<i>mMass</i> data miner: an open source alternative for mass spectrometric data analysis

Strohalm, Martin; Hassman, Martin; Košata, Bedřich; Kodı́ček, Milan

doi:10.1002/rcm.3444

Cited by 474 publications

(400 citation statements)

References 7 publications

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“…Calibration was carried out with an external standard using a mix of peptides (5,000 to 20,000 Da; Bruker Daltonics, Inc.). Data analysis and area quantification of the spectra were performed using the mMass package software tools described by Strohalm et al (29) and ImageJ 1.41 (http: //rsbweb.nih.gov/ij/download.html), respectively.…”

Section: Methodsmentioning

confidence: 99%

Microcin E492 Amyloid Formation Is Retarded by Posttranslational Modification

Marcoleta

Marín

Mercado

et al. 2013

Journal of Bacteriology

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b Microcin E492, a channel-forming bacteriocin with the ability to form amyloid fibers, is exported as a mixture of two forms: unmodified (inactive) and posttranslationally modified at the C terminus with a salmochelin-like molecule, which is an essential modification for conferring antibacterial activity. During the stationary phase, the unmodified form accumulates because expression of the maturation genes mceIJ is turned off, and microcin E492 is rapidly inactivated. The aim of this work was to demonstrate that the increase in the proportion of unmodified microcin E492 augments the ability of this bacteriocin to form amyloid fibers, which in turn decreases antibacterial activity. To this end, strains with altered proportions of the two forms were constructed. The increase in the expression of the maturation genes augmented the antibacterial activity during all growth phases and delayed the loss of activity in the stationary phase, while the ability to form amyloid fibers was markedly reduced. Conversely, a higher expression of microcin E492 protein produced concomitant decreases in the levels of the modified form and in antibacterial activity and a substantial increase in the ability to form amyloid fibers. The same morphology for these fibers, including those formed by only the unmodified version, was observed. Moreover, seeds formed using exclusively the nonmodified form were remarkably more efficient in amyloid formation with a shorter lag phase, indicating that the nucleation process is probably improved. Unmodified microcin E492 incorporation into amyloid fibers was kinetically more efficient than the modified form, probably due to the existence of a conformation that favors this process.

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Section: Methodsmentioning

confidence: 99%

Microcin E492 Amyloid Formation Is Retarded by Posttranslational Modification

Marcoleta

Marín

Mercado

et al. 2013

Journal of Bacteriology

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“…Las masas obtenidas se compararon con las masas teóricas según PeptideMass de ExPASy (Wilkins et al, 1999) y con mMass 3.9.0 (Strohalm et al, 2008). Se comprobó la presencia de picos con relaciones m/z correspondientes a las masas teóricas de los fragmentos monocargados generados (figuras 5 y 6).…”

Section: Comprobación De La Secuencia De Los Conectores Fviiia1 Y Fviunclassified

Producción heteróloga y caracterización bioquímica del procoagulante humano Factor VIII para ensayos de cristalización de macromoléculas proteicas

Hernández-Carvajal

Arce-Solano

Mena-Aguilar

et al. 2017

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<p class="p1">A pesar de la relevancia médica y el impacto económico en los sistemas de salud, las enfermedades cardiovasculares, tales como infartos cardíacos y accidentes cerebrovasculares, siguen siendo la principal causa de morbilidad y mortalidad en los países en vías de desarrollo. Esto se debe a que las bases estructurales y funcionales de los procesos de formación de los coágulos sanguíneos o trombos solo se conocen de forma incompleta. La trombina juega un papel esencial en estos procesos y los fundamentos atómico-moleculares de su interacción con otros factores que participan en el proceso de coagulación son poco conocidos, en particular el reconocimiento de importantes sustratos como los factores V y VIII, así como el receptor de plaquetas PAR1. Dada la importancia de estos factores, en esta investigación se produjeron fragmentos del factor VIII humano (FVIII) y se caracterizaron bioquímicamente para realizar ensayos de cristalización de complejos FVIII·Trombina. Para ello, (1) se sobreexpresaron heterólogamente los conectores ácidos entre los dominios del factor VIII (denominados FVIIIa1, FVIIIa2 y FVIIIa3), (2) se purificaron y caracterizaron estos fragmentos recombinantes, (3) se formaron sus complejos con la trombina y (4) se inició la búsqueda de las condiciones de cristalización de estos complejos proteicos. La producción del FVIII, y en particular la determinación de las condiciones en las que crecen cristales del tamaño y calidad apropiados, son un auténtico cuello de botella en los estudios de estructura-función, por ello se considera que la optimización de estos procesos permitirá obtener un mayor número de cristales de proteína de calidad adecuada para futuros estudios de difracción de rayos X.</p>

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“…Instrument calibration was performed prior all analysis and mass accuracy was notably below 1 ppm using Thermo Pierce calibration solution and automated instrument protocol. All possible C-terminal processing metabolites were simulated in silico using mMass [25] to generate survey accurate masses.…”

Section: Peptide Fragments Identificationmentioning

confidence: 99%

“…PC1 (P63239) and PC2 (P21661) protein sequences were obtained from the The Universal Protein Resource (UniProt) databases. In silico protein digestions, peptide mass fingerprinting and MS/MS fragment ion fragmentation were performed using mMass [25]. Data analyses were performed using Thermo Scientific SIEVE (ver 2.1) and PINPOINT (ver 1.4) software (San Jose, CA, USA).…”

Section: Protein Extraction From S9 Fraction and Pc1/pc2 Ms Analysismentioning

confidence: 99%

Tachykinins Processing is Significantly Impaired in PC1 and PC2 Mutant Mouse Spinal Cord S9 Fractions

et al. 2015

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mMass data miner: an open source alternative for mass spectrometric data analysis

Cited by 474 publications

References 7 publications

Microcin E492 Amyloid Formation Is Retarded by Posttranslational Modification

Microcin E492 Amyloid Formation Is Retarded by Posttranslational Modification

Producción heteróloga y caracterización bioquímica del procoagulante humano Factor VIII para ensayos de cristalización de macromoléculas proteicas

Tachykinins Processing is Significantly Impaired in PC1 and PC2 Mutant Mouse Spinal Cord S9 Fractions

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