2015
DOI: 10.1002/prca.201400164
|View full text |Cite
|
Sign up to set email alerts
|

Abstract: Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identif… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
3
1

Citation Types

1
261
0

Year Published

2015
2015
2022
2022

Publication Types

Select...
9
1

Relationship

0
10

Authors

Journals

citations
Cited by 311 publications
(262 citation statements)
references
References 53 publications
1
261
0
Order By: Relevance
“…Today, mass-spectrometry(MS)-based shotgun proteomics is reaching a level of maturity that makes it a powerful and broadly applicable technology for researchers in biology and biomedical sciences 1,2 . Consistent automatic processing of spectra and the identification of peptides, proteins and posttranslational modifications (PTMs) with the help of search engines [3][4][5][6][7] and reliable workflows have become standard computational tasks for which satisfactory solutions exist for single studies as well as communitywide data reanalysis [8][9][10] . Sophisticated computational proteomics platforms enable the quantification of proteins and PTMs over many samples in a large variety of labeling or label-free formats 11 .…”
mentioning
confidence: 99%
“…Today, mass-spectrometry(MS)-based shotgun proteomics is reaching a level of maturity that makes it a powerful and broadly applicable technology for researchers in biology and biomedical sciences 1,2 . Consistent automatic processing of spectra and the identification of peptides, proteins and posttranslational modifications (PTMs) with the help of search engines [3][4][5][6][7] and reliable workflows have become standard computational tasks for which satisfactory solutions exist for single studies as well as communitywide data reanalysis [8][9][10] . Sophisticated computational proteomics platforms enable the quantification of proteins and PTMs over many samples in a large variety of labeling or label-free formats 11 .…”
mentioning
confidence: 99%
“…Recently, Trans-Proteomic Pipeline (TPP) has been enabled with Amazon Web Services cloud computing to speed up data analysis pipeline at a very low cost 23 . An Automated Proteomics Pipeline (APP) was also implemented using Java to integrate a set of tools and allow distributed execution on most available computers with minimal setup 24 .…”
Section: Resultsmentioning
confidence: 99%
“…Thus, the first pipelines emerged, including viz., the trans-proteomic pipeline (TPP) 21,22 , OpenMS 23 , MaxQuant 24,25 , and PatternLab for proteomics 26 , each having its own set of advantages and limitations. In what followed, SkyLine 27 and Galaxy 28 emerged to overcome some of the limitations of the aforementioned tools at the time.…”
Section: Introductionmentioning
confidence: 99%