Abstract：
:Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications of unknown masses up to ± 500 Da. In a proteome-wide data set on HEK293 cells (9,513 proteins and 396,736 peptides), this approach matched an additional 184,000 modified peptides, which were linked to biological and chemical modifications representing 523 distinct mass bins, including phosphorylation, glycosylation and methylation. We localized all unknown modification masses to specific regions within a peptide. Known modifications were assigned to the correct amino acids with frequencies >90%. We conclude that at least one-third of unassigned spectra arise from peptides with substoichiometric modifications.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Chick JM,Kolippakkam D,Nusinow DP,Zhai B,Rad R,Huttlin EL,Gygi SPdoi
10.1038/nbt.3267subject
Has Abstractpub_date
2015-07-01 00:00:00pages
743-9issue
7eissn
1087-0156issn
1546-1696pii
nbt.3267journal_volume
33pub_type
杂志文章abstract：:The use of DNA variants in the mapping of the human genome and in the positional cloning of monogenic disease genes is well established. Determining the genetic bases of the more common "multifactorial" diseases, however, presents a major challenge. The genetics of these diseases are complicated by the interplay betwe...
journal_title：Nature biotechnology
pub_type： 杂志文章,评审
doi：10.1038/nbt0198-33
更新日期：1998-01-01 00:00:00
abstract：:We describe wavelength-shifting molecular beacons, which are nucleic acid hybridization probes that fluoresce in a variety of different colors, yet are excited by a common monochromatic light source. The twin functions of absorption of energy from the excitation light and emission of that energy in the form of fluores...
journal_title：Nature biotechnology
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abstract：:A detailed understanding of the function of neural networks and how they are supported by a dynamic vascular system requires fast three-dimensional imaging in thick tissues. Here we present confocal light field microscopy, a method that enables fast volumetric imaging in the brain at depths of hundreds of micrometers....
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journal_title：Nature biotechnology
pub_type： 杂志文章
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abstract：:The scale and capabilities of single-cell RNA-sequencing methods have expanded rapidly in recent years, enabling major discoveries and large-scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single-cell and/or si...
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journal_title：Nature biotechnology
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journal_title：Nature biotechnology
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journal_title：Nature biotechnology
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更新日期：2016-09-01 00:00:00
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journal_title：Nature biotechnology
pub_type： 杂志文章
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更新日期：2017-09-01 00:00:00
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journal_title：Nature biotechnology
pub_type： 杂志文章
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abstract：:Previous reports have demonstrated the growth of undifferentiated human embryonic stem (HES) cells on mouse embryonic fibroblast (MEF) feeders and on laminin- or Matrigel-coated plastic surfaces supplemented with MEF-conditioned medium. These xenosupport systems run the risk of cross-transfer of animal pathogens from ...
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更新日期：2007-02-01 00:00:00
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journal_title：Nature biotechnology
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更新日期：2006-01-01 00:00:00
abstract：:The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single ce...
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abstract：:RNA-guided gene drives capable of spreading genomic alterations made in laboratory organisms through wild populations could be used to address environmental and public health problems. However, the possibility of unintended genome editing occurring through the escape of strains from laboratories, coupled with the pros...
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更新日期：2015-12-01 00:00:00
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journal_title：Nature biotechnology
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更新日期：2005-04-01 00:00:00
abstract：:Nitrile hydratase (NHase), which catalyzes the hydration of nitriles to amides, has been used in the industrial production of acrylamide and nicotinamide. Recent studies on NHases, which are roughly classified into iron and cobalt types according to the metal involved, have clarified the photoactivation mechanism, the...
journal_title：Nature biotechnology
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更新日期：1998-08-01 00:00:00
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journal_title：Nature biotechnology
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