TY - JOUR

T1 - Performance evaluation of the Q Exactive HF-X for shotgun proteomics

AU - Kelstrup, Christian D

AU - Bekker-Jensen, Dorte B

AU - Arrey, Tabiwang N

AU - Hogrebe, Alexander

AU - Harder, Alexander

AU - Olsen, Jesper V

PY - 2018/1

Y1 - 2018/1

N2 - Progress in proteomics is mainly driven by advances in mass spectrometric (MS) technologies. Here we benchmarked the performance of the latest MS instrument in the benchtop Orbitrap series, the Q Exactive HF-X, against its predecessor for proteomics applications. A new peak picking algorithm, a brighter ion source and optimized ion transfers enable productive MS/MS acquisition above 40 Hz at 7500 resolution. The hardware and software improvements collectively resulted in improved peptide and protein identifications across all comparable conditions, with an increase of up to fifty percent at short LC-MS gradients, yielding identification rates of more than one thousand unique peptides per minute. Alternatively, the Q Exactive HF-X is capable of achieving the same proteome coverage as its predecessor in approximately half the gradient time or at 10-fold lower sample loads. The Q Exactive HF-X also enables rapid phosphoproteomics with routine analysis of more than five thousand phosphopeptides with short single-shot 15-minute LC-MS/MS measurements, or 16,700 phosphopeptides quantified across ten conditions in six gradient hours using TMT10-plex and offline peptide fractionation. Finally, exciting perspectives for data independent acquisition are highlighted with reproducible identification of 55,000 unique peptides covering 5900 proteins in half-an-hour of MS analysis.

AB - Progress in proteomics is mainly driven by advances in mass spectrometric (MS) technologies. Here we benchmarked the performance of the latest MS instrument in the benchtop Orbitrap series, the Q Exactive HF-X, against its predecessor for proteomics applications. A new peak picking algorithm, a brighter ion source and optimized ion transfers enable productive MS/MS acquisition above 40 Hz at 7500 resolution. The hardware and software improvements collectively resulted in improved peptide and protein identifications across all comparable conditions, with an increase of up to fifty percent at short LC-MS gradients, yielding identification rates of more than one thousand unique peptides per minute. Alternatively, the Q Exactive HF-X is capable of achieving the same proteome coverage as its predecessor in approximately half the gradient time or at 10-fold lower sample loads. The Q Exactive HF-X also enables rapid phosphoproteomics with routine analysis of more than five thousand phosphopeptides with short single-shot 15-minute LC-MS/MS measurements, or 16,700 phosphopeptides quantified across ten conditions in six gradient hours using TMT10-plex and offline peptide fractionation. Finally, exciting perspectives for data independent acquisition are highlighted with reproducible identification of 55,000 unique peptides covering 5900 proteins in half-an-hour of MS analysis.

KW - Journal Article

U2 - 10.1021/acs.jproteome.7b00602

DO - 10.1021/acs.jproteome.7b00602

M3 - Journal article

C2 - 29183128

VL - 17

SP - 727

EP - 738

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 1

ER -