A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

Marlon D.M. Santos; Diogo B. Lima; André R.F. Silva; Louise U. Kurt; Milan A. Clasen; Antônio F.M. Pinto; James J. Moresco; John R. Yates; Priscila Aquino; Valmir C. Barbosa; Juliana S.G. Fischer; Paulo C. Carvalho

doi:10.1016/j.jprot.2019.04.021

A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

Marlon D.M. Santos, Diogo B. Lima, André R.F. Silva, Louise U. Kurt, Milan A. Clasen, Antônio F.M. Pinto, James J. Moresco, John R. Yates, Priscila Aquino, Valmir C. Barbosa, Juliana S.G. Fischer, Paulo C. Carvalho

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.

Original language	English (US)
Article number	103371
Journal	Journal of Proteomics
Volume	202
DOIs	https://doi.org/10.1016/j.jprot.2019.04.021
State	Published - Jun 30 2019
Externally published	Yes

Keywords

Bioinformatics
Differential proteomics
Dimethyl
PatternLab

ASJC Scopus subject areas

Biophysics
Biochemistry

Access to Document

10.1016/j.jprot.2019.04.021

Cite this

Santos, M. D. M., Lima, D. B., Silva, A. R. F., Kurt, L. U., Clasen, M. A., Pinto, A. F. M., Moresco, J. J., Yates, J. R., Aquino, P., Barbosa, V. C., Fischer, J. S. G., & Carvalho, P. C. (2019). A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics. Journal of Proteomics, 202, Article 103371. https://doi.org/10.1016/j.jprot.2019.04.021

@article{a2b9270cb09847758a7ec227f9f25e0b,

title = "A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics",

abstract = "We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.",

keywords = "Bioinformatics, Differential proteomics, Dimethyl, PatternLab",

author = "Santos, {Marlon D.M.} and Lima, {Diogo B.} and Silva, {Andr{\'e} R.F.} and Kurt, {Louise U.} and Clasen, {Milan A.} and Pinto, {Ant{\^o}nio F.M.} and Moresco, {James J.} and Yates, {John R.} and Priscila Aquino and Barbosa, {Valmir C.} and Fischer, {Juliana S.G.} and Carvalho, {Paulo C.}",

note = "Funding Information: This work was supported by Fiocruz, the Brazilian National Research Council (CNPq)and Graduate Studies Agency (CAPES), National Institute of General Medical Sciences (8 P41 GM103533), and a FAPERJ BBP grant. Funding Information: This work was supported by Fiocruz, the Brazilian National Research Council (CNPq) and Graduate Studies Agency (CAPES) , National Institute of General Medical Sciences ( 8 P41 GM103533 ), and a FAPERJ BBP grant. Publisher Copyright: {\textcopyright} 2019",

year = "2019",

month = jun,

day = "30",

doi = "10.1016/j.jprot.2019.04.021",

language = "English (US)",

volume = "202",

journal = "Journal of Proteomics",

issn = "1874-3919",

publisher = "Elsevier",

}

TY - JOUR

T1 - A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

AU - Santos, Marlon D.M.

AU - Lima, Diogo B.

AU - Silva, André R.F.

AU - Kurt, Louise U.

AU - Clasen, Milan A.

AU - Pinto, Antônio F.M.

AU - Moresco, James J.

AU - Yates, John R.

AU - Aquino, Priscila

AU - Barbosa, Valmir C.

AU - Fischer, Juliana S.G.

AU - Carvalho, Paulo C.

N1 - Funding Information: This work was supported by Fiocruz, the Brazilian National Research Council (CNPq)and Graduate Studies Agency (CAPES), National Institute of General Medical Sciences (8 P41 GM103533), and a FAPERJ BBP grant. Funding Information: This work was supported by Fiocruz, the Brazilian National Research Council (CNPq) and Graduate Studies Agency (CAPES) , National Institute of General Medical Sciences ( 8 P41 GM103533 ), and a FAPERJ BBP grant. Publisher Copyright: © 2019

PY - 2019/6/30

Y1 - 2019/6/30

N2 - We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.

AB - We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.

KW - Bioinformatics

KW - Differential proteomics

KW - Dimethyl

KW - PatternLab

UR - http://www.scopus.com/inward/record.url?scp=85065536909&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85065536909&partnerID=8YFLogxK

U2 - 10.1016/j.jprot.2019.04.021

DO - 10.1016/j.jprot.2019.04.021

M3 - Article

C2 - 31034900

AN - SCOPUS:85065536909

SN - 1874-3919

VL - 202

JO - Journal of Proteomics

JF - Journal of Proteomics

M1 - 103371

ER -

A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this