Abstract
Traditional bottom-up mass spectrometry-based proteomics relies on the use of an enzyme, often trypsin, to generate small peptides (typically < 25 amino acids long). In top-down proteomics, proteins remain intact and are directly measured within the mass spectrometer. This technique, while inherently simpler than bottom-up proteomics, generates data which must be processed and analyzed using software tools “purpose-built” for the job. In this chapter, we will show the analysis of intact protein spectra through deconvolution, deisotoping, and searching with ProSight Lite, a free, vendor-agnostic tool for the analysis of top-down mass spectrometry data. We will illustrate with two examples of intact protein fragmentation spectra and discuss the iterative use of the software to characterize proteoforms and discover the sites of post-translational modifications.
| Original language | English (US) |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Publisher | Humana Press Inc |
| Pages | 381-394 |
| Number of pages | 14 |
| DOIs | |
| State | Published - Jan 1 2017 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 1558 |
| ISSN (Print) | 1064-3745 |
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Keywords
- Bioinformatics
- Intact protein
- Mass spectrometry
- ProSight lite
- Proteomics
- Top-down
ASJC Scopus subject areas
- Molecular Biology
- Genetics
Cite this
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Bioinformatics analysis of top-down mass spectrometry data with proSight lite. / Dehart, Caroline J.; Fellers, Ryan T.; Fornelli, Luca; Kelleher, Neil L.; Thomas, Paul M.
Methods in Molecular Biology. Humana Press Inc, 2017. p. 381-394 (Methods in Molecular Biology; Vol. 1558).Research output: Chapter in Book/Report/Conference proceeding › Chapter
TY - CHAP
T1 - Bioinformatics analysis of top-down mass spectrometry data with proSight lite
AU - Dehart, Caroline J.
AU - Fellers, Ryan T.
AU - Fornelli, Luca
AU - Kelleher, Neil L.
AU - Thomas, Paul M.
PY - 2017/1/1
Y1 - 2017/1/1
N2 - Traditional bottom-up mass spectrometry-based proteomics relies on the use of an enzyme, often trypsin, to generate small peptides (typically < 25 amino acids long). In top-down proteomics, proteins remain intact and are directly measured within the mass spectrometer. This technique, while inherently simpler than bottom-up proteomics, generates data which must be processed and analyzed using software tools “purpose-built” for the job. In this chapter, we will show the analysis of intact protein spectra through deconvolution, deisotoping, and searching with ProSight Lite, a free, vendor-agnostic tool for the analysis of top-down mass spectrometry data. We will illustrate with two examples of intact protein fragmentation spectra and discuss the iterative use of the software to characterize proteoforms and discover the sites of post-translational modifications.
AB - Traditional bottom-up mass spectrometry-based proteomics relies on the use of an enzyme, often trypsin, to generate small peptides (typically < 25 amino acids long). In top-down proteomics, proteins remain intact and are directly measured within the mass spectrometer. This technique, while inherently simpler than bottom-up proteomics, generates data which must be processed and analyzed using software tools “purpose-built” for the job. In this chapter, we will show the analysis of intact protein spectra through deconvolution, deisotoping, and searching with ProSight Lite, a free, vendor-agnostic tool for the analysis of top-down mass spectrometry data. We will illustrate with two examples of intact protein fragmentation spectra and discuss the iterative use of the software to characterize proteoforms and discover the sites of post-translational modifications.
KW - Bioinformatics
KW - Intact protein
KW - Mass spectrometry
KW - ProSight lite
KW - Proteomics
KW - Top-down
UR - http://www.scopus.com/inward/record.url?scp=85011551479&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85011551479&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-6783-4_18
DO - 10.1007/978-1-4939-6783-4_18
M3 - Chapter
C2 - 28150248
AN - SCOPUS:85011551479
T3 - Methods in Molecular Biology
SP - 381
EP - 394
BT - Methods in Molecular Biology
PB - Humana Press Inc
ER -