MALDI-TOF MS: An Evolving Approach to Cancer Profiling

New research suggests MALDI-TOF MS has an important place in the future of cancer diagnostics and therapeutics

Jake Moskowitz, DVM, PhD
May 17, 2022 | 4 min read

Tools that facilitate accurate cancer diagnoses in the early stages of disease and direct clinicians to more effective treatment strategies are critical to improving patient outcomes. Screening for informative biomarkers has become a highly effective method of detecting both increased risk of, and the presence of, cancer. However, pathophysiological heterogeneity across different cancers presents a significant challenge to discovering and developing effective biomarker-based diagnostics and therapeutics.

The discovery process requires high-throughput technologies that can efficiently generate promising candidate biomarkers with clinical relevance. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a promising tool that can efficiently identify informative biomolecules from minimally invasive patient samples, which may substantially improve biomarker discovery across a wide range of cancers. Translating these findings into sensitive and specific diagnostic tests and informed personalized treatment strategies presents an opportunity to significantly improve patient outcomes.

A practical approach to discovery

Extensive research has enabled the subclassification of cancers according to common molecular signatures. These categorizations provide a better understanding of biological pathways that include potential diagnostic biomarkers or therapeutic targets. In MALDI-TOF MS, analytes in complex biological samples are ionized and accelerated into a time-of-flight mass analyzer, providing access to the mass spectra of molecules such as proteins, peptides, lipids, carbohydrates, and nucleotides. This versatility is especially advantageous for biomarker development because it provides a wide range of potentially clinically informative biomolecules.

Currently, the relatively limited range of cancer biomarkers often forces health care providers to rely heavily on invasive biopsies. The development of novel biomarker tests can help patients circumvent these painful procedures. Thus, less invasive samples, such as saliva, blood, or urine that contain complex mixtures of metabolites and are amenable to deconstruction by MALDI-TOF MS, may hold the key to painless, reliable detection of early-stage cancer. However, identification and validation of biomarkers that are consistently effective across patients remains a considerable challenge.

Most potential biomarkers are likely to fail during follow-up validation studies. Thus, biomarker discovery demands the high-throughput generation of candidate markers to improve the chances of identifying a clinically informative biomolecule. In many ways, MALDI-TOF MS is uniquely suited to address these challenges. MALDI-TOF MS produces mass spectra from intact molecules, avoiding the need for extensive sample preparation. Moreover, the instrument can analyze samples in a matter of seconds and hundreds of samples can be added to the target plate simultaneously, making this technology an efficient way to collect large data sets from patient samples containing complex mixtures of biomolecules. Given these favorable characteristics, MALDI-TOF MS is highly amenable to the large sample sizes required to conduct cancer biomarker studies.

Recent progress towards novel biomarkers

Prostate cancer is among the most commonly diagnosed cancers worldwide, indicating a great need for accurate early diagnostics. Currently, prostate-specific antigen (PSA) testing is used for noninvasive surveillance of prostate cancer. However, the PSA test is plagued by a high false-positive rate, so patients are frequently overdiagnosed and still require a confirmatory biopsy after a positive PSA test.1 As a result, researchers are turning to new methods to identify more accurate biomarkers for prostate cancer.

Although biomarker discovery studies commonly focus on protein molecules, MALDI-TOF MS facilitates the use of more diverse molecules as candidate markers. Recently, a research team led by Dr. Boguslaw Buszewski of Nicolaus Copernicus University in Poland used MALDI-TOF technology to screen the lipid profiles of urine samples from 121 prostate cancer patients and 18 healthy controls. Using MALDI-TOF, Buszewski’s group was able to discriminate between healthy patients and those with prostate cancer using the urine lipid profile, suggesting the potential use for this approach to diagnostics.2

Similarly, Dr. Xin Li of Kyoto University used MALDI-TOF MS to evaluate the lipid metabolites of 75 patients with prostate cancer and 44 control subjects with benign prostatic hyperplasia. Notably, Li’s team found that the ratio of two lipid types, phosphatidylcholines and lysophosphatidylcholine, was significantly different in patients with prostate cancer compared to those with prostatic hyperplasia.3 This finding was confirmed in an additional validation cohort consisting of 133 total patients, suggesting that this is a consistent difference. Though it is unclear whether these lipid biomarkers are sensitive and specific enough to constitute a new diagnostic test of early-stage disease, the versatility and efficiency of MALDI-TOF MS was instrumental in this novel approach to noninvasive prostate cancer screening.

Informing better treatment strategies

Companies focused on cancer treatment have also integrated MALDI-TOF MS into their pipelines to facilitate further molecular characterization of disease toward developing new therapeutic strategies. Based in Boulder, Colorado, Biodesix, Inc. aims to provide both diagnostic and therapeutic solutions for health providers addressing lung diseases such as non-small cell lung cancer (NSCLC). Biodesix recently demonstrated that a MALDI-TOF MS-based proteomics approach can distinguish NSCLC patients that are more likely to respond to immunotherapy-based treatment from those who are not.4 In an ongoing clinical trial, Biodesix used MALDI-TOF MS to evaluate various markers in blood samples from approximately 2,000 enrolled patients prior to starting their prescribed treatment regimens. Remarkably, their approach successfully stratified patients into responder and nonresponder groups based on significant differences in overall survival. In this case, robust molecular data provided by MALDI-TOF MS could empower health care providers to preempt which patients would benefit from immunotherapy while steering potential nonresponders to alternative treatment strategies.

A launching point for cancer profiling

Though other spectrometry methods can provide more complete information about individual compounds, MALDI-TOF MS is well-suited for the high-throughput detection of diverse biomolecules from complex samples. Given the dramatic heterogeneity found in individual patients and across cancer types, tools that can extract large datasets from noninvasive patient samples will be critical for detailed molecular profiling. Already, MALDI-TOF MS has begun to identify large numbers of candidate biomarkers for early-stage diagnostics for follow-up validation studies, which may guide health care providers toward the most effective treatment options for patients.


  1. Ilic D, Djulbegovic M, Jung JH, et al. Prostate cancer screening with prostate-specific antigen (PSA) test: a systematic review and meta-analysis. BMJ. 2018;362:k3519. doi:10.1136/bmj.k3519.
  2. Buszewska-Forajta M, Pomastowski P, Monedeiro F, et al. New approach in determination of urinary diagnostic markers for prostate cancer by MALDI-TOF MS. Talanta. 2022;236:122843. doi:10.1016/j.talanta.2021.122843.
  3. Li X, Nakayama K, Goto T, et al. High level of phosphatidylcholines/lysophosphatidylcholine ratio in urine is associated with prostate cancer. Cancer Sci. 2021;112(10):4292-4302. doi:10.1111/cas.15093.
  4. Rich P, Mitchell RB, Schaefer E, et al. Real-world performance of blood-based proteomic profiling in first-line immunotherapy treatment in advanced stage non-small cell lung cancer. J Immunother Cancer. 2021;9(10):e002989. doi:10.1136/jitc-2021-002989.