Technical Field

The invention relates to a computer implemented method for calibrating a customer mass spectrometry instrument for quantifier-qualifier-ratio check, a computer implemented method for quantifier-qualifier-ratio check, computer programs and a mass spectrometry system. The method may be used for in-vitro-diagnostic assays.

Background art

Quantifier-Qualifier peak area ratio, denoted QQ ratio, are known to be an important quality control measure to check peak identity and interferences within every measured patient sam ple. Using the QQ ratio is a well-established approach for liquid chromatography-mass spec trometry (LC-MS) assays and considered by a number of guidelines, such as from the Clin ical & Laboratory Standards Institute (CLSI) C62-A, “Guideline for quality control in fo rensic-toxicological analyses” by the “Society of Toxicological and Forensic Chemistry” (GTFCh). Target values for QQ ratios for checking peak identity and interferences may be set either during assay development, validation, or with calibrating the assay. Setting of tar get values is done on a specific instrument. Respective acceptance criteria may be defined during assay development or are just set according to guidelines recommendations.

For example, using QQ ratio as quality measure to check peak identity and interferences is described in US 2017/0108478 Al, WO 2018/207228 Al, WO 2018/136825 A1 and US 20120318970 Al. Although this ratio is specific for an analyte, robustness deficiencies can be observed, spe cifically in comparison to peak area ratios between analyte and internal standard. Moreover, there may be distinct differences between different instruments and temporal drifts and shifts. For laboratory devices, target values for this ratio are usually defined after develop ment or during validation or verification on a specific instrument. To overcome the robust ness deficiency, broad acceptance ranges may be applied or the target needs to be adjusted with every batch-wise calibration. For fully automated in-vitro-diagnostics run on multiple instruments this approach may not be feasible and suitable.

An overview of usual tuning and calibration routines for mass spectrometry instruments is given by Fabio Garofolo: "LC-MS Instrument Calibration : Chan/ Analytical Validation" In: "Analytical Method Validation and Instrument Performance Verification", John Wiley & Sons, Inc., Hoboken, NJ, USA, ISBN: 978-0-471-25953-4, pages 197-220, DOI: 10.1002/0471463728. chl3. An overview of equipment qualification and validation is given by Ludwig Huber et al.: "Equipment Qualification and Computer System Validation : Chan/Analytical Validation" In: "Analytical Method Validation and Instrument Perfor mance Verification", 15 January 2004, John Wiley & Sons, Inc., Hoboken, NJ, USA, ISBN: 978-0-471-25953-4, pages 255-276, DOI: 10.1002/0471463728.chl7.

Problem to be solved

It is therefore an objective of the present invention to provide methods and devices for quan- tifier-qualifier-ratio check, which avoid the above-described disadvantages of known meth ods and devices. In particular, the method and the device shall allow reliable and completely automatic analysis of samples with mass spectrometry devices.

Summary

This problem is addressed by computer implemented methods, computer programs and a mass spectrometry system with the features of the independent claims. Advantageous em bodiments which might be realized in an isolated fashion or in any arbitrary combinations are listed in the dependent claims as well as throughout the specification. As used in the following, the terms “have”, “comprise” or “include” or any arbitrary gram matical variations thereof are used in a non-exclusive way. Thus, these terms may both refer to a situation in which, besides the feature introduced by these terms, no further features are present in the entity described in this context and to a situation in which one or more further features are present. As an example, the expressions “A has B”, “A comprises B” and “A includes B” may both refer to a situation in which, besides B, no other element is present in A (i.e. a situation in which A solely and exclusively consists of B) and to a situation in which, besides B, one or more further elements are present in entity A, such as element C, elements C and D or even further elements.

Further, it shall be noted that the terms “at least one”, “one or more” or similar expressions indicating that a feature or element may be present once or more than once typically will be used only once when introducing the respective feature or element. In the following, in most cases, when referring to the respective feature or element, the expressions “at least one” or “one or more” will not be repeated, non-withstanding the fact that the respective feature or element may be present once or more than once.

Further, as used in the following, the terms "preferably", "more preferably", "particularly", "more particularly", "specifically", "more specifically" or similar terms are used in conjunc tion with optional features, without restricting alternative possibilities. Thus, features intro duced by these terms are optional features and are not intended to restrict the scope of the claims in any way. The invention may, as the skilled person will recognize, be performed by using alternative features. Similarly, features introduced by "in an embodiment of the inven tion" or similar expressions are intended to be optional features, without any restriction re garding alternative embodiments of the invention, without any restrictions regarding the scope of the invention and without any restriction regarding the possibility of combining the features introduced in such way with other optional or non-optional features of the invention.

In a first aspect of the present invention, a computer implemented method for calibrating a customer mass spectrometry instrument for quantifier-qualifier-ratio check is disclosed.

The term “computer implemented method” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limita tion, to a method involving at least one computer and/or at least one computer network. The computer and/or computer network may comprise at least one processor which is configured for performing at least one of the method steps of the method according to the present in vention. Preferably several of the method steps may be performed by the computer and/or computer network. The method may be performed partially or completely automatically, specifically without user interaction. The term “automatically” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a process which is performed completely by means of at least one computer and/or computer network and/or machine, in particular without manual action and/or interaction with a user.

The terms “calibration” and “calibrating” are broad terms and are to be given its ordinary and customary meaning to a person of ordinary skill in the art and are not to be limited to a special or customized meaning. The terms specifically may refer, without limitation, to an operation or a process of operation of determining a relationship, specifically a calibration function, of measurement values delivered by a device with those of a calibration standard. In particular, the calibration may be a relationship between measurement value and target value. The calibration may be a relationship between target value for quantifier-qualifier- ratios from measurements determined with a customer mass spectrometry instrument and target values for quantifier-qualifier-ratios of a calibration standard, in particular determined on a manufacturer-site.

The term “mass spectrometry (MS) instrument” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a mass analyzer configured for detecting at least one analyte based on mass to charge ratio. The mass spectrometry instrument may be or may comprise at least one quad- rupole mass spectrometry device. The MS instrument may be a tandem mass spectrometry (MS/MS) instrument or a triple quadrupole MS/MS. Specifically, the mass spectrometry in strument may be configured for Multiple Reaction Monitoring (MRM).

The mass spectrometry instrument may specifically be or may comprise a liquid chromatog raphy mass spectrometry device. The term “liquid chromatography mass spectrometry de vice” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a combination of liquid chromatography with mass spectrometry. The liquid chromatography mass spectrometry de vice may be or may comprise at least one high-performance liquid chromatography (HPLC) device or at least one micro liquid chromatography (pLC) device. The liquid chromatog raphy mass spectrometry device may comprise a liquid chromatography (LC) device and a mass spectrometry (MS) device, wherein the LC device and the MS are coupled via at least one interface. The interface coupling a liquid chromatography device and the MS may com prise at least one ionization source configured for generating of molecular ions and for trans ferring of the molecular ions into the gas phase. The term “liquid chromatography (LC) de vice” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to an analytical module con figured to separate one or more analytes of interest of a sample from other components of the sample for detection of the one or more analytes with the mass spectrometry instrument. The LC device may be based on any separation principle deemed appropriate by the skilled person; in an embodiment, the LC device may be reverse phase chromatography, hydropho bic interaction chromatography, ion exchange chromatography, size exclusion chromatog raphy, affinity chromatography, or chiral chromatography; in a further embodiment, the LC device is reverse phase chromatography. The LC device may comprise at least one LC col umn. For example, the LC device may be a single-column LC device or a multi-column LC device having a plurality of LC columns. The LC column may have a stationary phase through which a mobile phase is pumped in order to separate and/or elute and/or transfer the analytes of interest.

The term “multiple reaction monitoring”, also denoted multiple transition monitoring, as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a method used in mass spectrometry, spe cifically in tandem mass spectrometry, in which multiple product ions from one or more precursor ions are monitored. As used herein, the term “monitored” is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, with out limitation, to determining and/or detecting of multiple product ions.

The term “customer” as used herein is a broad term and is to be given its ordinary and cus tomary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to an owner or operator of a mass spectrometry instrument, in particular obtained from one or more of a seller, vendor, or supplier. The term “customer mass spectrometry instrument” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifi cally may refer, without limitation, to a mass spectrometry instrument of the customer.

The term “quantifier”, also denoted as quantifier ion, as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, with out limitation, to an ion characterizing a compound of interest. Generally, the most abundant and/or most reliably detected transition or fragment is used for quantifying the compound. Specifically, the quantifier ion may have on a mass spectrum of the compound a peak of a maximum signal intensity. The term “qualifier”, also denoted as qualifier ion, as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifi cally may refer, without limitation, to another ion characterizing the compound of interest having a different mass-to-charge ratio compared to the quantifier ion. The qualifier may be used for confirmation of identity of the compound. Generally, a second transition or frag ment is used as qualifier. The term “quantifier-qualifier-ratio”, also denoted as quantifier- qualifier peak area ratio, as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a ratio be tween signal intensity of the peak of the qualifier ion and the signal intensity of the peak of the quantifier ion and/or to a ratio between peak area of the peak of the quantifier ion and peak area of the peak of the qualifier ion.

The term “quantifier-qualifier-ratio check” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limita tion, to a quality control measure to check peak identity and interferences within a sample. Using the quantifier-qualifier-ratio is a well-established approach for liquid chromatog raphy-mass spectrometry assays and considered by a number of guidelines, such as from the Clinical & Laboratory Standards Institute (CLSI) C62-A, “Guideline for quality control in forensic-toxicological analyses” by the “Society of Toxicological and Forensic Chemistry” (GTFCh). For the quantifier-qualifier-ratio check determined quantifier-qualifier-ratios are compared to target values for quantifier-qualifier-ratios and are validated in view of at least one acceptance criterion.

The term "quality control", as used herein, is known to the skilled person. In an embodiment, quality control is the process of ensuring that processes performed and/or goods produced by an entity are in conformity with pre-defmed quality criteria. In a further embodiment, quality control in sample measurement, in particular in measurement of medical samples such as patient samples, e.g. in clinical diagnostics and/or clinical chemistry, comprises en suring that the analysis results obtained with a specific measuring method correspond to the results obtainable with a gold standard method and, therefore, in an embodiment correspond to the results theoretically obtainable, within a pre-specified range.

The method comprises the following steps which, as an example, may be performed in the given order. It shall be noted, however, that a different order is also possible. Further, it is also possible to perform one or more of the method steps once or repeatedly. Further, it is possible to perform two or more of the method steps simultaneously or in a timely overlap ping fashion. The method may comprise further method steps which are not listed. The term “step” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a work step, a process step or a stage of an operation or a procedure.

The method comprises the following steps: a) at least one manufacturer-site standardization, wherein a set of samples of a subject and a set of calibrator samples are measured in multiple replicates on a plurality of mass spectrometry instruments, wherein each measurement comprises multiple reac tion monitoring with quantifier and qualifier transition for analyte and internal stand ard, wherein at least three adjustment factors are determined from the measurements of the set of samples of a subject and the set of calibrator samples, wherein a first adjustment factor a depends on a difference between analyte and internal standard, wherein a second adjustment factor b depends on a difference between samples of a subject and calibrator samples for analyte quantifier-qualifier-ratio, wherein a third adjustment factor g depends on a difference between samples of a subject and calibra tor samples for the internal standard quantifier-qualifier-ratio; b) at least one transfer step, wherein the adjustment factors are electronically transferred to a customer mass spectrometry instrument; c) at least one customer-site calibration, wherein the customer-site calibration comprises at least one calibration measurement, wherein a set of calibrator samples is measured on the customer mass spectrometry instrument and quantifier-qualifier-ratios are de termined therefrom, wherein target values for quantifier-qualifier-ratios for analyte and for internal standard are set by applying the adjustment factors on the determined quantifier-qualifier-ratios. For performing a quality check based on quantifier-qualifier-ratios at least one target value is used to which the measured quantifier-qualifier-ratio is compared. However, the target value may change or vary from mass spectrometry instruments to mass spectrometry instru ments. Thus, it may be advantageous to use for quality check target values for a specific customer mass spectrometry instrument. Even changes in time are possible. Thus, it may be advantageous to use for quality check target values which may be adjusted or adapted re peatedly in time on the customer- site. Moreover, for calibration usually a low number of calibrator samples is measured and composition of those calibrator samples might be differ ent compared to samples of a subject. Thus, the quality check based on the quantifier-quali- fier-ratio would be strongly affected by measurement imprecision and biased by matrix dif ferences between calibrator and samples of a subject. To overcome these issues, the present invention proposes a data transfer approach. On the manufacturer-site a set of samples of a subject and the calibrator samples may be measured in multiple replicates on multiple in struments during step a). Three adjustment factors may be determined in step a) and may be electronically transferred to the customer mass spectrometry instrument in step b). At the customer-site in step c) a calibration measurement may be performed on the calibrator sam ples and initial target values for the quantifier-qualifier-ratios for analyte and for internal standard may be determined. The adjustment factors may be applied to the initial target val ues to calculate adjusted target values for analyte and internal standard quantifier-qualifier- ratios. The adjusted target values are instrument specific, traceable to samples of a subject and have a better accuracy due to multiple data points used. Due to assay specific calibration frequency temporal drifts and shifts can be corrected periodically. For subsequent sample analysis at least one acceptance criterion may be used to validate the measured quantifier- qualifier-ratio. The acceptance criterion or a plurality of acceptance criteria may be deter mined during assay development. The at least one acceptance criterion may be neither in strument specific nor may change over time. The at least one acceptance criterion may be electronically transferred to customer instrument by application parameter file.

The term “manufacturer” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to at least one producer of the mass spectrometry instrument. The term “manufacturer” may further refer to a single manufacturer producing all parts of the mass spectrometry instrument and/or to a plurality of manufacturers such as suppliers for specific components of the mass spectrom etry instrument. The manufacturer may be the final manufacturer providing the final product for use by a customer. The term “manufacturer-site” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, with out limitation, to all processes which were performed by the manufacturer before providing the mass spectrometry instrument to the customer. All reagents, columns, calibrators, system reagents, disposables may be produced by or for the manufacturer. In contrary at the cus tomer-site, the customer can place samples of a subject and control samples as non-manu facturer components on the instrument.

The term “standardization” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a process of determining an estimation of imprecision of measured quantifier-qualifier-ratios and bias by matrix differences between calibrator and samples of a subject and providing a correction therefor. The standardization may comprise determining for each measurement of a sample a chromatogram. The term "chromatogram" is known to the skilled person. In an embodi ment, the term relates to a correlation plot of a quantitative measure of signals obtained from a sample and determined by an MS instrument with the progress of a chromatographic sep aration, in an embodiment over time, e.g. retention time, and/or elution volume. In an em bodiment, said quantitative measure of signals correlates with the concentration of at least part of sample constituents, in particular with the analyte; thus, the quantitative measure of signals may in particular be a signal intensity. The chromatogram may be an MS chromato gram, in a further embodiment an MS/MS chromatogram. As will be understood by the skilled person, the aforesaid representation may be, but does not have to be, a graphical representation; the representation may, however, also be provided e.g. as a list of value pairs, e.g. elution time / quantifier value pairs and/or elution time / qualifier value pairs, or as a mathematical model. Said quantitative measure of signals may comprise an analyte signal intensity and/or an internal standard signal intensity. Said quantitative measure of signals may comprise an analyte quantifier, an internal standard quantifier, an analyte qualifier and/or an internal standard qualifier. Thus, in an embodiment, in particular in case the MS is tandem MS, determining at least one chromatogram comprises measuring at least one of an analyte quantifier, an internal standard quantifier, an analyte qualifier and/or an internal standard qualifier over time and/or elution time, as specified above. As the skilled person understands, elution time may be replaced by any other measure of LC progress deemed appropriate by the skilled person, in particular by elution volume or by retention time.

The term “sample” as used herein is a broad term and is to be given its ordinary and custom ary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to any arbitrary sample such as a biological sample. In an embodiment, the sample is a liquid sample, in a further embodiment an aqueous sample. In an embodiment, the sample is selected from the group consisting of: a physiological fluid, including blood, serum, plasma, saliva, ocular lens fluid, lacrimal fluid, cerebrospinal fluid, sweat, urine, milk, ascites, mucus, synovial fluid, peritoneal fluid, and amniotic fluid; lavage fluid; tissue, cells, or the like. The sample may, however, also be a natural or industrial liquid, in particular surface or ground water, sewage, industrial wastewater, processing fluid, soil eluates, and the like. In an embodiment, the sample comprises or is suspected to comprise at least one chemical compound of interest, i.e. a chemical which shall be determined, which is referred to as "analyte". The sample may comprise one or more further chemical compounds, which are not to be determined and which are commonly referred to as "matrix". The sample may be used directly as obtained from the respective source or may be subjected to one or more pretreatment and/or a sample preparation step(s). Thus, the sample may be pretreated by physical and/or chemical meth ods, in an embodiment by centrifugation, filtration, mixing, homogenization, chromatog raphy, precipitation, dilution, concentration, contacting with a binding and/or detection rea gent, and/or any other method deemed appropriate by the killed person. In, i.e. before, dur ing, and/or after, the sample preparation step, one or more internal standard(s) may be added to the sample. The sample may be spiked with the internal standard. For example, an internal standard may be added to the sample at a predefined concentration. The internal standard may be selected such that it is easily identifiable under normal operating conditions of a mass spectrometry instrument. The concentration of the internal standard may be pre-deter- mined and significantly higher than the concentration of the analyte.

As used herein, the term “internal standard”, in an embodiment, relates to an analyte which is present with a defined concentration in a sample. Thus, in an embodiment, the concentra tion of the internal standard is known; it is, however, also envisaged that the concentration of the standard is unknown, but is the same for at least the sample of interest and at least one calibration sample; in such case, in an embodiment, the concentration of the internal standard is the same for all samples analyzed. The internal standard, in an embodiment, is structurally similar to the analyte, in a further embodiment is structurally identical to the analyte. In particular in the latter case, in an embodiment, the internal standard is an isotope-labelled molecule, in particular an isotope-labelled version of the analyte, e.g. a ² H (deuterated), ¹⁵ N, and/or ¹³ C-labelled derivative. The internal standard sample may be a sample comprising at least one internal standard substance with a known, e.g. pre-determined, concentration. For further details with respect to the standard sample, reference is made e.g. to EP 3 425 369 Al. The term “subject” as used herein is a broad term and is to be given its ordinary and custom ary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a mammal. In an embodiment of the invention said subject is a human. Specifically, the subject may be a patient. The patient in accordance with the present invention may, typically, suffer from or shall be suspected to suffer from a disease, i.e. it may already show some or all of the nega tive symptoms associated with the said disease. The term “sample of a subject” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a biological sample of the subject under test. The set of patient samples may comprise a plurality of different samples of at least one sub ject. The set of patient sample may be a set of representative samples. Typically, the set of patient samples may comprise 5 to 30 samples. However, the set of patient samples may comprise more than 30 samples.

The term “calibrator sample”, is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or cus tomized meaning. The term specifically may refer, without limitation, to an arbitrary sample having a known concentration of a substance of the calibrator sample. For example, concen tration values for the calibrator samples may be determined by a reference laboratory. For example, the calibrator sample may be at least one commercial calibrator. The set of calibra tor samples may comprise a plurality of different calibrator samples. The calibrator samples may be or may comprise samples having an assigned target value. For example, the set of calibrator samples may comprise two to three calibrator samples. The set of calibrator sam ples may comprise at least one calibrator sample. The set of calibrator samples may comprise 4 to 10 calibrator samples.

The term “adjustment factor”, is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or cus tomized meaning. The term specifically may refer, without limitation, to a factor for correct ing initial target values for quantifier-qualifier-ratios for analyte and/or for internal standard determined on the customer mass spectrometry instrument for measurement imprecision and bias due to matrix differences between calibrator and samples of a subject.

The method comprises determining at least three adjustment factors from the measurements of the set of samples of a subject and the set of calibrator samples. The method may comprise evaluating the determined chromatograms and determining quantifier-qualifier-ratios there from. The evaluating may comprise determining a peak area of the quantifier peak of the chromatogram and determining a peak area of the qualifier peak of the chromatogram. The evaluating may comprise determining a ratio of the peak area of the quantifier peak and the peak area of the qualifier peak. Step a) may comprise determining median quantifier-quali- fier-ratios for analyte and internal standard for calibrator samples and samples of a subject for each of the plurality of mass spectrometry instruments. The adjustment factors may be determined by using inter-instrument means. The first adjustment factor a depends on a dif ference, in particular a relation, between analyte and internal standard. In step a) the first adjustment factor a may be determined by a = R _m ean,AQN /AQL/ Rmean, IQN/IQL, wherein Rmean _,AQN /AQL > ^{s a} mean of the analyte quantifier-qualifier-ratios of the multiple measure ments of step a) and R _me an,iQN / _/Qi is ^a mean of the internal standard quantifier-qualifier- ratios of the multiple measurements of step a). The second adjustment factor b depends on a difference between samples of a subject and calibrator samples for analyte quantifier-quali- fier-ratio. In step a) the second adjustment factor b may be determined by b =

Rmean, patient ,AQN / AQL / Rmean, calibrator ,AQN / AQL wherein R _m ean, patient, AQN /AQL ^a mean of the analyte quantifier-qualifier-ratios of the multiple measurements of the samples of a sub ject of step a) and Rmean, caiibr ator _, AQN / AQL is a mean of analyte quantifier-qualifier-ratios of the multiple measurements of the calibrator samples of step a). The third adjustment factor g depends on a difference between samples of a subject and calibrator samples for the inter nal standard quantifier-qualifier-ratio. In step a) the third adjustment factor g may be deter mined by Y Rynean, patient, IQN /IQL/ Rmean, calibrator, IQN /IQL wherein

Rmean, patient, iQN/iQL > ^{s a} mean of the internal standard quantifier-qualifier-ratios of the mul tiple measurements of the samples of a subject of step a) and R _me an, calibrator, IQN/IQL is ^a mean of internal standard quantifier-qualifier-ratios of the multiple measurements of the cal ibrator samples of step a).

The term “transfer”, is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to unidirectional or bidirec tional information exchange, in particular data exchange. The transfer may comprise trans ferring information from a computational device, e.g. a computer, such as to send or output information, e.g. onto another device. The transfer may be performed via at least one com munication interface. The term “communication interface” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to an item or element forming a boundary configured for transferring information. In particular, the communication interface may be configured for transferring information from a computational device, e.g. a computer, such as to send or output infor mation, e.g. onto another device. Additionally or alternatively, the communication interface may be configured for transferring information onto a computational device, e.g. onto a com puter, such as to receive information. The communication interface may specifically provide means for transferring or exchanging information. In particular, the communication interface may provide a data transfer connection, e.g. Bluetooth, NFC, inductive coupling or the like. As an example, the communication interface may be or may comprise at least one port com prising one or more of a network or internet port, a USB-port and a disk drive. The commu nication interface may be at least one web interface. The term “electronically transferring”, is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifi cally may refer, without limitation, to a transfer using at least one electronic data transfer technique, in particular using at least one transmission protocol. Specifically, the electronic transfer may comprise at least one download of at least one parameter file from a dedicated database. The transfer may comprise that the customer mass spectrometry retrieves infor mation from the manufacturer. The term “retrieving” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, with out limitation, to receiving data and/or downloading data such as from a data server.

The term “customer-site” calibration is a broad term and is to be given its ordinary and cus tomary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a calibration which is conducted by a customer. Thus, the calibration may be conducted without the man ufacturer. However, the manufacturer may provide support to the customer if required.

The present invention proposes to split the calibration into two parts. In a first part, at the manufacturer-site a standardization may be performed and, in a second part, a calibration is performed on the customer mass spectrometry instrument. The standardization may be con ducted before the customer-site calibration is carried out. The customer-site calibration com prises at least one calibration measurement, wherein a set of calibrator samples is measured on the customer mass spectrometry instrument. The set of calibrator samples used for the customer-site calibration may be identical to the set of calibrator samples used for the man ufacturer-site standardization. The set of calibrator samples may be provided by the manu facturer. The calibration measurement may comprise a plurality of measurements such as for a plurality of calibrator samples of the set of calibrator samples and multiple replicates. The calibration measurement may comprise multiple reaction monitoring with quantifier and qualifier transition for analyte and/or internal standard. The calibration measurement may comprise determining for each measurement of a sample at least one chromatogram. The calibration measurement may comprise determining initial target values for quantifier-qual ifier-ratios for analyte and for internal standard. The initial target values may be determined by evaluating chromatograms and determining quantifier-qualifier-ratios therefrom.

The target values for quantifier-qualifier-ratios for analyte and for internal standard are set by applying the adjustment factors on the determined quantifier-qualifier-ratios, also de noted initial target values. In step c), all quantifier-qualifier-ratios determined during the calibration measurement may be used for setting the target values. In particular, all calibrator levels and all calibrator replicates for analyte and internal standard may be used for setting the target values. The target value for the quantifier-qualifier-ratio R for analyte quantifier AQN and analyte qualifier AQL may be set by with R being a quantifier-qualifier peak area ratio of a single measurement, IQN being an internal standard quantifier, IQL being an internal standard qualifier, and N being a total number of quantifier-qualifier-ratios used for calculation. The target value for a quantifier- qualifier-ratio R for internal standard quantifier IQN and internal standard qualifier IQL is set by with R being a quantifier-qualifier peak area ratio of a single measurement, AQN being an analyte quantifier, AQL being an analyte qualifier, and N being a total number of quantifier- qualifier-ratios used for calculation. These target values may be instrument specific, based on native patient samples and have better accuracy due to multiple data points used. Due to assay specific calibration frequency temporal changes can be corrected periodically.

In a further aspect, a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument is disclosed. The method comprises performing a calibration of the customer mass spectrometry instrument according to a computer imple mented method for calibrating a customer mass spectrometry instrument for quantifier-qual- ifier-ratio check according to the present invention. Thus, for definitions and embodiments of the method for quantifier-qualifier-ratio check reference is made to definitions and em bodiments of the method for calibrating a customer mass spectrometry instrument for quan- tifier-qualifier-ratio check according to the present invention as described in detail above or in more detail below. The method comprises at least one sample measurement using the customer mass spectrom etry instrument. The method further comprises at least one sample analysis step, wherein during sample analysis for every sample measurement quantifier-qualifier-ratios for analyte and/or internal standard are determined and compared to the target values under considera tion of at least one acceptance criterion.

The term “sample measurement” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to a pro cess of measuring a sample under test using the mass spectrometry instrument. The term “sample analysis” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or cus tomized meaning. The term specifically may refer, without limitation, to a process of evalu ating the signals of the mass spectrometry instrument. The sample analysis may comprise determining at least one chromatogram. The sample analysis may comprise evaluating the chromatogram and determining the at least one quantifier-qualifier-ratio.

The term “acceptance criterion” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to an arbitrary criterion characterizing a quantifier-qualifier-ratio as acceptable or as rejected. The acceptance criterion or a plurality of acceptance criteria may be determined during assay development. The at least one acceptance criterion may be neither instrument specific nor may change over time. The at least one acceptance criterion may be electronically transferred to customer instrument by application parameter file. The acceptance criterion may comprise at least one tolerance limit or tolerance range. The acceptance criterion may be used for peak identity check. The acceptance criterion may be used to distinguish between quantifier ions and interferences. The acceptance criterion may characterize whether or not the quantifier- qualifier-ratios measured with the customer mass spectrometry instrument are appropriate. Quantifier-qualifier-ratios below the tolerance limit or within the tolerance range may be validated. The method further may comprise flagging each of sample measurements which fails the acceptance criterion. Quantifier-qualifier-ratios above the tolerance limit or not within the tolerance range may be flagged and need further review by the operator or user of the customer mass spectrometry instrument.

Further disclosed and proposed herein is a computer program product having program code means, wherein the program code means can be stored or are stored on a storage medium, for performing a computer implemented method for calibrating a customer mass spectrom etry instrument for quantifier-qualifier-ratio check according to the present invention and/or a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument according to the present invention, when the pro-gram code means are executed on a computer or on a computer network.

Further disclosed and proposed herein is computer program product having program code means, wherein the program code means can be stored or are stored on a storage medium, for performing a computer implemented method for calibrating a customer mass spectrom etry instrument for quantifier-qualifier-ratio check according to the present invention and/or a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument according to the present invention, when the program code means are executed on a computer or on a computer network. Specifically, the program code means may be stored on a computer-readable data carrier and/or on a computer-readable storage medium.

As used herein, the terms “computer-readable data carrier” and “computer-readable storage medium” specifically may refer to non-transitory data storage means, such as a hardware storage medium having stored thereon computer-executable instructions. The computer- readable data carrier or storage medium specifically may be or may comprise a storage me dium such as a random-access memory (RAM) and/or a read-only memory (ROM).

Thus, specifically, one, more than one or even all of method steps a) to c) as indicated above may be performed by using a computer or a computer network, preferably by using a com puter program.

Further disclosed and proposed herein is a data carrier having a data structure stored thereon, which, after loading into a computer or computer network, such as into a working memory or main memory of the computer or computer network, may execute one or both of the methods according to one or more of the embodiments disclosed herein.

Further disclosed and proposed herein is a computer program product with program code means stored on a machine-readable carrier, in order to perform one or both of the methods according to one or more of the embodiments disclosed herein, when the program is executed on a computer or computer network. As used herein, a computer program product refers to the program as a tradable product. The product may generally exist in an arbitrary format, such as in a paper format, or on a computer-readable data carrier and/or on a computer- readable storage medium. Specifically, the computer program product may be distributed over a data network.

Finally, disclosed and proposed herein is a modulated data signal which contains instructions readable by a computer system or computer network, for performing one or both of the meth ods according to one or more of the embodiments disclosed herein.

Referring to the computer-implemented aspects of the invention, one or more of the method steps or even all of the method steps of one or both of the methods according to one or more of the embodiments disclosed herein may be performed by using a computer or computer network. Thus, generally, any of the method steps including provision and/or manipulation of data may be performed by using a computer or computer network. Generally, these method steps may include any of the method steps, typically except for method steps requir ing manual work, such as providing the samples and/or certain aspects of performing the actual measurements.

In a further aspect of the present invention a mass spectrometry system for determining a concentration of at least one analyte in a sample is disclosed. The mass spectrometry system comprising: a manufacture-site calibration system comprising a plurality of mass spectrometry instruments configured for measuring a set of samples of a subject and a set of cali brator samples in multiple replicates, wherein each of the mass spectrometry instru ments is configured for multiple reaction monitoring with quantifier and qualifier transition for analyte and internal standard, wherein the manufacture-site calibration system comprises at least one processing unit configured for determining at least three adjustment factors from the measurements of the set of samples of a subject and the set of calibrator samples, wherein a first adjustment factor a depends on a difference between analyte and internal standard, wherein a second adjustment factor b depends on a difference between samples of a subject and calibrator samples for analyte quantifier-qualifier-ratio, wherein a third adjustment factor g depends on a difference between samples of a subject and calibrator samples for the internal stand ard quantifier-qualifier-ratio; at least one communication interface configured for electronically transferring the adjustment factors from the manufacture-site calibration system to at least one cus tomer mass spectrometry instrument, and - the at least one customer mass spectrometry instrument, wherein the customer mass spectrometry instrument is configured for performing at least one calibration meas urement, wherein, in the calibration measurement, a set of calibrator samples is meas ured on the customer mass spectrometry instrument, wherein the customer mass spectrometry instrument comprises at least one evaluation device configured for de termining quantifier-qualifier-ratios from the calibration measurement, wherein the evaluation device is configured for setting target values for quantifier-qualifier-ratios for analyte and for internal standard by applying the adjustment factors on the deter mined quantifier-qualifier-ratios.

The mass spectrometry instruments may be liquid chromatography mass spectrometer (LC- MS) devices.

The customer mass spectrometry instrument may be configured for performing at least one sample measurement. The evaluation device may be configured for performing at least one sample analysis, wherein during sample analysis for every sample measurement quantifier- qualifier-ratios for analyte and/or internal standard are determined and compared to the tar get values under consideration of at least one acceptance criterion.

The term “processing unit” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to an arbitrary device adapted to perform the method step(s) as described above, in an embodiment by using at least one data processing device and, in a further embodiment, by using at least one pro cessor and/or at least one application-specific integrated circuit. Thus, as an example, the at least one processing unit may comprise at least one data processing unit having a software code stored thereon comprising a number of computer commands. The processing unit may provide one or more hardware elements for performing one or more of the indicated opera tions and/or may provide one or more processors with software running thereon for perform ing one or more of the method steps.

The term “evaluation device” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to an arbitrary device adapted to perform the method step(s) as described above, in an embodiment by using at least one data processing device and, in a further embodiment, by using at least one processor and/or at least one application-specific integrated circuit. Thus, as an example, the at least one evaluation device may comprise at least one data processing unit having a software code stored thereon comprising a number of computer commands. The evaluation device may provide one or more hardware elements for performing one or more of the indi cated operations and/or may provide one or more processors with software running thereon for performing one or more of the method steps.

The system may be configured for performing a computer implemented method for calibrat ing a customer mass spectrometry instrument for quantifier-qualifier-ratio check according to the present invention and/or a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument according to the present invention. Thus, for definitions and embodiments of the system reference is made to the embodiments and definitions of the methods according to the present invention as described above and as de scribed in more detail below.

Summarizing and without excluding further possible embodiments, the following embodi ments may be envisaged:

Embodiment 1 : A computer implemented method for calibrating a customer mass spectrom etry instrument for quantifier-qualifier-ratio check, the method comprises the following steps: a) at least one manufacturer-site standardization, wherein a set of samples of a subject and a set of calibrator samples are measured in multiple replicates on a plurality of mass spectrometry instruments, wherein each measurement comprises multiple reac tion monitoring with quantifier and qualifier transition for analyte and internal stand ard, wherein at least three adjustment factors are determined from the measurements of the set of samples of a subject and the set of calibrator samples, wherein a first adjustment factor a depends on a difference between analyte and internal standard, wherein a second adjustment factor b depends on a difference between samples of a subject and calibrator samples for analyte quantifier-qualifier-ratio, wherein a third adjustment factor g depends on a difference between samples of a subject and cali brator samples for the internal standard quantifier-qualifier-ratio; b) at least one transfer step, wherein the adjustment factors are electronically transferred to a customer mass spectrometry instrument; c) at least one customer-site calibration, wherein the customer-site calibration com prises at least one calibration measurement, wherein a set of calibrator samples is measured on the customer mass spectrometry instrument and quantifier-qualifier-ra tios are determined therefrom, wherein target values for quantifier-qualifier-ratios for analyte and for internal standard are set by applying the adjustment factors on the determined quantifier-qualifier-ratios.

Embodiment 2: The method according to the preceding embodiment, wherein in step c) all quantifier-qualifier-ratios determined during the calibration measurement are used for set ting the target values, wherein all calibrator levels and all calibrator replicates for analyte and internal standard are used for setting the target values.

Embodiment 3 : The method according to any one the preceding embodiments, wherein the target value for the quantifier-qualifier-ratio R for analyte quantifier AQN and analyte qual ifier AQL is set by with R being a quantifier-qualifier peak area ratio of a single measurement, IQN being an internal standard quantifier, IQL being an internal standard qualifier, and N being a total number of quantifier-qualifier-ratios used for calculation.

Embodiment 4: The method according to any one the preceding embodiments, wherein the target value for a quantifier-qualifier-ratio R for internal standard quantifier IQN and internal standard qualifier IQL is set by - - å ^R AQN/AQL+å ^R IQN/IQL

RIQN/IQL = Y - - ^ - , with R being a quantifier-qualifier peak area ratio of a single measurement, AQN being an analyte quantifier, AQL being an analyte qualifier, and N being a total number of quantifier- qualifier-ratios used for calculation.

Embodiment 5: The method according to any one the preceding embodiments, wherein in step a) the first adjustment factor a is determined by a = R _me an,AQN/ AQL/ Rmean, IQN/IQL , wherein R _m ean,AQN /AQL is ^a mean of the analyte quantifier-qualifier-ratios of the multiple measurements of step a) and R _m ean,iQN /IQL - ^{1' S a} mean of the internal standard quantifier- qualifier-ratios of the multiple measurements of step a).

Embodiment 6: The method according to any one the preceding embodiments, wherein in step a) the second adjustment factor b is determined by b = Rmean, _] patient, _, AQN / AQL / Rmean, calibrator, AQN /AQL ·: wherein Rmean, patient, AQN /AQL is a mean ofthe analyte quantifier- qualifier-ratios of the multiple measurements of the samples of a subject of step a) and Rmean, calibrator, AQN /AQL is a mean of analyte quantifier-qualifier-ratios of the multiple measurements of the calibrator samples of step a). Embodiment 7: The method according to any one the preceding embodiments, wherein in step a) the second adjustment factor g is determined by g = R _mea n, patient, IQN/IQL/ Rmean, calibrator ,IQN /i _Q L wherein Rmean, patient, IQN/IQL is a mean of the internal standard quantifier-qualifier-ratios of the multiple measurements of the samples of a subject of step a) and R _mea n, calibrator, IQN/IQL is ^a mean of internal standard quantifier-qualifier-ratios of the multiple measurements of the calibrator samples of step a).

Embodiment 8: The method according to any one the preceding embodiments, wherein step a) comprises determining median quantifier-qualifier-ratios for analyte and internal standard for calibrator samples and samples of a subject for each of the plurality of mass spectrometry instruments.

Embodiment 9: The method according to the preceding embodiment, wherein the adjustment factors are determined by using inter-instrument means.

Embodiment 10: The method according to any one the preceding embodiments, wherein the mass spectrometry instruments used in steps a) and c) are liquid chromatography mass spec trometer (LC-MS) devices.

Embodiment 11 : A computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument, wherein the method comprises performing a cali bration of the customer mass spectrometry instrument according to a computer implemented method for calibrating a customer mass spectrometry instrument for quantifier-qualifier-ra tio check according to any one of the preceding embodiments, wherein the method comprises at least one sample measurement using the customer mass spectrometry instrument, wherein the method further comprises at least one sample analysis step, wherein during sample anal ysis for every sample measurement quantifier-qualifier-ratios for analyte and/or internal standard are determined and compared to the target values under consideration of at least one acceptance criterion.

Embodiment 12: The method according to the preceding embodiment, wherein the method further comprises flagging each of sample measurements which fails the acceptance crite rion.

Embodiment 13: The method according to the preceding embodiment, wherein the method further comprises review of flagged sample measurements. Embodiment 14: A computer program product having program code means, wherein the program code means can be stored or are stored on a storage medium, for performing a computer implemented method for calibrating a customer mass spectrometry instrument for quantifier-qualifier-ratio check according to any one of the preceding embodiments, refer ring to a method for calibrating a customer mass spectrometry instrument and/or a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument according to any of the preceding embodiments, referring to a method for quan- tifier-qualifier-ratio check, when the program code means are executed on a computer or on a computer network.

Embodiment 15: A computer program product having program code means, wherein the program code means can be stored or are stored on a storage medium, for performing a computer implemented method for calibrating a customer mass spectrometry instrument for quantifier-qualifier-ratio check according to any one of the preceding embodiments, refer ring to a method for calibrating a customer mass spectrometry instrument and/or a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument according to any of the preceding embodiments, referring to a method for quan- tifier-qualifier-ratio check, when the program code means are executed on a computer or on a computer network.

Embodiment 16: A mass spectrometry system for determining a concentration of at least one analyte in a sample comprising: a manufacture-site calibration system comprising a plurality of mass spectrometry instruments configured for measuring a set of samples of a subject and a set of cali brator samples in multiple replicates, wherein each of the mass spectrometry instru ments is configured for multiple reaction monitoring with quantifier and qualifier transition for analyte and internal standard, wherein the manufacture-site calibration system comprises at least one processing unit configured for determining at least three adjustment factors from the measurements of the set of samples of a subject and the set of calibrator samples, wherein a first adjustment factor a depends on a difference between analyte and internal standard, wherein a second adjustment factor b depends on a difference between samples of a subject and calibrator samples for analyte quantifier-qualifier-ratio, wherein a third adjustment factor g depends on a difference between samples of a subject and calibrator samples for the internal stand ard quantifier-qualifier-ratio; at least one communication interface configured for electronically transferring the adjustment factors from the manufacture-site calibration system to at least one cus tomer mass spectrometry instrument, and

- the at least one customer mass spectrometry instrument, wherein the customer mass spectrometry instrument is configured for performing at least one calibration meas urement, wherein, in the calibration measurement, a set of calibrator samples is meas ured on the customer mass spectrometry instrument, wherein the customer mass spectrometry instrument comprises at least one evaluation device configured for de termining quantifier-qualifier-ratios from the calibration measurement, wherein the evaluation device is configured for setting target values for quantifier-qualifier-ratios for analyte and for internal standard by applying the adjustment factors on the deter mined quantifier-qualifier-ratios.

Embodiment 17: The system according to the preceding embodiment, wherein the system is configured for performing a computer implemented method for calibrating a customer mass spectrometry instrument for quantifier-qualifier-ratio check according to any one of the pre ceding embodiments, referring to a method for calibrating a customer mass spectrometry instrument and/or a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument according to any of the preceding embodiments, referring to a method for quantifier-qualifier-ratio check.

Embodiment 18: The system according to any one of the preceding embodiments referring to a system, wherein the mass spectrometry instruments are liquid chromatography mass spectrometer (LC-MS) devices.

Short description of the Figures

Further optional features and embodiments will be disclosed in more detail in the subsequent description of embodiments, preferably in conjunction with the dependent claims. Therein, the respective optional features may be realized in an isolated fashion as well as in any arbi trary feasible combination, as the skilled person will realize. The scope of the invention is not restricted by the preferred embodiments. The embodiments are schematically depicted in the Figures. Therein, identical reference numbers in these Figures refer to identical or functionally comparable elements. In the Figures:

Figure 1 shows an embodiment of a mass spectrometry system according to the present invention;

Figure 2 shows a flow chart of a computer implemented method for calibrating a cus tomer mass spectrometry instrument for quantifier-qualifier-ratio check ac cording to the present invention and a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument according to the present invention; and

Figures 3A and 3B experimental results.

Detailed description of the embodiments

Figure 1 shows an embodiment of a mass spectrometry system 110 according to the present invention. The mass spectrometry system 110 comprises a manufacture-site calibration sys tem 112 comprising a plurality of mass spectrometry instruments 114 configured for meas uring a set of samples of a subject and a set of calibrator samples in multiple replicates. Each of the mass spectrometry instruments 114 is configured for multiple reaction monitoring with quantifier and qualifier transition for analyte and internal standard. The mass spectrom etry (MS) instruments 114 may be mass analyzers configured for detecting at least one ana lyte based on mass to charge ratio. Each of the mass spectrometry instruments 114 may be or may comprise at least one quadrupole mass spectrometry device. The MS instruments 114 may be tandem mass spectrometry (MS/MS) instruments or triple quadrupole MS/MS. Spe cifically, the mass spectrometry instruments 114 may be configured for Multiple Reaction Monitoring (MRM).

The mass spectrometry instruments 114 may specifically be or may comprise a liquid chro matography mass spectrometry device. The liquid chromatography mass spectrometry de vice may be or may comprise at least one high-performance liquid chromatography (HPLC) device or at least one micro liquid chromatography (pLC) device. The liquid chromatog raphy mass spectrometry device may comprise a liquid chromatography (LC) device and a mass spectrometry (MS) device, wherein the LC device and the MS are coupled via at least one interface. The interface coupling a liquid chromatography device and the MS may com- prise at least one ionization source configured for generating of molecular ions and for trans ferring of the molecular ions into the gas phase. The liquid chromatography (LC) device may be configured to separate one or more analytes of interest of a sample from other components of the sample for detection of the one or more analytes with the mass spectrometry instru ment 114. The LC device may be based on any separation principle deemed appropriate by the skilled person; in an embodiment, the LC device may be reverse phase chromatography, hydrophobic interaction chromatography, ion exchange chromatography, size exclusion chromatography, affinity chromatography, or chiral chromatography; in a further embodi ment, the LC device is reverse phase chromatography. The LC device may comprise at least one LC column. For example, the LC device may be a single-column LC device or a multi- column LC device having a plurality of LC columns. The LC column may have a stationary phase through which a mobile phase is pumped in order to separate and/or elute and/or trans fer the analytes of interest.

The manufacturer may be at least one producer of the mass spectrometry instrument 114. The manufacturer may be a single manufacturer producing all parts of the mass spectrometry instrument 114 and/or to a plurality of manufacturers such as suppliers for specific compo nents of the mass spectrometry instrument 114. The manufacturer may be the final manu facturer providing the final product for use by a customer. The manufacturer-site” as used herein is a broad term and is to be given its ordinary and customary meaning to a person of ordinary skill in the art and is not to be limited to a special or customized meaning. The term specifically may refer, without limitation, to all processes which were performed by the manufacturer before providing the mass spectrometry instrument to the customer. All rea gents, columns, calibrators, system reagents, disposables may be produced by or for the manufacturer. In contrary at the customer-site, the customer can place samples of a subject and control samples as non-manufacturer components on the instrument.

The manufacture-site calibration system 112 comprises at least one processing unit 116 con figured for determining at least three adjustment factors from the measurements of the set of samples of a subject and the set of calibrator samples. The processing unit 116 may be adapted to determining the three adjustment factors by using at least one data processing device and, in a further embodiment, by using at least one processor and/or at least one application-specific integrated circuit. Thus, as an example, the at least one processing unit 116 may comprise at least one data processing unit having a software code stored thereon comprising a number of computer commands. The processing unit 116 may provide one or more hardware elements for performing one or more of the indicated operations and/or may provide one or more processors with software running thereon for performing the determin ing of the adjustment factors.

The adjustment factors may be determined during a manufacturer-site standardization. The standardization may be or may comprise a process of determining an estimation of impreci sion of measured quantifier-qualifier-ratios and bias by matrix differences between calibra tor and samples of a subject and providing a correction therefor. The standardization may comprise determining for each measurement of a sample a chromatogram. The chromato gram may be a correlation plot of a quantitative measure of signals obtained from a sample and determined by an MS instrument 114 with the progress of a chromatographic separation, in an embodiment over time, e.g. retention time, and/or elution volume. In an embodiment, said quantitative measure of signals correlates with the concentration of at least part of sam ple constituents, in particular with the analyte; thus, the quantitative measure of signals may in particular be a signal intensity. The chromatogram may be an MS chromatogram, in a further embodiment an MS/MS chromatogram. As will be understood by the skilled person, the aforesaid representation may be, but does not have to be, a graphical representation; the representation may, however, also be provided e.g. as a list of value pairs, e.g. elution time / quantifier value pairs and/or elution time / qualifier value pairs, or as a mathematical model. Said quantitative measure of signals may comprise an analyte signal intensity and/or an in ternal standard signal intensity. Said quantitative measure of signals may comprise an ana lyte quantifier, an internal standard quantifier, an analyte qualifier and/or an internal standard qualifier. Thus, in an embodiment, in particular in case the MS is tandem MS, determining at least one chromatogram comprises measuring at least one of an analyte quantifier, an internal standard quantifier, an analyte qualifier and/or an internal standard qualifier over time and/or elution time, as specified above. As the skilled person understands, elution time may be replaced by any other measure of LC progress deemed appropriate by the skilled person, in particular by elution volume or by retention time.

The adjustment factors may be or may comprise factors for correcting initial target values for quantifier-qualifier-ratios for analyte and/or for internal standard determined on a cus tomer mass spectrometry instrument 118 for measurement imprecision and bias due to ma trix differences between calibrator and samples of a subject. The processing unit 116 may be configured for determining at least three adjustment factors from the measurements of the set of samples of a subject and the set of calibrator samples. The processing unit may be configured for evaluating the determined chromatograms and determining quantifier-quali- fier-ratios therefrom. The processing unit 116 may be or may comprise at least one evalua tion device. The evaluating may comprise determining a peak area of the quantifier peak of the chromatogram and determining a peak area of the qualifier peak of the chromatogram. The evaluating may comprise determining a ratio of the peak area of the quantifier peak and the peak area of the qualifier peak. The processing unit 116 may be configured for determin ing median quantifier-qualifier-ratios for analyte and internal standard for calibrator samples and samples of a subject for each of the plurality of mass spectrometry instruments. The adjustment factors may be determined by using inter-instrument means. The first adjustment factor a depends on a difference between analyte and internal standard. The first adjustment factor a may be determined by cc — Rmean,AQN / AQL / Rmean, IQN /IQL _> wherein Rmean,AQN / AQL is a mean of the analyte quantifier-qualifier-ratios of the multiple measurements and Rmean, IQN /iQL -is a mean of the internal standard quantifier-qualifier-ratios of the multiple measurements. The second adjustment factor b depends on a difference between samples of a subject and calibrator samples for analyte quantifier-qualifier-ratio. The second adjustment factor b may be determined by b — Rmean, patient ,AQN / AQL / Rmean, calibrator ,AQN / AQL _? wherein Rmean, patient, AQN /AQL > ^s a mean of the analyte quantifier-qualifier-ratios of the mul tiple measurements of the samples of a subject and R _m ean,caiibrator ,AQN / AQL - is ^a mean of analyte quantifier-qualifier-ratios of the multiple measurements of the calibrator samples. The third adjustment factor g depends on a difference between samples of a subject and calibrator samples for the internal standard quantifier-qualifier-ratio. The third adjustment factor g may be determined by g — R _m ean, patient, IQN /IQL! Rmean, calibrator ,IQN /iQL _> wherein Rmean, patient, iQN /iQL is a mean of the internal standard quantifier-qualifier-ratios of the mul tiple measurements of the samples of a subject and R _mea n, calibrator, IQN /IQL - ^{1' S a} mean of in ternal standard quantifier-qualifier-ratios of the multiple measurements of the calibrator samples.

The mass spectrometry system 110 comprises at least one communication interface 120 con figured for electronically transferring the adjustment factors from the manufacture-site cali bration system 112 to the customer mass spectrometry instrument 118. In Figure 1, the com munication interface 120 is denoted as two dashed lines. The transfer may be a unidirectional or bidirectional information exchange, in particular data exchange. The transfer may com prise transferring information from a computational device, e.g. a computer, such as to send or output information, e.g. onto another device. The communication interface 120 may form a boundary configured for transferring information. In particular, the communication inter face 120 may be configured for transferring information from a computational device, e.g. a computer, such as to send or output information, e.g. onto another device. Additionally or alternatively, the communication interface 120 may be configured for transferring infor mation onto a computational device, e.g. onto a computer, such as to receive information. The communication interface 120 may specifically provide means for transferring or ex changing information. In particular, the communication interface 120 may provide a data transfer connection, e.g. Bluetooth, NFC, inductive coupling or the like. As an example, the communication interface 120 may be or may comprise at least one port comprising one or more of a network or internet port, a USB-port and a disk drive. The communication inter face 120 may be at least one web interface. The electronic transferring may be performed by using at least one electronic data transfer technique, in particular using at least one transmis sion protocol. Specifically, the electronic transfer may comprise at least one download of at least one parameter file from a dedicated database. The transfer may comprise that the cus tomer mass spectrometry 118 retrieves information from the manufacturer such as by receiv ing data and/or downloading data such as from a data server.

The mass spectrometry system 110 comprises the at least one customer mass spectrometry instrument 118. The customer mass spectrometry instrument 118 is located at a customer site 122. The customer mass spectrometry instrument 118 is configured for performing at least one calibration measurement, wherein, in the calibration measurement, a set of calibra tor samples is measured on the customer mass spectrometry instrument 118. The customer mass spectrometry instrument 118 comprises at least one evaluation device 124 configured for determining quantifier-qualifier-ratios from the calibration measurement. The evaluation device 124 is configured for setting target values for quantifier-qualifier-ratios for analyte and for internal standard by applying the adjustment factors on the determined quantifier- qualifier-ratios.

The target values for quantifier-qualifier-ratios for analyte and for internal standard are set by applying the adjustment factors on the determined quantifier-qualifier-ratios, also de noted initial target values. All quantifier-qualifier-ratios determined during the calibration measurement may be used for setting the target values. In particular, all calibrator levels and all calibrator replicates for analyte and internal standard may be used for setting the target values. The target value for the quantifier-qualifier-ratio R for analyte quantifier AQN and analyte qualifier AQL may be set by with R being a quantifier-qualifier peak area ratio of a single measurement, IQN being an internal standard quantifier, IQL being an internal standard qualifier, and N being a total number of quantifier-qualifier-ratios used for calculation. The target value for a quantifier- qualifier-ratio R for internal standard quantifier IQN and internal standard qualifier IQL is set by with R being a quantifier-qualifier peak area ratio of a single measurement, AQN being an analyte quantifier, AQL being an analyte qualifier, and N being a total number of quantifier- qualifier-ratios used for calculation. These target values may be instrument specific, based on native patient samples and have better accuracy due to multiple data points used. Due to assay specific calibration frequency temporal changes can be corrected periodically.

The customer mass spectrometry instrument 118 may be configured for performing at least one sample measurement. The evaluation device 124 may be configured for performing at least one sample analysis, wherein during sample analysis for every sample measurement quantifier-qualifier-ratios for analyte and/or internal standard are determined and compared to the target values under consideration of at least one acceptance criterion.

The mass spectrometry system 110 may be configured for performing a quality check based on quantifier-qualifier-ratios. For the quality check based on quantifier-qualifier-ratios at least one target value is used to which the measured quantifier-qualifier-ratio is compared. However, the target value may change or vary from mass spectrometry instruments to mass spectrometry instruments. Thus, it may be advantageous to use for quality check target val ues for a specific customer mass spectrometry instrument. Even changes in time are possible. Thus, it may be advantageous to use for quality check target values which may be adjusted or adapted repeatedly in time on the customer- site. Moreover, for calibration usually a low number of calibrator samples is measured and composition of those calibrator samples might be different compared to samples of a subject. Thus, the quality check based on the quanti- fier-qualifier-ratio would be strongly affected by measurement imprecision and biased by matrix differences between calibrator and samples of a subject. To overcome these issues, the present invention proposes a data transfer approach. On the manufacturer-site 112 a set of samples of a subject and the calibrator samples may be measured in multiple replicates on multiple instruments. Three adjustment factors may be determined and may be electron ically transferred to the customer mass spectrometry instrument 118. At the customer-site 122 a calibration measurement may be performed on the calibrator samples and initial target values for the quantifier-qualifier-ratios for analyte and for internal standard may be deter mined. The adjustment factors may be applied to the initial target values to calculate adjusted target values for analyte and internal standard quantifier-qualifier-ratios. The adjusted target values are instrument specific, traceable to samples of a subject and have a better accuracy due to multiple data points used. Due to assay specific calibration frequency temporal drifts and shifts can be corrected periodically. For subsequent sample analysis at least one ac ceptance criterion may be used to validate the measured quantifier-qualifier-ratio.

The acceptance criterion may characterize a quantifier-qualifier-ratio as acceptable or as re jected. The acceptance criterion or a plurality of acceptance criteria may be determined dur ing assay development. The at least one acceptance criterion may be neither instrument spe cific nor may change over time. The at least one acceptance criterion may be electronically transferred to customer instrument by application parameter file. The acceptance criterion may comprise at least one tolerance limit or tolerance range. The acceptance criterion may be used for peak identity check. The acceptance criterion may be used to distinguish between quantifier ions and interferences. The acceptance criterion may characterize whether or not the quantifier-qualifier-ratios measured with the customer mass spectrometry instrument 118 are appropriate. Quantifier-qualifier-ratios below the tolerance limit or within the tolerance range may be validated. The method further may comprise flagging each of sample meas urements which fails the acceptance criterion. Quantifier-qualifier-ratios above the tolerance limit or not within the tolerance range may be flagged and need further review by the oper ator or user of the customer mass spectrometry instrument.

The present invention proposes to split the calibration into two parts. In a first part, at the manufacturer-site 112 a standardization may be performed and, in a second part, a calibration is performed on the customer mass spectrometry instrument 118. The standardization may be conducted before the customer-site calibration is carried out. The customer-site calibra tion comprises at least one calibration measurement, wherein a set of calibrator samples is measured on the customer mass spectrometry instrument 118. The set of calibrator samples used for the customer-site calibration may be identical to the set of calibrator samples used for the manufacturer-site standardization. The set of calibrator samples may be provided by the manufacturer. The calibration measurement may comprise a plurality of measurements such as for a plurality of calibrator samples of the set of calibrator samples and multiple replicates. The calibration measurement may comprise multiple reaction monitoring with quantifier and qualifier transition for analyte and/or internal standard. The calibration meas urement may comprise determining for each measurement of a sample at least one chroma togram. The calibration measurement may comprise determining initial target values for quantifier-qualifier-ratios for analyte and for internal standard. The initial target values may be determined by evaluating chromatograms and determining quantifier-qualifier-ratios therefrom. Figure 2 shows a flow chart of a computer implemented method for calibrating a customer mass spectrometry instrument 118 for quantifier-qualifier-ratio check according to the pre sent invention and a computer implemented method for quantifier-qualifier-ratio check on a customer mass spectrometry instrument 118 according to the present invention. The method comprises the following steps: a) (denoted with reference number 126) at least one manufacturer-site standardiza tion, wherein a set of samples of a subject and a set of calibrator samples are measured in multiple replicates on a plurality of mass spectrometry instruments 114, wherein each measurement comprises multiple reaction monitoring with quantifier and qualifier transition for analyte and internal standard, wherein at least three adjustment factors are determined from the measurements of the set of samples of a subject and the set of calibrator samples, wherein a first adjustment factor a depends on a difference between analyte and internal standard, wherein a second adjustment factor b depends on a difference between samples of a sub ject and calibrator samples for analyte quantifier-qualifier-ratio, wherein a third adjustment factor g depends on a difference between samples of a subject and calibrator samples for the internal standard quantifier-qualifier-ratio; b) (denoted with reference number 128) at least one transfer step, wherein the adjustment factors are electronically transferred to a customer mass spectrometry instrument 118; c) (denoted with reference number 130) at least one customer-site calibration, wherein the customer-site calibration comprises at least one calibration measurement, wherein a set of calibrator samples is measured on the customer mass spectrometry instrument 118 and quantifier-qualifier-ratios are determined therefrom, wherein target values for quantifier-qualifier-ratios for analyte and for internal standard are set by applying the adjustment factors on the determined quantifier-qualifier-ratios.

The computer implemented method for quantifier-qualifier-ratio check on the customer mass spectrometry instrument 118 comprises steps a) to c). In addition, the method for quantifier- qualifier-ratio check comprises at least one sample measurement (denoted with reference number 132) using the customer mass spectrometry instrument 118. The method further comprises at least one sample analysis step (denoted with reference number 134), wherein during sample analysis for every sample measurement quantifier-qualifier-ratios for analyte and/or internal standard are determined and compared to the target values under considera tion of at least one acceptance criterion.

Figures 3A and 3B show experimental results of a testosterone test case, in particular an LCMS assay for testosterone quantification in human serum or plasma. Automated sample preparation was done on a robotic workstation, LC separation was done on a commercial HPLC system, and mass spectrometric detection was done by multiple reaction monitoring with quantifier and qualifier transition for analyte and internal standard, respectively. For the manufacturer-site standardization on two mass spectrometry instruments 114 for two days two replicates calibrators and patient samples were measured. Median quantifier-qual ifier-ratios for calibrators and patient samples on both mass spectrometry instruments 114 were calculated. By using inter-instrument means the adjustment factors a, b, g were determined:

- a = 1.001

- b = 1.003

- g = 0.998. On the customer-site 122, sample measurement under customer conditions were performed. On the customer’s mass spectrometry instrument 118 for one day three replicates of the two calibrator levels were measured und used for calibration and setting of the target values. 30 patient samples were measured over 10 days in multiple replicates and a quantifier-qualifier- ratio check was applied.

Figures 3A and 3B show the experimental results for the testosterone test case. Figure 3A shows the quantifier-qualifier-ratio for the analyte QQana as a function of an area ratio. The area ratio is a ratio of peak area of the analyte quantifier and of the internal standard quanti- Tier. Figure 3B shows the quantifier-qualifier-ratio for the internal standard QQISTD as a func tion of the of the area ratio. The solid lines show the target values for analyte 1.15 and for internal standard 1.14. Moreover, the acceptance range of ± 20% is depicted. It is shown that the target values for analyte 1.15 and for internal standard 1.14 determined with the adjust ment factors from the manufacturer-site standardization are suitable for the whole measure ment range of the customer mass spectrometry instrument.

List of reference numbers mass spectrometry system manufacturer-site mass spectrometry instruments processing unit mass spectrometry instrument communication interface customer- site evaluation device manufacturer-site standardization transfer step, customer-site calibration sample measurement sample analysis step