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.jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117 J+Am+Soc+Mass+Spectrom
2015 ; 26
(11
): 1820-6
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From raw data to biological discoveries: a computational analysis pipeline for
mass spectrometry-based proteomics
#MMPMID26002791
Lavallée-Adam M
; Park SK
; Martínez-Bartolomé S
; He L
; Yates JR 3rd
J Am Soc Mass Spectrom
2015[Nov]; 26
(11
): 1820-6
PMID26002791
show ga
In the last two decades, computational tools for mass spectrometry-based
proteomics data analysis have evolved from a few stand-alone software solutions
serving specific goals, such as the identification of amino acid sequences based
on mass spectrometry spectra, to large-scale complex pipelines integrating
multiple computer programs to solve a collection of problems. This software
evolution has been mostly driven by the appearance of novel technologies that
allowed the community to tackle complex biological problems, such as the
identification of proteins that are differentially expressed in two samples under
different conditions. The achievement of such objectives requires a large suite
of programs to analyze the intricate mass spectrometry data. Our laboratory
addresses complex proteomics questions by producing and using algorithms and
software packages. Our current computational pipeline includes, among other
things, tools for mass spectrometry raw data processing, peptide and protein
identification and quantification, post-translational modification analysis, and
protein functional enrichment analysis. In this paper, we describe a suite of
software packages we have developed to process mass spectrometry-based proteomics
data and we highlight some of the new features of previously published programs
as well as tools currently under development. Graphical Abstract ?.