2013
DOI: 10.1074/mcp.o113.028258
|View full text |Cite
|
Sign up to set email alerts
|

High-throughput Database Search and Large-scale Negative Polarity Liquid Chromatography–Tandem Mass Spectrometry with Ultraviolet Photodissociation for Complex Proteomic Samples

Abstract: The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new … Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
1
1
1
1

Citation Types

3
86
0

Year Published

2014
2014
2018
2018

Publication Types

Select...
6
1

Relationship

2
5

Authors

Journals

citations
Cited by 34 publications
(89 citation statements)
references
References 48 publications
(55 reference statements)
3
86
0
Order By: Relevance
“…GluC, which cleaves C-terminal to glutamic acid (and at slower rates, aspartic acid (60)), enabled the identification of more than 4,200 unique peptides, a greater than 7-fold increase over our previous NETD results with the enzyme (24). These peptides mapped back to 857 proteins, which also outmatches the best results achieved to date for any protease in negative mode approaches (25). Chymotrypsin and AspN performed considerably well, too, illustrating the flexibility AI-NETD can offer for peptide anion characterization.…”
Section: Multiple Proteases For Single-shot Negative Modementioning
confidence: 57%
See 3 more Smart Citations
“…GluC, which cleaves C-terminal to glutamic acid (and at slower rates, aspartic acid (60)), enabled the identification of more than 4,200 unique peptides, a greater than 7-fold increase over our previous NETD results with the enzyme (24). These peptides mapped back to 857 proteins, which also outmatches the best results achieved to date for any protease in negative mode approaches (25). Chymotrypsin and AspN performed considerably well, too, illustrating the flexibility AI-NETD can offer for peptide anion characterization.…”
Section: Multiple Proteases For Single-shot Negative Modementioning
confidence: 57%
“…Negative mode approaches for the characterization of peptide anions offer a valuable dimension to proteomic analyses (21,24,25,66), especially as biologically relevant posttranslational modifications and other analytes that pose challenges to canonical positive mode techniques continue to emerge (7,53,(67)(68)(69)(70)(71)(72). Platforms for shotgun analysis of complex mixtures of peptide anions have been introduced, most notably using UVPD and NETD; however, these approaches have yet to provide considerable proteomic depth (fewer than ϳ800 total proteins identified in a given experiment), restricting the degree to which peptide anion characterization can benefit the proteomic community.…”
Section: Discussionmentioning
confidence: 99%
See 2 more Smart Citations
“…7 Ultraviolet photodissociation (UVPD) is a more recent activation technique that has gained traction and has been applied to a broad range of proteomics applications. [8][9][10][11][12][13][14][15] In particular, UVPD using 193 nm photons generates very rich fragmentation patterns, 10,15 providing high sequence coverage of peptides.…”
Section: Introductionmentioning
confidence: 99%