A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS.
Mukul K MidhaUlrike KusebauchDavid D ShteynbergMichal MaesSamuel L BaderPanga Jaipal ReddyDavid S CampbellNitin S BaligaRobert L MoritzPublished in: Scientific data (2020)
Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries that are generally derived from a priori measurements of peptides for each species. Although Escherichia coli (E. coli) is among the best studied model organisms, so far there is no spectral assay library for the bacterium publicly available. Here, we generated a spectral assay library for 4,014 of the 4,389 annotated E. coli proteins using one- and two-dimensional fractionated samples, and ion mobility separation enabling deep proteome coverage. We demonstrate the utility of this high-quality library with robustness in quantitation of the E. coli proteome and with rapid-chromatography to enhance throughput by targeted DIA-MS. The spectral assay library supports the detection and quantification of 91.5% of all E. coli proteins at high-confidence with 56,182 proteotypic peptides, making it a valuable resource for the scientific community. Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28).
Keyphrases
- mass spectrometry
- escherichia coli
- optical coherence tomography
- liquid chromatography
- high throughput
- data analysis
- ms ms
- high performance liquid chromatography
- dual energy
- gas chromatography
- tandem mass spectrometry
- capillary electrophoresis
- multiple sclerosis
- high resolution
- healthcare
- biofilm formation
- computed tomography
- cancer therapy
- mental health
- loop mediated isothermal amplification
- amino acid
- klebsiella pneumoniae
- cystic fibrosis
- machine learning
- electronic health record
- high speed
- artificial intelligence
- gram negative
- solid phase extraction
- real time pcr
- quantum dots
- genetic diversity