PeptideClassifier for protein inference and targeted quantitative proteomics

Qeli, Ermir; Ahrens, Christian H.

doi:10.1038/nbt0710-647

Cited by 82 publications

(87 citation statements)

References 15 publications

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“…Oxidation (M), deamidation (NQ), and methylation (DE) were used as variable modifications and carbamidomethylation (C) as a fixed modification. Using the decoy option of MS-GFϩ, we filtered the list of peptide spectrum matches (PSMs) to an estimated overall false discovery rate (FDR) of 0.2%, classified the PSMs with PeptideClassifier (27), and further considered only peptides (tryptic or semitryptic) that unambiguously imply one bacterial protein sequence. The FDR at the peptide level amounted to about 1.5%, and that at the protein level amounted to about 2.5% when requiring two peptides or three spectra for protein identification.…”

Section: Methodsmentioning

confidence: 99%

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

Koch

Delmotte

Ahrens

et al. 2014

Appl Environ Microbiol

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cRhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. In this study, Bradyrhizobium japonicum USDA 110 was found to be able to utilize oxalate as the sole carbon source. A proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. A mutant of the key pathway genes oxc (for oxalyl-coenzyme A decarboxylase) and frc (for formyl-coenzyme A transferase) was constructed and shown to be (i) impaired in growth on arabinose and (ii) unable to grow on oxalate. Oxalate was detected in roots and, at elevated levels, in root nodules of four different B. japonicum host plants. Mixed-inoculation experiments with wild-type and oxc-frc mutant cells revealed that oxalotrophy might be a beneficial trait of B. japonicum at some stage during legume root nodule colonization.

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Section: Methodsmentioning

confidence: 99%

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

Koch

Delmotte

Ahrens

et al. 2014

Appl Environ Microbiol

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“…Ratios were corrected for unequal mixing of labeled and unlabeled proteins in each sample by the geometric median of light-to-heavy ratios of all peptides in that sample. Peptides were classified according to their information content according to Qeli and Ahrens (2010). Class 1a peptides unambiguously identify a single unique protein sequence, class 1b is only ambiguous regarding protein isoforms, class 2a and 2b identify a distinct gene model, while class 2a peptides additionally identifies a proper subset.…”

Section: Nano-lc-ms/ms Protein Identification Quantification and Anmentioning

confidence: 99%

Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism

et al. 2014

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ORCID IDs: 0000-0002-7487-8014 (S.S.); 0000-0002-2594-509X (S.S.M.)Nitrogen (N) is a key nutrient that limits global primary productivity; hence, N-use efficiency is of compelling interest in agriculture and aquaculture. We used Chlamydomonas reinhardtii as a reference organism for a multicomponent analysis of the N starvation response. In the presence of acetate, respiratory metabolism is prioritized over photosynthesis; consequently, the N-sparing response targets proteins, pigments, and RNAs involved in photosynthesis and chloroplast function over those involved in respiration. Transcripts and proteins of the Calvin-Benson cycle are reduced in N-deficient cells, resulting in the accumulation of cycle metabolic intermediates. Both cytosolic and chloroplast ribosomes are reduced, but via different mechanisms, reflected by rapid changes in abundance of RNAs encoding chloroplast ribosomal proteins but not cytosolic ones. RNAs encoding transporters and enzymes for metabolizing alternative N sources increase in abundance, as is appropriate for the soil environmental niche of C. reinhardtii. Comparison of the N-replete versus N-deplete proteome indicated that abundant proteins with a high N content are reduced in N-starved cells, while the proteins that are increased have lower than average N contents. This sparing mechanism contributes to a lower cellular N/C ratio and suggests an approach for engineering increased N-use efficiency.

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“…The FDR distributions of all search algorithms were aligned to allow for overall peptide identifications with greater than 95% probability. For protein inference, peptides were classified according to their information content according to Qeli and Ahrens (2010). The Occam's Razor approach (Nesvizhskii et al, 2003) was applied to each peptide class from high to low information content to report a minimal set of proteins explaining the identified peptides by proteins and protein groups.…”

Section: N Quantitative Shotgun Proteomicsmentioning

confidence: 99%

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

et al. 2014

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We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42°C for 24 h and back to 25°C for ‡8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.

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PeptideClassifier for protein inference and targeted quantitative proteomics

Cited by 82 publications

References 15 publications

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

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