<scp>MSDA</scp>, a proteomics software suite for in‐depth <scp>M</scp>ass <scp>S</scp>pectrometry <scp>D</scp>ata <scp>A</scp>nalysis using grid computing

Carapito, Christine; Burel, Alexandre; Guterl, Patrick; Walter, Alexandre; Varrier, Fabrice; Bertile, Fabrice; Dorsselaer, Alain Van

doi:10.1002/pmic.201300415

Cited by 56 publications

(58 citation statements)

References 19 publications

(20 reference statements)

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“…Optional modifications were set as follows: carbamidomethylation of cysteine residues, oxidation of methionine residues, and acetylation of protein N-termini. Database generation, OMSSA searches and automatic extraction of protein functional annotations (gene ontologies) were performed using our home-made “Mass Spectrometry Data Analysis” software suite [64]. …”

Section: Methodsmentioning

confidence: 99%

Litter size manipulation in laboratory mice: an example of how proteomic analysis can uncover new mechanisms underlying the cost of reproduction

et al. 2014

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BackgroundLife history theories predict that investment in current reproduction comes at a cost for future reproduction and survival. Oxidative stress is one of the best documented mechanisms underlying costs of reproduction to date. However, other, yet to be described molecular mechanisms that play a short term role during reproduction may explain the negative relationships underlying the cost of reproduction. To identify such new mechanisms, we used a global proteomic determination of liver protein profiles in laboratory adult female mice whose litter size had been either reduced or enlarged after birth. This litter size manipulation was expected to affect females by either raising or decreasing their current reproductive effort. At the same time, global parameters and levels of oxidative stress were also measured in all females.ResultsBased on plasma analyses, females with enlarged litters exhibited increased levels of oxidative stress at the date of weaning compared to females with reduced litters, while no significant difference was found between both the latter groups and control females. None of the liver proteins related to oxidative balance were significantly affected by the experimental treatment. In contrast, the liver protein profiles of females with enlarged and reduced litters suggested that calcium metabolism and cell growth regulation were negatively affected by changes in the number of pup reared.ConclusionsPlasma oxidative stress levels in reproductive mice revealed that the degree of investment in reproduction can actually incur a cost in terms of plasmatic oxidative stress, their initial investment in reproduction being close to maximum and remaining at a same level when the energy demand of lactation is reduced. Liver proteomic profiles in reproductive females show that hepatic oxidative stress is unlikely to be involved in the cost of reproduction. Reproductive females rather exhibited liver protein profiles similar to those previously described in laboratory ageing mice, thus suggesting that hepatic cell pro-ageing processes may be involved in the cost of reproduction. Overall, our data illustrate how a proteomic approach can unravel new mechanisms sustaining life-history trade-offs, and reproduction costs in particular.

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Section: Methodsmentioning

confidence: 99%

Litter size manipulation in laboratory mice: an example of how proteomic analysis can uncover new mechanisms underlying the cost of reproduction

et al. 2014

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“…A second round search was performed to identify Nt-acetyl peptides in position >2 and semi-specific internal peptides. The Recover module of MSDA37 was used to create a subset “mgf” files by removing all identified spectra from the first round search, spectra with no peak above the m/z ratio of the 1+ charged state precursor ion and spectra which did not include at least six peaks higher than 2 times the intensity of the background noise. The second round search was performed using enzyme semi-specificity (only one end of a peptide needs to match the cleavage specificity) and as previously described.…”

Section: Methodsmentioning

confidence: 99%

Trafficking of the exported P. falciparum chaperone PfHsp70x

Rhiel

Bittl

Tribensky

et al. 2016

Sci Rep

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Plasmodium falciparum extensively modifies its chosen host cell, the mature human erythrocyte. This remodelling is carried out by parasite-encoded proteins that are exported into the host cell. To gain access to the human red blood cell, these proteins must cross the parasitophorous vacuole, a membrane bound compartment surrounding the parasite that is generated during the invasion process. Many exported proteins carry a so-called PEXEL/HT signal that directs their transport. We recently reported the unexpected finding of a species-restricted parasite-encoded Hsp70, termed PfHsp70x, which is exported into the host erythrocyte cytosol. PfHsp70x lacks a classical PEXEL/HT motif, and its transport appears to be mediated by a 7 amino acid motif directly following the hydrophobic N-terminal secretory signal. In this report, we analyse this short targeting sequence in detail. Surprisingly, both a reversed and scrambled version of the motif retained the capacity to confer protein export. Site directed mutagenesis of glutamate residues within this region leads to a block of protein trafficking within the lumen of the PV. In contrast to PEXEL-containing proteins, the targeting signal is not cleaved, but appears to be acetylated. Furthermore we show that, like other exported proteins, trafficking of PfHsp70x requires the vacuolar translocon, PTEX.

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“…Searches were performed without any molecular weight or isoelectric point restrictions against an in-house generated protein database composed of all vertebrate protein sequences extracted from UniProtKB (Release-2014_02, TaxonomyID = 7742, 2,187,035 entries). The database was concatenated in-house using the Mass Spectrometry Data Analysis (MSDA) software suite (Carapito et al, 2014). Known contaminant proteins such as human keratins and porcine trypsin were included in this vertebrate database and therefore only reversed copies of all sequences were added to obtain a target-decoy database of 4,374,070 entries (Elias & Gygi, 2010).…”

Section: Data Interpretation and Protein Identificationmentioning

confidence: 99%

Differentiation between fresh and frozen–thawed sea bass (Dicentrarchus labrax) fillets using two-dimensional gel electrophoresis

et al. 2015

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This study aimed to identify a protein marker that can differentiate between fresh skinless and frozen-thawed sea bass (Dicentrarchus labrax) fillets using the two-dimensional polyacrylamide gel electrophoresis (2-DE) technique. Distinct gel patterns, due to proteins with low molecular weight and low isoelectric points, distinguished fresh fillets from frozen-thawed ones. Frozen-thawed fillets showed two specific protein spots as early as the first day of the study. However, these spots were not observed in fresh fillets until at least 13days of storage between 0 and 4°C, fillets were judged, beyond this period, fish were unfit for human consumption as revealed by complementary studies on fish spoilage indicators namely total volatile basic nitrogen and biogenic amines. Mass spectrometry identified the specific proteins as parvalbumin isoforms. Parvalbumins may thus be useful markers of differentiation between fresh and frozen-thawed sea bass fillets.

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MSDA, a proteomics software suite for in‐depth Mass Spectrometry Data Analysis using grid computing

Cited by 56 publications

References 19 publications

Litter size manipulation in laboratory mice: an example of how proteomic analysis can uncover new mechanisms underlying the cost of reproduction

Litter size manipulation in laboratory mice: an example of how proteomic analysis can uncover new mechanisms underlying the cost of reproduction

Trafficking of the exported P. falciparum chaperone PfHsp70x

Differentiation between fresh and frozen–thawed sea bass (Dicentrarchus labrax) fillets using two-dimensional gel electrophoresis

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