TECHNICAL RESOURCES · 上机检测

Instrument Run

Q: How much data does one PE150 run produce?

In PE150 mode read length reaches up to 2×300 bp and throughput is up to 25 B reads per flow cell, covering WGS / WES / RNA-seq / scRNA-seq.

Q: Can you hold Q30 for whole-genome sequencing?

The WGS standard is Q30 ≥ 85%, and runs are monitored in real time — dropping below 80% triggers an alert and a re-run assessment.

Q: Which instruments do you run for long-read sequencing?

Long-read work uses PacBio Revio / Sequel IIe and Oxford Nanopore PromethION 24 / MinION Mk1C.

Q: My sample amount is very small — can I still do proteomics?

Yes: the Bruker timsTOF HT is suited to ultra-low sample loads (< 100 ng) and is used for low-input, single-cell and deep plasma proteomics.

Q: What does a library need before it can go on the instrument?

Library concentration ≥ 2 nM (Illumina standard) diluted in EB buffer, expected fragment distribution with no significant adapter-dimer peaks, equimolar pooling, and a flow cell model matched to the library type.

Covering NGS and third-generation sequencing (TGS), meeting every need from short to long reads and from bulk to single cell

Methodology note · content is citable as-is

KEY POINTS

PE150 mode, read length up to 2×300 bp
up to 25 B reads per flow cell
Q30 ≥ 85% (WGS)
supports WGS / WES / RNA-seq / scRNA-seq

01Sequencing Platforms

Covering NGS and third-generation sequencing (TGS), meeting every need from short to long reads and from bulk to single cell

Illumina NGS Platform

short reads · high throughput · high accuracy

Model

Illumina NovaSeq X Plus / NovaSeq 6000 / NextSeq 2000

Technical Highlights

PE150 mode, read length up to 2×300 bp
up to 25 B reads per flow cell
Q30 ≥ 85% (WGS)
supports WGS / WES / RNA-seq / scRNA-seq

Applicable Omics

genomics (WGS/WES), transcriptomics (RNA-seq), single-cell sequencing

PacBio TGS Platform

long reads · HiFi accuracy · direct methylation sequencing

Model

PacBio Revio / Sequel IIe

Technical Highlights

HiFi reads: 15–25 kb average, >99.9% accuracy
up to 90 Gb HiFi data per run
direct DNA-methylation (5mC) detection
ideal for complex-genome assembly and structural-variant detection

Applicable Omics

whole-genome sequencing (large genomes), full-length transcript sequencing, methylation sequencing

Oxford Nanopore Platform

ultra-long reads · real-time sequencing · direct methylation detection

Model

Oxford Nanopore PromethION 24 / MinION Mk1C

Technical Highlights

ultra-long reads: 30–50 kb average, >1 Mb maximum
PCR-free direct sequencing with reduced bias
real-time data output—analyze while sequencing
suited to metagenomics, viral assembly and structural variation

Applicable Omics

metagenome sequencing, large-genome assembly, viral-diversity research

02Mass-Spectrometry Platforms

Top-tier Thermo Fisher and Bruker MS systems covering high-precision proteomics and metabolomics detection

Thermo Orbitrap Astral

ultra-fast scanning · high sensitivity · 4D proteomics

Technical Highlights

scan rate: up to 200 Hz (Astral mass analyzer)
resolution: up to 480,000 FWHM (Orbitrap)
>12,000 proteins identified per DIA run
dynamic range: > 5 orders of magnitude

Applications

4D proteomics (DIA/DDA/PRM), PTM analysis, large-cohort clinical studies

Bruker timsTOF HT

ion-mobility separation · PASEF technology · ultra-high sensitivity

Technical Highlights

mobility resolution: up to 300–500 1/K0
PASEF mode improves ion utilization 10–20×
scan rate: up to 100 Hz MS/MS
suited to ultra-low sample loads (< 100 ng）场景

Applications

low-input proteomics, single-cell proteomics, deep plasma proteomics

Thermo Q Exactive HF-X

high resolution · accurate mass · for both metabolomics and proteomics

Technical Highlights

resolution: up to 240,000 FWHM (@ m/z 200)
mass accuracy: < 1 ppm（外标校准）
dynamic range: > 4 orders of magnitude
supports DDA / DIA / PRM acquisition modes

Applications

metabolomics (LC-MS/MS untargeted + targeted), proteomics (DIA/DDA), PTM analysis

03Standard Run Procedure

Standardized procedure from library/sample loading to data output

Run Preparation

library/sample QC recheck, flow-cell/column preparation

Pooling & Loading

libraries pooled at equimolar ratios, diluted and loaded onto the flow cell

Sequencing / Acquisition

run per preset protocol with real-time monitoring of Q30/resolution

Real-Time QC

data quality checked every 12–24 h; parameters adjusted as needed

Data Output

raw data (FASTQ/RAW/WIFF) transferred to storage servers

04Platform Parameter Comparison

Platform	Read length / resolution	Throughput (per run)	Accuracy / mass accuracy	Run time
Illumina NovaSeq X Plus	PE 2×150 bp	up to 25 B reads	Q30 ≥ 85%	approx. 24–48 h
PacBio Revio	HiFi 15–25 kb	up to 90 Gb	accuracy > 99.9%	approx. 24 h
Nanopore PromethION	ultra-long reads 30–50 kb	up to 150 Gb	accuracy ~98% (HAC model)	real-time (interruptible)
Orbitrap Astral	resolution 480,000	~200 Hz scan rate	mass accuracy < 1 ppm	sample-dependent (hours)
timsTOF HT	mobility resolution ~400	~100 Hz MS/MS	mass accuracy < 1 ppm	sample-dependent (hours)

05In-Run QC Monitoring

Key metrics monitored in real time during runs to ensure data meets delivery standards

Sequencing QC Metrics

Q30 ≥ 85%

NGS Q30 (error rate ≤ 0.1%) ratio; below 80% triggers an alert and re-run assessment.

Coverage uniformity: per-sample coverage CV < 0.2
Mapping rate: reference-genome mapping rate ≥ 70%
Duplication rate: WGS duplication rate < 20%

MS QC Metrics

MS1 resolution ≥ 60,000

MS1 resolution ≥ 60,000 for proteomics DIA; ≥ 35,000 for metabolomics.

Retention-time drift: within batch < 1 秒
QC-sample RSD: metabolite peak-area RSD < 15%
Identifications: HeLa DIA single injection > 8,000 proteins

Alert & Response Mechanism

real-time monitoring · rapid response

QC reports are generated every 12 hours during runs; technicians act on the following rules:

Yellow alert: Q30 drop within 3%—continue running with enhanced monitoring
Orange alert: Q30 < 80% 或 QC RSD > 20%—pause and assess
Red alert: severe deviation—terminate the run, troubleshoot and re-run

06Pre-Run Checklist

Pre-run checklist for sequencing samples

library concentration ≥ 2 nM (Illumina standard); use EB buffer when diluting to working concentration
library fragment distribution as expected (Agilent TapeStation), no significant adapter-dimer peaks
libraries pooled at equimolar ratios to avoid over-representation of any sample
clustering-efficiency forecast: expected reads per sample matching the study design
flow-cell model matched to library type (NovaSeq X Plus uses X-series flow cells)

Pre-run checklist for MS samples

protein/metabolite extracts fully depleted of host proteins/salts (lines flushed with LC-MS-grade water/acetonitrile)
column equilibrated ≥ 30 min; retention-time stability RSD < 1%
pooled QC prepared and pre-injected ≥ 5 times until the system stabilizes
mass axis calibrated (external calibration; mass deviation < 1 ppm）
injection order randomized to avoid batch effects on quantification

Q&AFAQ

How much data does one PE150 run produce?

In PE150 mode read length reaches up to 2×300 bp and throughput is up to 25 B reads per flow cell, covering WGS / WES / RNA-seq / scRNA-seq.

Can you hold Q30 for whole-genome sequencing?

The WGS standard is Q30 ≥ 85%, and runs are monitored in real time — dropping below 80% triggers an alert and a re-run assessment.

Which instruments do you run for long-read sequencing?

Long-read work uses PacBio Revio / Sequel IIe and Oxford Nanopore PromethION 24 / MinION Mk1C.

My sample amount is very small — can I still do proteomics?

Yes: the Bruker timsTOF HT is suited to ultra-low sample loads (< 100 ng) and is used for low-input, single-cell and deep plasma proteomics.

What does a library need before it can go on the instrument?

Library concentration ≥ 2 nM (Illumina standard) diluted in EB buffer, expected fragment distribution with no significant adapter-dimer peaks, equimolar pooling, and a flow cell model matched to the library type.