb Protoc 2011(8):993–994. https://doi.
org/10.1101/pdb.prot5651
31. Doucette AA, Vieira DB, Orton DJ, Wall MJ
(2014) Resolubilization of precipitated intact
membrane proteins with cold formic acid for
analysis by mass spectrometry. J Proteome Res
13(12):6001–6012.
https://doi.org/10.
1021/pr500864a
32. Wessel D, Flugge UI (1984) A method for the
quantitative recovery of protein in dilute solution in the presence of detergents and lipids.
Anal Biochem 138(1):141–143. https://doi.
org/10.1016/0003-2697(84)90782-6
548
Carolina Mehaffy et al.
doi.org/10.1074/mcp.RA118.000821
18. Duncan C, Jamieson FB, Troudt J, Izzo L,
Bielefeldt-Ohmann H, Izzo A, Mehaffy C
(2017) Whole transcriptomic and proteomic
analyses of an isogenic M. tuberculosis clinical
strain with a naturally occurring 15 kb genomic
deletion. PLoS One 12(6):e0179996. https://
doi.org/10.1371/journal.pone.0179996
19. Mehaffy C, Hess A, Prenni JE, Mathema B,
Kreiswirth B, Dobos KM (2010) Descriptive
proteomic analysis shows protein variability
between closely related clinical isolates of Mycobacterium
tuberculosis.
Proteomics
10:1966–1984.
https://doi.org/10.1002/
pmic.200900836
20. Bereman MS, Beri J, Sharma V, Nathe C,
Eckels J, MacLean B, MacCoss MJ (2016) An
automated pipeline to monitor system performance in liquid chromatography-tandem mass
spectrometry proteomic experiments. J Proteome Res 15(12):4763–4769. https://doi.org/
10.1021/acs.jproteome.6b00744
21. Bereman MS, Johnson R, Bollinger J, Boss Y,
Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ (2014) Implementation of statistical
process control for proteomic experiments via
LC MS/MS. J Am Soc Mass Spectrom 25
(4):581–587.
https://doi.org/10.1007/
s13361-013-0824-5
22. Bielow C, Mastrobuoni G, Kempa S (2016)
Proteomics quality control: quality control
software for MaxQuant results. J Proteome
Res 15(3):777–787. https://doi.org/10.
1021/acs.jproteome.5b00780
23. Dogu E, Mohammad-Taheri S, Abbatiello SE,
Bereman MS, MacLean B, Schilling B, Vitek O
(2017) MSstatsQC: longitudinal system suitability monitoring and quality control for targeted proteomic experiments. Mol Cell
Proteomics 16(7):1335–1347. https://doi.
org/10.1074/mcp.M116.064774
24. Taverner T, Karpievitch YV, Polpitiya AD,
Brown JN, Dabney AR, Anderson GA, Smith
RD (2012) DanteR: an extensible R-based tool
for quantitative analysis of -omics data. Bioinformatics 28(18):2404–2406. https://doi.
org/10.1093/bioinformatics/bts449
25. Bourmaud A, Gallien S, Domon B (2015) A
quality control of proteomic experiments based
on multiple isotopologous internal standards.
EuPA Open Proteom 8:16–21. https://doi.
org/10.1016/j.euprot.2015.07.010
26. Perez-Riverol Y, Alpi E, Wang R,
Hermjakob H, Vizcaino JA (2015) Making
proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 15(5–6):930–949. https://
doi.org/10.1002/pmic.201400302
27. Riffle M, Eng JK (2009) Proteomics data repositories.
Proteomics
9(20):4653–4663.
https://doi.org/10.1002/pmic.200900216
28. Demeure K, Quinton L, Gabelica V, De Pauw
E (2007) Rational selection of the optimum
MALDI matrix for top-down proteomics by
in-source
decay.
Anal
Chem
79
(22):8678–8685. https://doi.org/10.1021/
ac070849z
29. Guray MZ, Zheng S, Doucette AA (2017)
Mass spectrometry of intact proteins reveals
+98 u chemical artifacts following precipitation
in acetone. J Proteome Res 16(2):889–897.
https://doi.org/10.1021/acs.jproteome.
6b00841
30. Link AJ, LaBaer J (2011) Trichloroacetic acid
(TCA) precipitation of proteins. Cold Spring
Harb Protoc 2011(8):993–994. https://doi.
org/10.1101/pdb.prot5651
31. Doucette AA, Vieira DB, Orton DJ, Wall MJ
(2014) Resolubilization of precipitated intact
membrane proteins with cold formic acid for
analysis by mass spectrometry. J Proteome Res
13(12):6001–6012.
https://doi.org/10.
1021/pr500864a
32. Wessel D, Flugge UI (1984) A method for the
quantitative recovery of protein in dilute solution in the presence of detergents and lipids.
Anal Biochem 138(1):141–143. https://doi.
org/10.1016/0003-2697(84)90782-6
548
Carolina Mehaffy et al.