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Characterization of LysargiNase peptide fragmentation

ABSTRACT: Comparison of Lyarginase and tryptic digests with regard to fragmentation behaviour/effect of inclusing a ion in peptide assignment scoring

INSTRUMENT(S): QSTAR

ORGANISM(S): Escherichia Coli

SUBMITTER: Pitter Huesgen

LAB HEAD: Christopher M Overall

PROVIDER: PXD001378 | Pride | 2014-12-16

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	37144Aions.xls	Xls
	37144ET.aions.pep.xml	Pepxml
	37144ET.mzXML.gz	Mzxml
	37144ET.regular.pep.xml	Pepxml
	37144ETaion.xls	Xls

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Publications

LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification.

Huesgen Pitter F PF Lange Philipp F PF Rogers Lindsay D LD Solis Nestor N Eckhard Ulrich U Kleifeld Oded O Goulas Theodoros T Gomis-Rüth F Xavier FX Overall Christopher M CM

Nature methods 20141124 1

To improve proteome coverage and protein C-terminal identification, we characterized the Methanosarcina acetivorans thermophilic proteinase LysargiNase, which cleaves before lysine and arginine up to 55 °C. Unlike trypsin, LysargiNase-generated peptides had N-terminal lysine or arginine residues and fragmented with b ion-dominated spectra. This improved protein C terminal-peptide identification and several arginine-rich phosphosite assignments. Notably, cleavage also occurred at methylated or di ...[more]

PMID: 25419962

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LysargiNase cleavage specificity characterization

Project description:Determination of LysargiNase and tryptic ckeavage efficiency at dimethylated Lys residues

2014-12-16 | PXD001379 | Pride

Specificity profiling of LysargiNase in comparison to trypsin

Project description:Protease cleavage site preferences of LysargiNase (former name: ulilysin) and trypsin were tested using proteome-derived peptide libraries (Schilling et al Nature Protocols 2011)

2014-12-16 | PXD001122 | Pride

Mirroring the charged termini; ETD/HCD fragmentation characteristics of LysargiNase and tryptic peptides and their benefits for peptide sequencing in proteomics

Project description:A key step in proteomics is the digestion of proteins into peptides, so far largely done by using trypsin. Tryptic digestion leads to peptides that in ESI-MS attain predominantly two charges, via protonation at the free N-terminus and at the C-terminal basic residue Arginine or Lysine. These peptides can be readily sequenced and identified by collision-induced dissociation (CID) or higher-energy collisional dissociation (HCD), as the fragmentation rules are well understood. Here we explore the trypsin mirror protease, LysargiNase, which cleaves equally specifically at Arg and Lys, albeit at the N-terminal end. The resulting peptides are therefore practically tryptic-alike in length and sequence, except that the two charges are now both positioned at the N-terminus. We compare the chromatographic separation properties, gas phase fragmentation behavior and (phospho)proteome sequence coverage of tryptic and LysargiNase peptides using electron-transfer dissociation (ETD), and for comparison HCD. We find that tryptic and LysargiNase peptides fragment nearly as mirror images. For LysargiNase predominantly N-terminal peptide ions (c-ions/ETD, b-ions/HCD) are formed, whereas for trypsin C-terminal fragment ions dominate (z-ions/ETD, y-ions/HCD). Especially during ETD LysargiNase peptides fragment into low-complexity, but information rich sequence ladders. We observe that trypsin and LysargiNase chart distinct parts of the (phospho)proteome. Therefore, we conclude that the collective use LysargiNase and Trypsin will benefit a more in-depth and reliable analysis of (phospho)proteomes.

2016-12-02 | PXD004447 | Pride

Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF)

Project description:Data independent acquisition modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions in each window are sampled. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current in m/z and mobility windows. We extend an established targeted data extraction workflow by including the ion mobility dimension for both signal extraction and scoring, thereby increasing the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a very high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.

2020-12-17 | PXD017703 | Pride

Basic Strong Cation Exchange Chromatography, BaSCX, a Highly Efficient Approach for C-Terminomic Studies Using LysargiNase Digestion

Project description:Decoding protein C-termini is a challenging task in protein chemistry using conventional chemical/enzymatic approaches. With the rapid development in modern mass spectrometer, many advanced mass spectrometry (MS) based protein C-termini analysis approaches have been established. Although great progresses have been continually achieved, it is still nec-essary to develop more efficient approaches in order to discover a proteome-scale protein C-termini (C-terminome), and consequently to help understand their biological functions. In this report, we describe a simple method, termed BaSCX, for basic strong cation exchange chromatography, to study C-terminome.

2020-02-28 | PXD016317 | Pride

Characterization of LysargiNase for use in phosphoproteomics experiments, part 1

Project description:Use of parallel digest with LysargiNase (former name: ulilysin) and trypsin to cover complementary phosphosites / characterization of phospho-motifs preferentially identified by each protease

2014-12-16 | PXD001121 | Pride

Characterization of LysargiNase for use in phosphoproteomics experiments, partII

Project description:Use of parallel digest with LysargiNase and trypsin to cover complementary phosphosites / characterization of phospho-motifs preferentially identified by each protease

2014-12-16 | PXD001114 | Pride

Monoclonal antibody LC-MS/MS - Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics

Project description:Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics

2019-01-11 | PXD008690 | Pride

Yeast mirror LC-MS/MS - Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics

Project description:Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics

2019-01-11 | PXD011562 | Pride

E. coli mirror LC-MS/MS - Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics

Project description:Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomicsPrecision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics

2019-01-11 | PXD008688 | Pride

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