Check column ends cut cleanly and the distance that the column enters the injector.

Check all your fittings are re-tightened after system has been heated for a while.

Do an autotune and check your water/nitrogen levels to confirm MS is working.

Check to see if the syringe in the autosampler is worn or dirty. The plunger should give some resistance if you attempt to extract it from the syringe barrel, if there is no resistance, replace the syringe (or plunger). If the syringe is dirty replace it or clean it by removing the plunger and drawing solvents through it by applying vacuum to the bottom of the syringe barrel where the plunger fits in.

I have changed the syringe with a new one and filled new solvents. I will see reproducibility results tomorrow.

Officer Aksoy,

"Reproducibility" as term in "analytical chemistry" is: "dispersion of the results from mutually independent tests, using the same method to aliquots of the same sample under different conditions: different operators, different equipment or different laboratories". This is definition according ISO.

As I have understood, you have conducted experiments, within the frame of one and the same laboratory, by same equipment and same sample within the frame of a short period of time. If this happen, then you have decreasing in "repeatability", not in the "reproducibility".

This decreasing in repeatability is due to the change of column characteristics, meaning that you have changed method. Effecting the repeatability, of course, you in fact, effect the reproducibility as wellas, but within the frame of an interlaboratory analysis.

According ISO, also, "repeatability" as term refers to: "dispersion of the results from mutually independent tests, using the same method to aliquots of the same sample under same conditions: same operators, same equipment at the same laboratory over a short period of time".

Nevertheless, both repeatability and reproducibility decrease in even without any manipulations relating instrumentation using GC-MS, due to common instability of the data. Between day analysis of multicomponent samples has shown standard deviation (SD) ca. 15 % using GCxGC technique by RxiR-5Sil column. This combination has been described as among best ones of GC. The LOD is 0.1 pg (or 10-12 gram), which is a high value, generally. Applying preliminary chemical substitution to given analytes, for example, you can obtain even stronger increasing in SD.

In spite of, GC-MS is already routinely implemented in the analytical practice and has well established analytical protocols, including searchable databases, there are many other mass spectrometric methods. Some of them have provided spectacular high accuracy and precision of analytical information, at reduced (or without) sample pretreatments, allowing even direct assay (for example refs. [10,11]). They have superior insrumental characteristics over those ones of GC-hybrid variant of MS. Large number of them are applicable to multicomponent analysis allowing, for example, simultaneous analysis of 26 000 metabolites in one sample in same run. Concentration LODs are within ranges fmol to zmol (10-21 mol) (mass spectrometry, operating with ICR or Orbitrap analyzers). Both analyzers have ultra-high resolving power. And, thus, they allow direct determination of analytes in complex multicomponent mixtures. Some of them operate at ambient conditions. Any sources of random errors associated with chemical pretreatment of sample are strongly reduced. There have been reported other advantages particularly applicable to your operative work. Even they could have many more instrumental characteristics suitable for routine utilization for chemical analysis in forenscics, which from a research standpoint in the field of analytical chemistry, only, cannot be evaluated enough precisely (for example contributions like those reported in ref. [6]). Nevertheless that many of those methods have not still developed routine quantitative procedures; protocols and/or databases (or minimum such as developments are not public available or are only scarce represented). You can see, for example ref. [8].

In this context, please pay attention to references [1-11], containing the new trends in the analytical instrumentation, associated with mass spectrometry. Some reports are direct associated with forensic chemistry, even some of them used case objects. In ref. [1], however, it is not included MALDI-MS method. But it could be also routinely applicable (most probably) for such as purposes, due to it generally great instrumental features (refs. [10,11]). Relating MALDI-MS as instrumental features and applicability, you can pay attention to refs. [2-4], for example.

Please bear in mind that refs. [1-11] are only representative and they do not contain full instrumental characteristics to the methods. The reference sections to the papers are not completed. Most of them are not review-articles and/or monographs. In this context you can conduct a more comprehensive literature search towards, for example, the following authors, which mostly are discoverers to those methods and in parallel have conducted instrumental methodologic developments, exactly towards improvement of the instrumental characteristics:

- For MALDI-MS application for biomacromolecular imaging and in vivo assay (R. Caprioli). He has applied this method for clinical diagnostics, first. And the contributions are mainly associated with biomacromolecules and living systems.

- For quantitative analysis by MALDI mainly of low molecular weight analytes(M. Karas, F. Hillenkamp†). They are in parallel, discoverers to this method.

- Ambient DESI MS (R. Cooks) (He is it discoverer, as well)

- For ICR-MS (A. Marshall) (Also discoverer)

- For characteristics of Orbitrap analyzer (Ref. 7) (A. Makarov; He is also discoverer to it)

References

[Ref. 1] Forensic Chemistry and Ambient Mass Spectrometry: A Perfect Couple Destined for a Happy Marriage? D. Correa, J. Santos, L. Eberlin, M. Eberlin, S. Teunissen, Anal. Chem. 88 (2016) 2515-2526

[Ref. 2] Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification, J. Donfack, A. Wiley, Forensic Sci. Int. 16 (2015) 112-120

[Ref. 3] Absolute Quantitative MALDI Imaging Mass Spectrometry: A Case of Rifampicin in Liver Tissues, C. Chumbley, M. Reyzer, J. Allen, G. Marriner, L. Via, C. Barry, R. Caprioli, Anal. Chem. 88 (2016) 2392-2398

[Ref. 4] Fast quantitative determination of methylphenidate levels in rat plasma and brain ex vivo by MALDI-MS/MS, Arnold, A., Persike, M., Gorka, J., Dommett, E., Zimmermann, M., Karas, M., J. Mass Spectrom. 50 (2015) 963-971.

[Ref. 5] Fourier Transform ion cyclotron resonance mass spectrometry, A. Marshall, C. Hendrickson, G. Jackson, Mass Spectrom. Rev. 17 (1998) 1-35.

[Ref. 6] Rapid discrimination of bacteria using a miniature mass spectrometer, Pulliam, C., Wei, P., Snyder, D., Wang, X., Ouyang, Z., Pielak, R., R. Cooks, Analyst 141 (2016) 1633-1636.

[Ref. 7] The Orbitrap: a new mass spectrometer, Q. Hu, R. Noll, H. Li, A. Makarov, M. Hardman, R. Cooks, J. Mass Spectrom. 40 (2005) 430-443

[Ref. 8] MALDI Orbitrap mass spectrometry for fast and simplified analysis of novel street and designer drugs, K. Ostermann, A. Luf, N. Lutsch, R. Dieplinger, T. Mechtler, T. Metz, R. Schmid, D. Kasper, Clin. Chim. Acta 433 (2014) 254-258

[Ref. 9] Raman spectroscopy and laser desorption mass spectrometry for minimal destructive forensic analysis of black and color inkjet, printed documents, L. Heudt, D. Debois, T. Zimmerman, L. Koehler, B. Bano, F. Partouche, A. Duwez, B. Gilbert, E. De Pauw, Forensic Sci. Int. 219 (2012) 64-75

[Ref. 10] Single Hair Cocaine Consumption Monitoring b Mass Spectrometric Imaging, T. Porta, C Grivet, T. Kraemer, E. Varesio, G. Hopfgartner, Anal. Chem. 83 (2011) 4266-4272

[Ref. 11] Utilization of matrix-assisted laser desorption/ionization imaging mass spectrometry to search for cannabis in herb mixtures, K. Kuwayama, T. Yamamuro, K. Tsujikawa, H. Miyaguchi, T. Kanamori, Y. Iwata, H. Inoue, Anal. Bioanal. Chem. 406 (2014) 4789-4794

I think we have confirm that system is working properly by checking syringe, leak test, water and nitrogen ratio,  column performance, EM voltage (it gets high when ion source is dirty ). In additon, some compounds are not stable and do degrade in presence of light, metals, air and storage condition...

Use internal standart and check again. 

Thanks for all comments. All of them are very useful.

I think i have found the reason of the fault. I have been analyzing my samples in split mode 1/10. But when i used splitless mode, results became consistent. Service man told me that splitless liner that i use is one of the reasons. However %RSD which is bigger than %50 is still not normal. The other reason may be a congestion in split vent. We will check and see... 

I think the type of liner is rather important. There are split and splitless ones.