PXD004447

PXD004447 is an original dataset announced via ProteomeXchange.

Title	Mirroring the charged termini; ETD/HCD fragmentation characteristics of LysargiNase and tryptic peptides and their benefits for peptide sequencing in proteomics
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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:48:47.493.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liana Tsiatsiani
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-27 06:14:48	ID requested
1	2016-12-02 07:34:38	announced
2	2017-01-24 03:06:44	announced	Updated publication reference for PubMed record(s): 28111955.
⏵ 3	2023-11-14 08:48:48	announced	2023-11-14: Updated project metadata.

Tsiatsiani L, Giansanti P, Scheltema RA, van den Toorn H, Overall CM, Altelaar AF, Heck AJ, K/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics. J Proteome Res, 16(2):852-861(2017) [pubmed]

curator keyword: Technical

submitter keyword: fragmentation,ETD, HCD, LysargiNase, orbitrap, phosphoproteomics, trypsin

Albert JR Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands
contact email	A.J.R.Heck@uu.nl
lab head
Liana Tsiatsiani
contact affiliation	Dr. Ir.
contact email	l.tsiatsiani@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004447
     1. Label: PRIDE project
     2. Name: Mirroring the charged termini; ETD/HCD fragmentation characteristics of LysargiNase and tryptic peptides and their benefits for peptide sequencing in proteomics