https://doi.org/10.1016/j.jprot.2017.10.
006
3. Hoffmann E, Machelart A, Song OR, Brodin P
(2018) Proteomics of mycobacterium infection: moving towards a better understanding
of pathogen-driven immunomodulation. Front
Immunol 9:86. https://doi.org/10.3389/
fimmu.2018.00086
4. Parra J, Marcoux J, Poncin I, Canaan S, Herrmann JL, Nigou J, Burlet-Schiltz O, Riviere M
(2017) Scrutiny of Mycobacterium tuberculosis
19 kDa antigen proteoforms provides new
insights in the lipoglycoprotein biogenesis paradigm. Sci Rep 7:43682. https://doi.org/10.
1038/srep43682
5. Kruh-Garcia NA, Wolfe LM, Chaisson LH,
Worodria WO, Nahid P, Schorey JS, Davis JL,
Dobos KM (2014) Detection of Mycobacterium tuberculosis peptides in the exosomes of
patients with active and latent M. tuberculosis
infection using MRM-MS. PLoS One 9(7):
e103811. https://doi.org/10.1371/journal.
pone.0103811
6. Kruh-Garcia NA, Wolfe LM, Dobos KM
(2015) Deciphering the role of exosomes in
tuberculosis.
Tuberculosis
(Edinb)
95
(1):26–30. https://doi.org/10.1016/j.tube.
2014.10.010
7. Mehaffy C, Dobos KM, Nahid P, Kruh-Garcia
NA (2017) Second generation multiple reaction monitoring assays for enhanced detection
of ultra-low abundance Mycobacterium tuberculosis peptides in human serum. Clin Proteomics
14:21.
https://doi.org/10.1186/
s12014-017-9156-y
8. Donnelly DP, Rawlins CM, DeHart CJ,
Fornelli L, Schachner LF, Lin Z, Lippens JL,
Aluri KC, Sarin R, Chen B, Lantz C, Jung W,
Johnson KR, Koller A, Wolff JJ, Campuzano
IDG, Auclair JR, Ivanov AR, Whitelegge JP,
Pasa-Tolic L, Chamot-Rooke J, Danis PO,
Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher
NL, Agar JN (2019) Best practices and benchmarks for intact protein analysis for top-down
mass spectrometry. Nat Methods 16
(7):587–594.
https://doi.org/10.1038/
s41592-019-0457-0
9. Binz PA, Barkovich R, Beavis RC, Creasy D,
Horn DM, Julian RK Jr, Seymour SL, Taylor
CF, Vandenbrouck Y (2008) Guidelines for
reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol 26
(8):862. https://doi.org/10.1038/nbt0808862
10. Martinez-Bartolome S, Deutsch EW, Binz PA,
Jones AR, Eisenacher M, Mayer G, Campos A,
Canals F, Bech-Serra JJ, Carrascal M, Gay M,
Paradela A, Navajas R, Marcilla M, Hernaez
ML, Gutierrez-Blazquez MD, Velarde LF,
Aloria K, Beaskoetxea J, Medina-Aunon JA,
Albar JP (2013) Guidelines for reporting quantitative mass spectrometry based experiments
in proteomics. J Proteome 95:84–88. https://
doi.org/10.1016/j.jprot.2013.02.026
11. Taylor CF (2006) Minimum reporting requirements for proteomics: a MIAPE primer. Proteomics 6(Suppl 2):39–44. https://doi.org/10.
1002/pmic.200600549
12. Taylor CF, Binz PA, Aebersold R, Affolter M,
Barkovich R, Deutsch EW, Horn DM,
Huhmer A, Kussmann M, Lilley K, Macht M,
Mann M, Muller D, Neubert TA, Nickson J,
Patterson SD, Raso R, Resing K, Seymour SL,
Tsugita A, Xenarios I, Zeng R, Julian RK Jr
(2008) Guidelines for reporting the use of
mass spectrometry in proteomics. Nat Biotechnol 26(8):860–861. https://doi.org/10.
1038/nbt0808-860
13. Taylor CF, Paton NW, Lilley KS, Binz PA,
Julian RK Jr, Jones AR, Zhu W, Apweiler R,
Aebersold R, Deutsch EW, Dunn MJ, Heck AJ,
Leitner A, Macht M, Mann M, Martens L,
Neubert TA, Patterson SD, Ping P, Seymour
SL, Souda P, Tsugita A, Vandekerckhove J,
Vondriska TM, Whitelegge JP, Wilkins MR,
Xenarios I, Yates JR 3rd, Hermjakob H
(2007) The minimum information about a
proteomics experiment (MIAPE). Nat Biotechnol 25(8):887–893. https://doi.org/10.
1038/nbt1329
14. Bisson GP, Mehaffy C, Broeckling C, Prenni J,
Rifat D, Lun DS, Burgos M, Weissman D, Karakousis PC, Dobos K (2012) Upregulation of
the phthiocerol dimycocerosate biosynthetic
pathway by rifampin-resistant, rpoB mutant
Mycobacterium tuberculosis. J Bacteriol 194
(23):6441–6452. https://doi.org/10.1128/
JB.01013-12
15. Nieto Ramirez LM, Mehaffy C, Dobos KM
(2019) Protein profile of different cellular fractions from Mycobacterium tuberculosis strains
after exposure to isoniazid. Data Brief
24:103953. https://doi.org/10.1016/j.dib.
2019.103953
16. Nieto RL, Mehaffy C, Dobos KM (2016)
Comparing isogenic strains of Beijing genotype
Mycobacterium tuberculosis after acquisition of
isoniazid resistance: a proteomics approach.
Proteomics 16(9):1376–1380. https://doi.
org/10.1002/pmic.201500403
17. Nieto RL, Mehaffy C, Islam MN, Fitzgerald B,
Belisle J, Prenni J, Dobos K (2018) Biochemical characterization of isoniazid-resistant Mycobacterium tuberculosis: can the analysis of clonal
strains reveal novel targetable pathways? Mol
Proteomic Analyses
547
006
3. Hoffmann E, Machelart A, Song OR, Brodin P
(2018) Proteomics of mycobacterium infection: moving towards a better understanding
of pathogen-driven immunomodulation. Front
Immunol 9:86. https://doi.org/10.3389/
fimmu.2018.00086
4. Parra J, Marcoux J, Poncin I, Canaan S, Herrmann JL, Nigou J, Burlet-Schiltz O, Riviere M
(2017) Scrutiny of Mycobacterium tuberculosis
19 kDa antigen proteoforms provides new
insights in the lipoglycoprotein biogenesis paradigm. Sci Rep 7:43682. https://doi.org/10.
1038/srep43682
5. Kruh-Garcia NA, Wolfe LM, Chaisson LH,
Worodria WO, Nahid P, Schorey JS, Davis JL,
Dobos KM (2014) Detection of Mycobacterium tuberculosis peptides in the exosomes of
patients with active and latent M. tuberculosis
infection using MRM-MS. PLoS One 9(7):
e103811. https://doi.org/10.1371/journal.
pone.0103811
6. Kruh-Garcia NA, Wolfe LM, Dobos KM
(2015) Deciphering the role of exosomes in
tuberculosis.
Tuberculosis
(Edinb)
95
(1):26–30. https://doi.org/10.1016/j.tube.
2014.10.010
7. Mehaffy C, Dobos KM, Nahid P, Kruh-Garcia
NA (2017) Second generation multiple reaction monitoring assays for enhanced detection
of ultra-low abundance Mycobacterium tuberculosis peptides in human serum. Clin Proteomics
14:21.
https://doi.org/10.1186/
s12014-017-9156-y
8. Donnelly DP, Rawlins CM, DeHart CJ,
Fornelli L, Schachner LF, Lin Z, Lippens JL,
Aluri KC, Sarin R, Chen B, Lantz C, Jung W,
Johnson KR, Koller A, Wolff JJ, Campuzano
IDG, Auclair JR, Ivanov AR, Whitelegge JP,
Pasa-Tolic L, Chamot-Rooke J, Danis PO,
Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher
NL, Agar JN (2019) Best practices and benchmarks for intact protein analysis for top-down
mass spectrometry. Nat Methods 16
(7):587–594.
https://doi.org/10.1038/
s41592-019-0457-0
9. Binz PA, Barkovich R, Beavis RC, Creasy D,
Horn DM, Julian RK Jr, Seymour SL, Taylor
CF, Vandenbrouck Y (2008) Guidelines for
reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol 26
(8):862. https://doi.org/10.1038/nbt0808862
10. Martinez-Bartolome S, Deutsch EW, Binz PA,
Jones AR, Eisenacher M, Mayer G, Campos A,
Canals F, Bech-Serra JJ, Carrascal M, Gay M,
Paradela A, Navajas R, Marcilla M, Hernaez
ML, Gutierrez-Blazquez MD, Velarde LF,
Aloria K, Beaskoetxea J, Medina-Aunon JA,
Albar JP (2013) Guidelines for reporting quantitative mass spectrometry based experiments
in proteomics. J Proteome 95:84–88. https://
doi.org/10.1016/j.jprot.2013.02.026
11. Taylor CF (2006) Minimum reporting requirements for proteomics: a MIAPE primer. Proteomics 6(Suppl 2):39–44. https://doi.org/10.
1002/pmic.200600549
12. Taylor CF, Binz PA, Aebersold R, Affolter M,
Barkovich R, Deutsch EW, Horn DM,
Huhmer A, Kussmann M, Lilley K, Macht M,
Mann M, Muller D, Neubert TA, Nickson J,
Patterson SD, Raso R, Resing K, Seymour SL,
Tsugita A, Xenarios I, Zeng R, Julian RK Jr
(2008) Guidelines for reporting the use of
mass spectrometry in proteomics. Nat Biotechnol 26(8):860–861. https://doi.org/10.
1038/nbt0808-860
13. Taylor CF, Paton NW, Lilley KS, Binz PA,
Julian RK Jr, Jones AR, Zhu W, Apweiler R,
Aebersold R, Deutsch EW, Dunn MJ, Heck AJ,
Leitner A, Macht M, Mann M, Martens L,
Neubert TA, Patterson SD, Ping P, Seymour
SL, Souda P, Tsugita A, Vandekerckhove J,
Vondriska TM, Whitelegge JP, Wilkins MR,
Xenarios I, Yates JR 3rd, Hermjakob H
(2007) The minimum information about a
proteomics experiment (MIAPE). Nat Biotechnol 25(8):887–893. https://doi.org/10.
1038/nbt1329
14. Bisson GP, Mehaffy C, Broeckling C, Prenni J,
Rifat D, Lun DS, Burgos M, Weissman D, Karakousis PC, Dobos K (2012) Upregulation of
the phthiocerol dimycocerosate biosynthetic
pathway by rifampin-resistant, rpoB mutant
Mycobacterium tuberculosis. J Bacteriol 194
(23):6441–6452. https://doi.org/10.1128/
JB.01013-12
15. Nieto Ramirez LM, Mehaffy C, Dobos KM
(2019) Protein profile of different cellular fractions from Mycobacterium tuberculosis strains
after exposure to isoniazid. Data Brief
24:103953. https://doi.org/10.1016/j.dib.
2019.103953
16. Nieto RL, Mehaffy C, Dobos KM (2016)
Comparing isogenic strains of Beijing genotype
Mycobacterium tuberculosis after acquisition of
isoniazid resistance: a proteomics approach.
Proteomics 16(9):1376–1380. https://doi.
org/10.1002/pmic.201500403
17. Nieto RL, Mehaffy C, Islam MN, Fitzgerald B,
Belisle J, Prenni J, Dobos K (2018) Biochemical characterization of isoniazid-resistant Mycobacterium tuberculosis: can the analysis of clonal
strains reveal novel targetable pathways? Mol
Proteomic Analyses
547