Dataset Information

Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows

ABSTRACT: This study presents a comparative analysis of three LysC endopeptidases homologues from Achromobacter lyticus, Pseudomonas aeruginosa, and Lysobacter enzymogenes for mass spectrometry-based proteomics. Utilizing a protein aggregation capture (PAC) workflow with HeLa cell lysate, we assessed the enzymes' cleavage specificity, digestion efficiency, and performance across various experimental conditions. Results showed that while all three LysC homologues exhibited high cleavage specificity at lysine residues, A. lyticus LysC outperformed the two others with its superior peptide identification, digestion efficiency, and protein coverage, especially at shorter digestion times. Combination of A. lyticus LysC and Trypsin demonstrated the importance of employing LysC for significantly minimizing missed cleavage rates in tryptic digests. This study underscores A. lyticus LysC's potential as an optimal choice for enhancing mass spectrometry-based proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell Of Cervix

DISEASE(S): Cervix Carcinoma

SUBMITTER: Leander Van der Hoeven

LAB HEAD: Jesper Velgaard Olsen

PROVIDER: PXD068827 | Pride | 2026-02-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	202405022_EXPL5_EVO10_60SPD_TSB_SA_LysC100_TrypsinON_01.raw	Raw
	202405022_EXPL5_EVO10_60SPD_TSB_SA_LysC100_TrypsinON_02.raw	Raw
	202405022_EXPL5_EVO10_60SPD_TSB_SA_LysC100_TrypsinON_03.raw	Raw
	202405022_EXPL5_EVO10_60SPD_TSB_SA_LysC100_TrypsinON_04.raw	Raw
	202405022_EXPL5_EVO10_60SPD_TSB_SA_LysC200_TrypsinON_01.raw	Raw

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Publications

Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows.

van der Hoeven Leander Roeland LR Lechner Maico M Hernandez-Rollan Cristina C Batth Tanveer Singh TS Olsen Jesper V JV

Journal of proteome research 20251222 2

This study presents a comparative analysis of three LysC endopeptidase homologues from Achromobacter lyticus (A. lyticus),Pseudomonas aeruginosa and Lysobacter enzymogenes for mass spectrometry-based proteomics. Utilizing a protein aggregation capture workflow with HeLa cell lysates, we assessed the enzymes' cleavage specificity, digestion efficiency, and performance across various experimental conditions. Results showed that while all three LysC homologues exhibited ...[more]

PMID: 41428240

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Project description:Dear Sir or Madam, we report an in-depth proteogenomics study of Helicobacter pylori strain 26695 and provide the supporting MS data via ProteomExchange. The study includes 2 biological replicates with 6 different datasets: G1: in-gel digestion with trypsin, replicate 1 G2: in-gel digestion with trypsin, replicate 2 T1: SEC fractionation of low molecular weight (LMW) proteins and subsequent trypsin digestion, replicate 1 T2: SEC fractionation of LMW proteins and subsequent trypsin digestion, replicate 2 A1: SEC fractionation of LMW proteins and subsequent AspN digestion, replicate 1 A2: SEC fractionation of LMW proteins and subsequent AspN digestion, replicate 2 L1: SEC fractionation of LMW proteins and subsequent LysC digestion, replicate 1 L2: SEC fractionation of LMW proteins and subsequent LysC digestion, replicate 2 In our proteogenomics approach, we could identify four previously missing protein annotations and were able to correct sequences of six protein coding regions. Furthermore we identified signal peptidase cleavage sites for 72 different proteins. MGFs were generated by Maxquant 1.1 [1] using recalibration of peptide parent masses. For PRIDE (http://www.ebi.ac.uk/pride) submission, we made an additional database search with Mascot and X!Tandem using the SearchGUI [2]. Therefore we searched against a NCBI database of H. pylori strain 26695 complemented with the sequence corrections, signal peptide cleavage sites and missing annotations with the same configurations as described in materials and methods. For pride xml export we used the software PeptideShaker (http://code.google.com/p/peptide-shaker/). The complemented database has entries which will be submitted to the UniProtKB via SPIN. The entries have the according SPIN number as accession number. The NCBI accession numbers for the shortened sequences due to signal peptide cleavage are extended with “_1”. The fasta database is added to the submission. For additional information, please contact me: stephan.mueller@ufz.de Yours sincerely, Stephan Mueller References: [1] Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. Journal of proteome research. 2011;10:1794-805. [2] Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 2011;11:996-9.